The Virtual Brain Data Model
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The Virtual Brain Data Model

Release: 2024-01-01

Modified on: 2026-04-30
This version:
https://w3id.org/tvbo/2026-04-30/tvbo.owl
Revision:
0.4.0
Contributors:
The Virtual Brain Ontology contributors
Publisher:
https://www.thevirtualbrain.org/
See also:
https://w3id.org/tvbo/axioms
https://w3id.org/tvbo/data
Download serialization:
JSON-LD RDF/XML N-Triples TTL
License:
https://spdx.org/licenses/EUPL-1.2
Visualization:
Visualize with WebVowl
Cite as:
The Virtual Brain Data Model. Revision: 0.4.0. Retrieved from: https://w3id.org/tvbo/2026-04-30/tvbo.owl
Provenance of this page
Ontology Specification Draft

Abstract

This is a placeholder text for the abstract. The abstract should contain a couple of sentences summarizing the ontology and its purpose.

Introduction back to ToC

This is a place holder text for the introduction. The introduction should briefly describe the ontology, its motivation, state of the art and goals.

tvb-datamodel: Overview back to ToC

This ontology has the following classes and properties.

Classes

Object Properties

Data Properties

Annotation Properties

Named Individuals

tvb-datamodel: Description back to ToC

Metadata schema for simulation studies using The Virtual Brain neuroinformatics platform or other dynamic network models of large-scale brain activity.

Cross-reference for tvb-datamodel classes, object properties and data properties back to ToC

This section provides details for each class and property defined by tvb-datamodel.

Classes

Ac back to ToC or Class ToC

IRI: http://qudt.org/vocab/unit/A

Ampere
has super-classes
UnitEnum c

active (DevelopmentStatus)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/DevelopmentStatus#active

Actively developed with regular releases.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
DevelopmentStatus c

Additive noisec back to ToC or Class ToC

IRI: https://w3id.org/tvbo/AdditiveNoise

has super-classes
Stochasticity character c

Aggregationc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Aggregation

Specifies how to aggregate values across a dimension. Used for loss functions to define per-element loss with reduction.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

AggregationTypec back to ToC or Class ToC

IRI: https://w3id.org/tvbo/AggregationType

How to aggregate time series data
Is defined by
https://w3id.org/tvbo/struct
is equivalent to
first (AggregationType) c or last (AggregationType) c or mean (AggregationType) c or none (AggregationType) c or window (AggregationType) c
has super-classes
Thing c
has sub-classes
first (AggregationType) c, last (AggregationType) c, mean (AggregationType) c, none (AggregationType) c, window (AggregationType) c

Algorithmc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Algorithm

A complete specification of an iterative parameter tuning algorithm. Combines update rules, objectives, observations, and hyperparameters.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

AlgorithmIncludec back to ToC or Class ToC

IRI: https://w3id.org/tvbo/AlgorithmInclude

Reference to an included algorithm with optional argument overrides. Allows combining algorithms with different hyperparameter values.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

analysis (RequirementRole)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/RequirementRole#analysis

Post-processing / analysis tool.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
RequirementRole c

analysis_toolc back to ToC or Class ToC

IRI: https://bio.tools/ontology/operation_2945

Post-processing, signal analysis, or statistics.
has super-classes
ToolRole c

arbitrary_unit (UnitEnum)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/UnitEnum#arbitrary_unit

Arbitrary units (a.u.)
Is defined by
https://w3id.org/tvbo/struct
has super-classes
UnitEnum c

Argumentc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Argument

A function argument with explicit value specification. Value can be: literal (number/string), reference to input (input.key), or cross-observation reference (observation_name.output_key).
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

Attractorc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Attractor

has super-classes
Dynamical property c
has sub-classes
Fixed point c, Limit cycle c, Strange attractor c, Torus c

Backendc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Backend

A code-generation or simulation backend (JAX, TVB, PyRates, tvboptim, NetworkDynamics.jl, BifurcationKit.jl).
has super-classes
Thing c
is in domain of
provides capability op, supports task op
is in range of
executable on op
has members
BifurcationKit.jl ni, JAX ni, NetworkDynamics.jl ni, PyRates ni, TVB ni, tvboptim ni

Backend capabilityc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/BackendCapability

A feature a backend either provides or lacks (autodiff, JIT, GPU, vectorised RNG, delay buffer, stochastic solver, stiff solver, continuation solver, code generation, etc.). Used to gate task support.
has super-classes
Thing c
is in range of
provides capability op
has members
Automatic differentiation ni, Built-in model library ni, Continuation solver ni, Delay history buffer ni, DifferentialEquations.jl integrators ni, GPU execution ni, Julia JIT ni, Just-in-time compilation ni, NetworkX topology API ni, NumPy execution ni, Stiff solver ni, Stochastic solver ni, Symbolic code generation ni, Vectorised RNG ni

backend_runtime (ToolRole)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/ToolRole#backend_runtime

Optimized execution backend for another simulator.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
ToolRole c

BarabasiAlbert (StandardGraphType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/StandardGraphType#BarabasiAlbert

Barabasi-Albert preferential attachment (params: k)
Is defined by
https://w3id.org/tvbo/struct
has super-classes
StandardGraphType c

batch (DimensionType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/DimensionType#batch

Batch dimension (for parallel processing)
Is defined by
https://w3id.org/tvbo/struct
has super-classes
DimensionType c

BidsEntitiesc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/BidsEntities

BIDS filename entities (BEP017-aligned) for provenance and data discovery. Reusable on Network, BrainAtlas, Tractogram, or any dataset with BIDS-conformant naming.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

Bifurcationc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Bifurcation

has super-classes
Dynamical property c
has sub-classes
Bogdanov-Takens c, Fold of limit cycles c, Homoclinic c, Hopf c, Period doubling c, Pitchfork c, Saddle-node c, Transcritical c

Bifurcation eventc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/BifurcationEvent

Reified record of a bifurcation in a specific model along a specific parameter.
has super-classes
Thing c
is in domain of
bifurcation parameter op, bifurcation type op, critical value dp
is in range of
exhibits bifurcation op

bifurcation_analysisc back to ToC or Class ToC

IRI: http://www.wikidata.org/entity/Q858926

Dynamical systems bifurcation / continuation analysis.
has super-classes
ModelParadigm c, ToolRole c

bioconda (EcosystemEnum)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/EcosystemEnum#bioconda

Bioinformatics Conda channel.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
EcosystemEnum c

Bistablec back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Bistable

has super-classes
Dynamical regime c
is also defined as
named individual

Bogdanov-Takensc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/BogdanovTakens

has super-classes
Bifurcation c

BOLD (ImagingModality)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/ImagingModality#BOLD

Blood Oxygen Level Dependent signal.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
ImagingModality c

Bookc back to ToC or Class ToC

IRI: http://schema.org/Book

has super-classes
Thing c
has members
Abbott2005 ni, Arnold1968 ni, Arnold1968a ni, Duffing1918 ni, Eisenberg1975 ni, Ermentrout2010 ni, Guckenheimer1983 ni, GuckenheimerHolmes1983 ni, IzhikevichBook ni, Ott2002 ni, Ott2010 ni, Skiadas2008 ni, Sprott2010 ni, Strogatz2015 ni, Tufillaro1992 ni

both (Hemisphere)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Hemisphere#both

Is defined by
https://w3id.org/tvbo/struct
has super-classes
Hemisphere c

BoundaryConditionc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/BoundaryCondition

Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

BrainAtlasc back to ToC or Class ToC

IRI: http://uri.interlex.org/tgbugs/uris/readable/BrainAtlas

A schema for representing a version of a brain atlas.
has super-classes
Thing c
has members
space-MNI152_atlas-Yeo17_res-1_dseg ni, tpl-FSLMNI152_atlas-Schaefer2018_seg-17Networks_scale-1000_dseg ni, tpl-FSLMNI152_atlas-Schaefer2018_seg-17Networks_scale-100_dseg ni, tpl-FSLMNI152_atlas-Schaefer2018_seg-17Networks_scale-200_dseg ni, tpl-FSLMNI152_atlas-Schaefer2018_seg-17Networks_scale-300_dseg ni, tpl-FSLMNI152_atlas-Schaefer2018_seg-17Networks_scale-400_dseg ni, tpl-FSLMNI152_atlas-Schaefer2018_seg-17Networks_scale-500_dseg ni, tpl-FSLMNI152_atlas-Schaefer2018_seg-17Networks_scale-600_dseg ni, tpl-FSLMNI152_atlas-Schaefer2018_seg-17Networks_scale-700_dseg ni, tpl-FSLMNI152_atlas-Schaefer2018_seg-17Networks_scale-800_dseg ni, tpl-FSLMNI152_atlas-Schaefer2018_seg-17Networks_scale-900_dseg ni, tpl-FSLMNI152_atlas-Schaefer2018_seg-7Networks_scale-1000_dseg ni, tpl-FSLMNI152_atlas-Schaefer2018_seg-7Networks_scale-100_dseg ni, tpl-FSLMNI152_atlas-Schaefer2018_seg-7Networks_scale-200_dseg ni, tpl-FSLMNI152_atlas-Schaefer2018_seg-7Networks_scale-300_dseg ni, tpl-FSLMNI152_atlas-Schaefer2018_seg-7Networks_scale-400_dseg ni, tpl-FSLMNI152_atlas-Schaefer2018_seg-7Networks_scale-500_dseg ni, tpl-FSLMNI152_atlas-Schaefer2018_seg-7Networks_scale-600_dseg ni, tpl-FSLMNI152_atlas-Schaefer2018_seg-7Networks_scale-700_dseg ni, tpl-FSLMNI152_atlas-Schaefer2018_seg-7Networks_scale-800_dseg ni, tpl-FSLMNI152_atlas-Schaefer2018_seg-7Networks_scale-900_dseg ni, tpl-MNI152NLin2009b_atlas-hcpmmp1_desc-ordered_dseg ni, tpl-MNI152NLin2009c_atlas-DesikanKilliany_desc-ranked_dseg ni, tpl-MNI152Nlin2009c_atlas-Destrieux_desc-ranked_dseg ni

BrainRegionSeriesc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/BrainRegionSeries

A series whose values represent latitude
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

BranchSwitchc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/BranchSwitch

Specification for switching from a detected bifurcation point to a new branch (periodic orbits from Hopf, fold continuation, etc.). Each BranchSwitch says: "from which special point on the parent branch, continue what kind of object, with what settings." Override parent solver settings via the inline continuation field — only explicitly set attributes take effect; everything else is inherited from the parent Continuation.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

brown (NoiseType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/NoiseType#brown

Is defined by
https://w3id.org/tvbo/struct
has super-classes
NoiseType c

Burstingc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Bursting

has super-classes
Dynamical regime c
is also defined as
named individual

Cc back to ToC or Class ToC

IRI: http://www.wikidata.org/entity/Q15777

has super-classes
ProgrammingLanguageEnum c

C#c back to ToC or Class ToC

IRI: http://www.wikidata.org/entity/Q2370

has super-classes
ProgrammingLanguageEnum c

C++c back to ToC or Class ToC

IRI: http://www.wikidata.org/entity/Q2407

has super-classes
ProgrammingLanguageEnum c

Callablec back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Callable

Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c
has sub-classes
ClassReference c

capacitance (PhysicalDimension)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/PhysicalDimension#capacitance

Capacitance [M⁻¹ L⁻² T⁴ I²]
Is defined by
https://w3id.org/tvbo/struct
has super-classes
PhysicalDimension c

Casec back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Case

Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

channelc back to ToC or Class ToC

IRI: http://www.wikidata.org/entity/Q898786

Ion channel / sub-cellular molecular dynamics.
has super-classes
SimulationScale c

Chaoticc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Chaotic

has super-classes
Dynamical regime c
is also defined as
named individual

charge (PhysicalDimension)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/PhysicalDimension#charge

Electric charge [T I]
Is defined by
https://w3id.org/tvbo/struct
has super-classes
PhysicalDimension c

ClassReferencec back to ToC or Class ToC

IRI: https://w3id.org/tvbo/ClassReference

Reference to a class that can be instantiated and called. Used for external library classes (e.g., tvboptim.Bold, custom monitors). The class is instantiated with constructor_args, then called with call_args. Generalizable pattern: works for tvboptim, TVB, or any Python class.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Callable c

ClinicalImprovement (dbs)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/dbs/ClinicalImprovement

Relative improvement on a defined clinical score.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

ClinicalScale (dbs)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/dbs/ClinicalScale

A clinical assessment inventory or structured scale composed of multiple scores or items.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

ClinicalScore (dbs)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/dbs/ClinicalScore

Metadata about a clinical score or scale.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

cmc back to ToC or Class ToC

IRI: http://qudt.org/vocab/unit/CentiM

Centimetre
has super-classes
UnitEnum c

collocation (NumericalDiscretizationMethod)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/NumericalDiscretizationMethod#collocation

Orthogonal collocation at Gauss points.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
NumericalDiscretizationMethod c

Coloured noisec back to ToC or Class ToC

IRI: https://w3id.org/tvbo/ColoredNoise

has super-classes
Stochasticity character c

CommonCoordinateSpacec back to ToC or Class ToC

IRI: http://uri.interlex.org/tgbugs/uris/readable/CommonCoordinateSpace

A schema for representing a version of a common coordinate space.
has super-classes
Thing c
is in range of
coordinateSpace op
has members
MNI152NLin2009b ni, MNI152NLin2009c ni, MNI152NLin2009cAsym ni, MNI152NLin6Asym ni

compartmentalc back to ToC or Class ToC

IRI: http://www.wikidata.org/entity/Q5155691

Multi-compartment morphologically detailed models.
has super-classes
ModelParadigm c

Complete (StandardGraphType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/StandardGraphType#Complete

Complete graph (all-to-all)
Is defined by
https://w3id.org/tvbo/struct
has super-classes
StandardGraphType c

concentration (PhysicalDimension)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/PhysicalDimension#concentration

Concentration [L⁻³ N]
Is defined by
https://w3id.org/tvbo/struct
has super-classes
PhysicalDimension c

concept (DevelopmentStatus)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/DevelopmentStatus#concept

Minimal or no implementation; ideas / prototypes.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
DevelopmentStatus c

conda (EnvironmentType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/EnvironmentType#conda

Conda environment.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
EnvironmentType c

conda_forgec back to ToC or Class ToC

IRI: http://www.wikidata.org/entity/Q105593788

Conda-Forge community channel.
has super-classes
EcosystemEnum c

ConditionalBlockc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/ConditionalBlock

A single condition and its corresponding equation segment.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

conductance (PhysicalDimension)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/PhysicalDimension#conductance

Conductance [M⁻¹ L⁻² T³ I²]
Is defined by
https://w3id.org/tvbo/struct
has super-classes
PhysicalDimension c

conductance_basedc back to ToC or Class ToC

IRI: http://www.wikidata.org/entity/Q72484

Conductance-based / Hodgkin-Huxley-type models.
has super-classes
ModelParadigm c

Contact (dbs)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/dbs/Contact

Individual contact on a DBS electrode.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

Continuationc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Continuation

Complete specification of a numerical continuation / bifurcation analysis. All universal solver settings live directly here. Toolkit-specific string options go in the options slot. When used inside a BranchSwitch, only explicitly set attributes override the parent's values.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c
has members
eq_in_a ni, eq_in_a_full ni

ContinuationAlgorithmc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/ContinuationAlgorithm

Predictor-corrector algorithm for numerical continuation.
Is defined by
https://w3id.org/tvbo/struct
is equivalent to
MoorePenrose (ContinuationAlgorithm) c or Natural (ContinuationAlgorithm) c or PALC (ContinuationAlgorithm) c
has super-classes
Thing c
has sub-classes
MoorePenrose (ContinuationAlgorithm) c, Natural (ContinuationAlgorithm) c, PALC (ContinuationAlgorithm) c

continuous (EventType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/EventType#continuous

Triggered when condition function crosses zero (root-finding). Maps to ContinuousCallback / ContinuousComponentCallback.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
EventType c

continuous (SystemType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/SystemType#continuous

Continuous-time dynamics (e.g., ODE/SDE).
Is defined by
https://w3id.org/tvbo/struct
has super-classes
SystemType c

coo (SparseFormat)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/SparseFormat#coo

Coordinate list (data, row, col)
Is defined by
https://w3id.org/tvbo/struct
has super-classes
SparseFormat c

Coordinatec back to ToC or Class ToC

IRI: http://uri.interlex.org/tgbugs/uris/readable/Coordinate

A 3D coordinate with X, Y, Z values.
has super-classes
Thing c

Couplingc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Coupling

Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c
has members
Difference ni, FastLinearCoupling ni, HyperbolicTangent ni, KuramotoCoupling ni, Linear ni, PreSigmoidal ni, Scaling ni, Sigmoidal ni, SigmoidalJansenRit ni

CouplingInputc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/CouplingInput

has super-classes
Thing c
is also defined as
named individual

cranc back to ToC or Class ToC

IRI: http://www.wikidata.org/entity/Q901584

Comprehensive R Archive Network.
has super-classes
EcosystemEnum c

Creative workc back to ToC or Class ToC

IRI: http://schema.org/CreativeWork

has super-classes
Thing c
has members
Cakan ni, FitzHughNagumo ni, Halvorsen2000 ni, OttRiddled2014 ni, Stankevich2012 ni, Ulam1960s ni, Weisstein ni

csr (SparseFormat)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/SparseFormat#csr

Compressed Sparse Row (data, indices, indptr)
Is defined by
https://w3id.org/tvbo/struct
has super-classes
SparseFormat c

curl (OperatorType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/OperatorType#curl

Is defined by
https://w3id.org/tvbo/struct
has super-classes
OperatorType c

current (PhysicalDimension)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/PhysicalDimension#current

Electric current [I]
Is defined by
https://w3id.org/tvbo/struct
has super-classes
PhysicalDimension c

Cycle (StandardGraphType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/StandardGraphType#Cycle

Cycle graph (ring)
Is defined by
https://w3id.org/tvbo/struct
has super-classes
StandardGraphType c

data_standardc back to ToC or Class ToC

IRI: http://www.wikidata.org/entity/Q317623

Data format or exchange standard.
has super-classes
ModelParadigm c

Dataset (study)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/study/Dataset

A collection of subjects for a multi-subject study. Provides the subject/session structure needed for workflow rendering. Optionally backed by a BIDS directory layout.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c
has sub-classes
DBSDataset (dbs) c

DataSourcec back to ToC or Class ToC

IRI: https://w3id.org/tvbo/DataSource

Specification for loading external/empirical data.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

DBSDataset (dbs)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/dbs/DBSDataset

Collection of data related to a specific DBS study.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Dataset (study) c

DBSProtocol (dbs)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/dbs/DBSProtocol

A protocol describing DBS therapy, potentially bilateral or multi-lead.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

DBSSubject (dbs)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/dbs/DBSSubject

Human or animal subject receiving DBS.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Subject (study) c

degCc back to ToC or Class ToC

IRI: http://qudt.org/vocab/unit/DEG_C

Degree Celsius
has super-classes
UnitEnum c

dense (SparseFormat)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/SparseFormat#dense

Dense N×N array with gzip compression
Is defined by
https://w3id.org/tvbo/struct
has super-classes
SparseFormat c

DerivedObservationc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/DerivedObservation

Observation derived from one or more other observations. Examples: - fc (from bold) - single source transformation - fc_corr (from fc and fc_target) - multi-source comparison Unlike regular Observations, these don't generate monitor classes but are computed from existing observation values.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Observation c

DerivedParameterc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/DerivedParameter

Is defined by
https://w3id.org/tvbo/struct
has super-classes
Parameter c

DerivedVariablec back to ToC or Class ToC

IRI: https://w3id.org/tvbo/DerivedVariable

Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c
has members
A_ik (StefanescuJirsa3D derived variable) ni, Aik (StefanescuJirsa2D derived variable) ni, B_ik (StefanescuJirsa3D derived variable) ni, Bik (StefanescuJirsa2D derived variable) ni, C_ik (StefanescuJirsa3D derived variable) ni, Cik (StefanescuJirsa2D derived variable) ni, DK_o (KIonEx derived variable) ni, DNa_i (KIonEx derived variable) ni, DNa_o (KIonEx derived variable) ni, Fe_ext (ZerlautAdaptationFirstOrder derived variable) ni, Fi_ext (ZerlautAdaptationFirstOrder derived variable) ni, H (ReducedWongWang derived variable) ni, H_e (ReducedWongWangExcInh derived variable) ni, H_i (ReducedWongWangExcInh derived variable) ni, H_x (ReducedWongWangTvboptim derived variable) ni, I (Kuramoto derived variable) ni, I (KuramotoModel2 derived variable) ni, IE_i (StefanescuJirsa2D derived variable) ni, IE_i (StefanescuJirsa3D derived variable) ni, II_i (StefanescuJirsa2D derived variable) ni, II_i (StefanescuJirsa3D derived variable) ni, I_Cl (KIonEx derived variable) ni, I_K (KIonEx derived variable) ni, I_Na (KIonEx derived variable) ni, I_pump (KIonEx derived variable) ni, J_N_S_e (ReducedWongWangExcInh derived variable) ni, K_i (KIonEx derived variable) ni, K_o (KIonEx derived variable) ni, Na_i (KIonEx derived variable) ni, Na_o (KIonEx derived variable) ni, Q_V (LarterBreakspear derived variable) ni, Q_Z (LarterBreakspear derived variable) ni, SS0 (TsodyksMarkram derived variable) ni, SS1 (TsodyksMarkram derived variable) ni, S_e (ZerlautAdaptationFirstOrder derived variable) ni, S_i (ZerlautAdaptationFirstOrder derived variable) ni, T_V_e (ZerlautAdaptationFirstOrder derived variable) ni, T_V_i (ZerlautAdaptationFirstOrder derived variable) ni, T_e (ZerlautAdaptationFirstOrder derived variable) ni, T_i (ZerlautAdaptationFirstOrder derived variable) ni, T_m_e (ZerlautAdaptationFirstOrder derived variable) ni, T_m_i (ZerlautAdaptationFirstOrder derived variable) ni, U_e_e (ZerlautAdaptationFirstOrder derived variable) ni, U_e_i (ZerlautAdaptationFirstOrder derived variable) ni, U_i_e (ZerlautAdaptationFirstOrder derived variable) ni, U_i_i (ZerlautAdaptationFirstOrder derived variable) ni, V_e (ZerlautAdaptationFirstOrder derived variable) ni, V_i (ZerlautAdaptationFirstOrder derived variable) ni, V_temp (KIonEx derived variable) ni, V_thre_e (ZerlautAdaptationFirstOrder derived variable) ni, V_thre_i (ZerlautAdaptationFirstOrder derived variable) ni, Vcond (KIonEx derived variable) ni, a_i (StefanescuJirsa3D derived variable) ni, b_i (StefanescuJirsa3D derived variable) ni, beta (KIonEx derived variable) ni, c_i (StefanescuJirsa3D derived variable) ni, coupled_input (ZetterbergJansen derived variable) ni, coupling (ReducedWongWangExcInh derived variable) ni, d_i (StefanescuJirsa3D derived variable) ni, e_i (StefanescuJirsa2D derived variable) ni, e_i (StefanescuJirsa3D derived variable) ni, f_i (StefanescuJirsa2D derived variable) ni, f_i (StefanescuJirsa3D derived variable) ni, f_out_e (ZerlautAdaptationFirstOrder derived variable) ni, f_out_i (ZerlautAdaptationFirstOrder derived variable) ni, fe_e (ZerlautAdaptationFirstOrder derived variable) ni, fe_i (ZerlautAdaptationFirstOrder derived variable) ni, fi_e (ZerlautAdaptationFirstOrder derived variable) ni, fi_i (ZerlautAdaptationFirstOrder derived variable) ni, h (Epileptor2D derived variable) ni, h (Epileptor5D derived variable) ni, h (KIonEx derived variable) ni, h_i (StefanescuJirsa3D derived variable) ni, lc_0 (Kuramoto derived variable) ni, lc_0 (KuramotoModel2 derived variable) ni, lc_0 (LarterBreakspear derived variable) ni, lc_0 (SupHopf derived variable) ni, lc_0 (WilsonCowan derived variable) ni, lc_1 (EpileptorRestingState derived variable) ni, lc_1 (WilsonCowan derived variable) ni, lc_E (ZerlautAdaptationFirstOrder derived variable) ni, lc_I (ZerlautAdaptationFirstOrder derived variable) ni, m_Ca (LarterBreakspear derived variable) ni, m_K (LarterBreakspear derived variable) ni, m_Na (LarterBreakspear derived variable) ni, m_i (StefanescuJirsa2D derived variable) ni, m_i (StefanescuJirsa3D derived variable) ni, minf (KIonEx derived variable) ni, mu_G_e (ZerlautAdaptationFirstOrder derived variable) ni, mu_G_i (ZerlautAdaptationFirstOrder derived variable) ni, mu_Ge_e (ZerlautAdaptationFirstOrder derived variable) ni, mu_Ge_i (ZerlautAdaptationFirstOrder derived variable) ni, mu_Gi_e (ZerlautAdaptationFirstOrder derived variable) ni, mu_Gi_i (ZerlautAdaptationFirstOrder derived variable) ni, mu_V_e (ZerlautAdaptationFirstOrder derived variable) ni, mu_V_i (ZerlautAdaptationFirstOrder derived variable) ni, n_i (StefanescuJirsa2D derived variable) ni, n_i (StefanescuJirsa3D derived variable) ni, ninf (KIonEx derived variable) ni, output (EpileptorRestingState derived variable) ni, p_i (StefanescuJirsa3D derived variable) ni, phase (KuramotoModel2 derived variable) ni, r (KIonEx derived variable) ni, r_E (CakanObermayer derived variable) ni, r_I (CakanObermayer derived variable) ni, s_e (WilsonCowan derived variable) ni, s_i (WilsonCowan derived variable) ni, sigma_V_e (ZerlautAdaptationFirstOrder derived variable) ni, sigma_V_i (ZerlautAdaptationFirstOrder derived variable) ni, sigma_v1 (ZetterbergJansen derived variable) ni, sigma_v23 (ZetterbergJansen derived variable) ni, sigma_v45 (ZetterbergJansen derived variable) ni, sigma_y0_1 (JansenRit derived variable) ni, sigma_y0_3 (JansenRit derived variable) ni, sigma_y1_y2 (JansenRit derived variable) ni, signal (KuramotoModel2 derived variable) ni, v_pyr (JansenRit1995 derived variable) ni, v_pyr (ModelJansen1995 derived variable) ni, x (ReducedWongWang derived variable) ni, x (ReducedWongWangTvboptim derived variable) ni, x1cond (Epileptor2D derived variable) ni, x1cond (Epileptor5D derived variable) ni, x1cond (EpileptorRestingState derived variable) ni, x_e (ReducedWongWangExcInh derived variable) ni, x_e (WilsonCowan derived variable) ni, x_i (ReducedWongWangExcInh derived variable) ni, x_i (WilsonCowan derived variable) ni, xcond (KIonEx derived variable) ni, y2cond (Epileptor5D derived variable) ni, y2cond (EpileptorRestingState derived variable) ni, zcond (Epileptor2D derived variable) ni, zcond (Epileptor5D derived variable) ni, zcond (EpileptorRestingState derived variable) ni

Deterministicc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Deterministic

has super-classes
Stochasticity character c
is also defined as
named individual

dev (RequirementRole)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/RequirementRole#dev

Development / build dependency.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
RequirementRole c

DevelopmentStatusc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/DevelopmentStatus

Development status of the software. Based on repostatus.org categories.
Is defined by
https://w3id.org/tvbo/struct
is equivalent to
active (DevelopmentStatus) c or concept (DevelopmentStatus) c or inactive (DevelopmentStatus) c or moved (DevelopmentStatus) c or suspended (DevelopmentStatus) c or unsupported (DevelopmentStatus) c or wip (DevelopmentStatus) c
has super-classes
Thing c
has sub-classes
active (DevelopmentStatus) c, concept (DevelopmentStatus) c, inactive (DevelopmentStatus) c, moved (DevelopmentStatus) c, suspended (DevelopmentStatus) c, unsupported (DevelopmentStatus) c, wip (DevelopmentStatus) c

DifferentialOperatorc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/DifferentialOperator

Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

dimensionlessc back to ToC or Class ToC

IRI: http://qudt.org/vocab/unit/UNITLESS

Dimensionless (unitless)
has super-classes
UnitEnum c

DimensionTypec back to ToC or Class ToC

IRI: https://w3id.org/tvbo/DimensionType

Dimensions along which operations can be applied
Is defined by
https://w3id.org/tvbo/struct
is equivalent to
batch (DimensionType) c or frequency (DimensionType) c or mode (DimensionType) c or node (DimensionType) c or region (DimensionType) c or sample (DimensionType) c or state (DimensionType) c or time (DimensionType) c
has super-classes
Thing c
has sub-classes
batch (DimensionType) c, frequency (DimensionType) c, mode (DimensionType) c, node (DimensionType) c, region (DimensionType) c, sample (DimensionType) c, state (DimensionType) c, time (DimensionType) c

Dirichlet (BoundaryConditionType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/BoundaryConditionType#Dirichlet

Is defined by
https://w3id.org/tvbo/struct
has super-classes
BoundaryConditionType c

discrete (EventType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/EventType#discrete

Triggered when condition function returns true (checked at each step). Maps to DiscreteCallback / DiscreteComponentCallback.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
EventType c

discrete (SystemType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/SystemType#discrete

Discrete-time dynamics (e.g., maps, iterated updates).
Is defined by
https://w3id.org/tvbo/struct
has super-classes
SystemType c

Discretizationc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Discretization

Discretization method for boundary value problems in continuation (periodic orbits, connecting orbits, quasi-periodic tori). Specifies the method; method-specific numerics go in parameters.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

DiscretizationMethodc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/DiscretizationMethod

Is defined by
https://w3id.org/tvbo/struct
is equivalent to
FDM (DiscretizationMethod) c or FEM (DiscretizationMethod) c or FVM (DiscretizationMethod) c or Spectral (DiscretizationMethod) c
has super-classes
Thing c
has sub-classes
FDM (DiscretizationMethod) c, FEM (DiscretizationMethod) c, FVM (DiscretizationMethod) c, Spectral (DiscretizationMethod) c

Distributionc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Distribution

A probability distribution for sampling parameters or initial conditions. Standard distributions (Uniform, Gaussian) are specified by name and domain/parameters. Custom distributions use a Function for the PDF/sampling rule. Default name is Uniform when only domain is given.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

divergence (OperatorType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/OperatorType#divergence

Is defined by
https://w3id.org/tvbo/struct
has super-classes
OperatorType c

docker (EnvironmentType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/EnvironmentType#docker

Docker container.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
EnvironmentType c

dynamic_mean_field (ModelParadigm)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/ModelParadigm#dynamic_mean_field

Dynamic mean-field approximation (e.g., Deco et al.).
Is defined by
https://w3id.org/tvbo/struct
has super-classes
ModelParadigm c

Dynamical propertyc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/DynamicalProperty

Top-level grouping for qualitative phase-space properties.
has super-classes
Thing c
has sub-classes
Attractor c, Bifurcation c, Dynamical regime c, Stochasticity character c

Dynamical regimec back to ToC or Class ToC

IRI: https://w3id.org/tvbo/DynamicalRegime

has super-classes
Dynamical property c
has sub-classes
Bistable c, Bursting c, Chaotic c, Excitable c, Multistable c, Oscillatory c, Quiescent c

EcosystemEnumc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/EcosystemEnum

Package ecosystem or registry the software is distributed through.
Is defined by
https://w3id.org/tvbo/struct
is equivalent to
conda_forge c or pypi c or maven c or npm c or cran c or bioconda (EcosystemEnum) c or github (EcosystemEnum) c or julia_registry (EcosystemEnum) c
has super-classes
Thing c
has sub-classes
bioconda (EcosystemEnum) c, conda_forge c, cran c, github (EcosystemEnum) c, julia_registry (EcosystemEnum) c, maven c, npm c, pypi c

Edgec back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Edge

An edge in a network. Two modes: explicit (source+target set, scalar parameters in YAML) or template (no source/target, N×N matrix measure in HDF5). Both coexist in the same edges list.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

EEG (ImagingModality)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/ImagingModality#EEG

Electroencephalography.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
ImagingModality c

EField (dbs)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/dbs/EField

Simulated electric field from DBS modeling.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

Electrode (dbs)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/dbs/Electrode

Implanted DBS electrode and contact geometry.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

ElementTypec back to ToC or Class ToC

IRI: https://w3id.org/tvbo/ElementType

Is defined by
https://w3id.org/tvbo/struct
is equivalent to
hexahedron (ElementType) c or quad (ElementType) c or tetrahedron (ElementType) c or triangle (ElementType) c
has super-classes
Thing c
has sub-classes
hexahedron (ElementType) c, quad (ElementType) c, tetrahedron (ElementType) c, triangle (ElementType) c

engine (RequirementRole)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/RequirementRole#engine

Primary simulation/processing engine.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
RequirementRole c

EnvironmentTypec back to ToC or Class ToC

IRI: https://w3id.org/tvbo/EnvironmentType

Is defined by
https://w3id.org/tvbo/struct
is equivalent to
conda (EnvironmentType) c or docker (EnvironmentType) c or singularity (EnvironmentType) c or venv (EnvironmentType) c
has super-classes
Thing c
has sub-classes
conda (EnvironmentType) c, docker (EnvironmentType) c, singularity (EnvironmentType) c, venv (EnvironmentType) c

Equationc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Equation

Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c
has sub-classes
TemporalApplicableEquation c
is in range of
equation (slot) op

ErdosRenyi (StandardGraphType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/StandardGraphType#ErdosRenyi

Erdos-Renyi random graph (params: p)
Is defined by
https://w3id.org/tvbo/struct
has super-classes
StandardGraphType c

Eventc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Event

A discrete or continuous event that modifies the system during simulation. Generalizes Stimulus: can represent external inputs (stimulus type), threshold-triggered state changes (continuous/discrete type), or time-scheduled interventions (preset_time type). Attaches to components (nodes/edges) or to the experiment level.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

EventTypec back to ToC or Class ToC

IRI: https://w3id.org/tvbo/EventType

Type of event triggering mechanism.
Is defined by
https://w3id.org/tvbo/struct
is equivalent to
continuous (EventType) c or discrete (EventType) c or preset_time (EventType) c or stimulus (EventType) c
has super-classes
Thing c
has sub-classes
continuous (EventType) c, discrete (EventType) c, preset_time (EventType) c, stimulus (EventType) c

Excitablec back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Excitable

has super-classes
Dynamical regime c
is also defined as
named individual

ExecutionConfigc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/ExecutionConfig

Configuration for computational execution (parallelization, precision, hardware).
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

Explorationc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Exploration

Parameter space exploration (grid search, sweep).
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

ExplorationAxisc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/ExplorationAxis

One axis of a parameter exploration grid. Points to an existing Parameter (by dotted reference, e.g. "ReducedWongWang.w" or "FastLinearCoupling.G") and supplies the sweep specification (domain, explored_values, or per-element overrides). No new Parameter is created.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

FDM (DiscretizationMethod)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/DiscretizationMethod#FDM

Finite Difference Method
Is defined by
https://w3id.org/tvbo/struct
has super-classes
DiscretizationMethod c

FEM (DiscretizationMethod)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/DiscretizationMethod#FEM

Finite Element Method
Is defined by
https://w3id.org/tvbo/struct
has super-classes
DiscretizationMethod c

female (SexEnum)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/SexEnum#female

Female
Is defined by
https://w3id.org/tvbo/struct
has super-classes
SexEnum c

field (ModelType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/ModelType#field

Spatially distributed neural-field models described by integro- differential or PDE formulations.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
ModelType c

FieldStateVariablec back to ToC or Class ToC

IRI: https://w3id.org/tvbo/FieldStateVariable

Is defined by
https://w3id.org/tvbo/struct
has super-classes
StateVariable c

Filec back to ToC or Class ToC

IRI: https://w3id.org/tvbo/File

Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

first (AggregationType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/AggregationType#first

First value in window
Is defined by
https://w3id.org/tvbo/struct
has super-classes
AggregationType c

Fixed pointc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/FixedPoint

has super-classes
Attractor c
is also defined as
named individual

Fold of limit cyclesc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/FoldOfLimitCycles

has super-classes
Bifurcation c

Fortranc back to ToC or Class ToC

IRI: http://www.wikidata.org/entity/Q83303

has super-classes
ProgrammingLanguageEnum c

frameworkc back to ToC or Class ToC

IRI: http://www.wikidata.org/entity/Q271680

Multi-paradigm simulation framework.
has super-classes
ToolRole c

FreeParameterc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/FreeParameter

One degree of freedom in an OptimizationStage. References an existing Parameter by dotted scope (e.g. "ReducedWongWang.w" or "FastLinearCoupling.G") and supplies optimization-specific metadata (heterogeneous, shape, bounds, initial value). No new Parameter is created here.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

frequency (DimensionType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/DimensionType#frequency

Frequency dimension (spectral analysis)
Is defined by
https://w3id.org/tvbo/struct
has super-classes
DimensionType c

from_branch (InitialStateMethod)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/InitialStateMethod#from_branch

Start from a point on a previously computed branch.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
InitialStateMethod c

Functionc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Function

A function with explicit input -> transformation -> output flow. Can be equation-based (symbolic) or software-based (callable). In a pipeline, functions are chained: output of one becomes input of next.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c
has sub-classes
LossFunction c

FunctionCallc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/FunctionCall

Invocation of a function in a pipeline. Can reference a defined Function by name, OR inline a callable directly for external library functions, OR inline an equation, OR use class_call for class instantiation. Mirrors Function attributes so pipeline steps can be self-contained. The `name` is an optional step label (used in pipelines for keyed access to step outputs); it is NOT a global identifier (singleton uses like `loss`, `observable` may omit it).
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

FVM (DiscretizationMethod)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/DiscretizationMethod#FVM

Finite Volume Method
Is defined by
https://w3id.org/tvbo/struct
has super-classes
DiscretizationMethod c

gaussian (NoiseType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/NoiseType#gaussian

Is defined by
https://w3id.org/tvbo/struct
has super-classes
NoiseType c

generic (ModelParadigm)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/ModelParadigm#generic

General-purpose, not specific to neuroscience.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
ModelParadigm c

generic (ModelType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/ModelType#generic

Generic / normal-form dynamical systems not specific to neural modelling (e.g. Generic2dOscillator, GenericLinear).
Is defined by
https://w3id.org/tvbo/struct
has super-classes
ModelType c

github (EcosystemEnum)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/EcosystemEnum#github

Distributed via GitHub releases.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
EcosystemEnum c

given (InitialStateMethod)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/InitialStateMethod#given

Use the model's default initial values directly.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
InitialStateMethod c

gradient (OperatorType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/OperatorType#gradient

Is defined by
https://w3id.org/tvbo/struct
has super-classes
OperatorType c

GraphGeneratorc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/GraphGenerator

Backend-agnostic graph generator specification. Captures the mathematical family (type) and its parameters so that each backend can emit the correct constructor call (Graphs.jl, NetworkX, etc.). The number of nodes is always taken from Network.number_of_nodes.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

Grid (StandardGraphType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/StandardGraphType#Grid

Grid/lattice graph (params: dims)
Is defined by
https://w3id.org/tvbo/struct
has super-classes
StandardGraphType c

H_per_mc back to ToC or Class ToC

IRI: http://qudt.org/vocab/unit/H-PER-M

Henry per metre (permeability)
has super-classes
UnitEnum c

Haskellc back to ToC or Class ToC

IRI: http://www.wikidata.org/entity/Q34010

has super-classes
ProgrammingLanguageEnum c

Hemispherec back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Hemisphere

Is defined by
https://w3id.org/tvbo/struct
is equivalent to
both (Hemisphere) c or left (Hemisphere) c or right (Hemisphere) c
has super-classes
Thing c
has sub-classes
both (Hemisphere) c, left (Hemisphere) c, right (Hemisphere) c

hexahedron (ElementType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/ElementType#hexahedron

Is defined by
https://w3id.org/tvbo/struct
has super-classes
ElementType c

HOCc back to ToC or Class ToC

IRI: http://www.wikidata.org/entity/Q5765633

NEURON's high-level interpreted language.
has super-classes
ProgrammingLanguageEnum c

Homoclinicc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/HomoclinicBifurcation

has super-classes
Bifurcation c
is also defined as
named individual

Hopfc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Hopf

has super-classes
Bifurcation c
has sub-classes
Subcritical Hopf c, Supercritical Hopf c
is also defined as
named individual

Hzc back to ToC or Class ToC

IRI: http://qudt.org/vocab/unit/HZ

Hertz (s⁻¹)
has super-classes
UnitEnum c

Hz_per_nA (UnitEnum)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/UnitEnum#Hz_per_nA

Hertz per nanoampere (neural gain)
Is defined by
https://w3id.org/tvbo/struct
has super-classes
UnitEnum c

IEEG (ImagingModality)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/ImagingModality#IEEG

Intracranial Electroencephalography.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
ImagingModality c

ImagingModalityc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/ImagingModality

Is defined by
https://w3id.org/tvbo/struct
is equivalent to
BOLD (ImagingModality) c or EEG (ImagingModality) c or IEEG (ImagingModality) c or MEG (ImagingModality) c or SEEG (ImagingModality) c
has super-classes
Thing c
has sub-classes
BOLD (ImagingModality) c, EEG (ImagingModality) c, IEEG (ImagingModality) c, MEG (ImagingModality) c, SEEG (ImagingModality) c

inactive (DevelopmentStatus)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/DevelopmentStatus#inactive

No longer actively developed; may still work.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
DevelopmentStatus c

InitialStatec back to ToC or Class ToC

IRI: https://w3id.org/tvbo/InitialState

How to obtain the starting equilibrium or periodic orbit for continuation. Most robust: time-integrate to steady state.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

InitialStateMethodc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/InitialStateMethod

Strategy for obtaining the starting equilibrium or periodic orbit.
Is defined by
https://w3id.org/tvbo/struct
is equivalent to
from_branch (InitialStateMethod) c or given (InitialStateMethod) c or newton (InitialStateMethod) c or time_integration (InitialStateMethod) c
has super-classes
Thing c
has sub-classes
from_branch (InitialStateMethod) c, given (InitialStateMethod) c, newton (InitialStateMethod) c, time_integration (InitialStateMethod) c

Integratorc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Integrator

Fixed-step or adaptive ODE integrator with TVB-specific extensions (noise, transient time, etc.). Inherits abs_tol, rel_tol from Solver. Overrides method default to 'euler'.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Solver c
has members
Dopri5 ni, Dopri853 ni, Euler ni, Heun ni, Identity ni, RungeKutta4thOrder ni, VODE ni

Javac back to ToC or Class ToC

IRI: http://www.wikidata.org/entity/Q251

has super-classes
ProgrammingLanguageEnum c

JavaScriptc back to ToC or Class ToC

IRI: http://www.wikidata.org/entity/Q2005

has super-classes
ProgrammingLanguageEnum c

Juliac back to ToC or Class ToC

IRI: http://www.wikidata.org/entity/Q4010477

has super-classes
ProgrammingLanguageEnum c

julia_registry (EcosystemEnum)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/EcosystemEnum#julia_registry

Julia General package registry.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
EcosystemEnum c

kgc back to ToC or Class ToC

IRI: http://qudt.org/vocab/unit/KiloGM

Kilogram
has super-classes
UnitEnum c

kg_per_s (UnitEnum)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/UnitEnum#kg_per_s

Kilogram per second
Is defined by
https://w3id.org/tvbo/struct
has super-classes
UnitEnum c

kHzc back to ToC or Class ToC

IRI: http://qudt.org/vocab/unit/KiloHZ

Kilohertz
has super-classes
UnitEnum c

kohm_cm (UnitEnum)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/UnitEnum#kohm_cm

Kilo-ohm centimetre (axial resistivity)
Is defined by
https://w3id.org/tvbo/struct
has super-classes
UnitEnum c

laplacian (OperatorType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/OperatorType#laplacian

Is defined by
https://w3id.org/tvbo/struct
has super-classes
OperatorType c

last (AggregationType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/AggregationType#last

Last value in window
Is defined by
https://w3id.org/tvbo/struct
has super-classes
AggregationType c

left (Hemisphere)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Hemisphere#left

Is defined by
https://w3id.org/tvbo/struct
has super-classes
Hemisphere c

length (PhysicalDimension)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/PhysicalDimension#length

Length [L]
Is defined by
https://w3id.org/tvbo/struct
has super-classes
PhysicalDimension c

Limit cyclec back to ToC or Class ToC

IRI: https://w3id.org/tvbo/LimitCycle

has super-classes
Attractor c
is also defined as
named individual

LossFunctionc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/LossFunction

A loss function for optimization with optional aggregation. Extends Function with aggregation specification for per-element losses.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Function c

mc back to ToC or Class ToC

IRI: http://qudt.org/vocab/unit/M

Metre
has super-classes
UnitEnum c

m_per_sc back to ToC or Class ToC

IRI: http://qudt.org/vocab/unit/M-PER-SEC

Metre per second
has super-classes
UnitEnum c

m_per_s2c back to ToC or Class ToC

IRI: http://qudt.org/vocab/unit/M-PER-SEC2

Metre per second squared (acceleration)
has super-classes
UnitEnum c

male (SexEnum)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/SexEnum#male

Male
Is defined by
https://w3id.org/tvbo/struct
has super-classes
SexEnum c

MATLABc back to ToC or Class ToC

IRI: http://www.wikidata.org/entity/Q182017

has super-classes
ProgrammingLanguageEnum c

Matrixc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Matrix

Adjacency matrix of a network.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

mavenc back to ToC or Class ToC

IRI: http://www.wikidata.org/entity/Q6795527

Maven Central Repository (Java).
has super-classes
EcosystemEnum c

max (ReductionType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/ReductionType#max

Maximum value
Is defined by
https://w3id.org/tvbo/struct
has super-classes
ReductionType c

mean (AggregationType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/AggregationType#mean

Average over time
Is defined by
https://w3id.org/tvbo/struct
has super-classes
AggregationType c

mean (ReductionType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/ReductionType#mean

Arithmetic mean
Is defined by
https://w3id.org/tvbo/struct
has super-classes
ReductionType c

mean_fieldc back to ToC or Class ToC

IRI: http://www.wikidata.org/entity/Q1368960

Mean-field reductions of spiking networks.
has super-classes
ModelParadigm c

mean_field (ModelType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/ModelType#mean_field

Mathematically derived mean-field models obtained by exact reduction of spiking networks (Ott-Antonsen ansatz, Lorentzian heterogeneity, etc.). Examples: MontbrioPazoRoxin, CoombesByrne, ReducedWongWang, ZerlautAdaptationFirstOrder.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
ModelType c

MEG (ImagingModality)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/ImagingModality#MEG

Magnetoencephalography.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
ImagingModality c

Meshc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Mesh

Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

min (ReductionType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/ReductionType#min

Minimum value
Is defined by
https://w3id.org/tvbo/struct
has super-classes
ReductionType c

mmc back to ToC or Class ToC

IRI: http://qudt.org/vocab/unit/MilliM

Millimetre
has super-classes
UnitEnum c

mm_per_msc back to ToC or Class ToC

IRI: http://qudt.org/vocab/unit/MilliM-PER-MilliSEC

Millimetre per millisecond (= m/s)
has super-classes
UnitEnum c

mmol_per_m3c back to ToC or Class ToC

IRI: http://qudt.org/vocab/unit/MilliMOL-PER-M3

Millimole per cubic metre (mmol/m³ ≈ mM)
has super-classes
UnitEnum c

mode (DimensionType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/DimensionType#mode

Mode dimension (e.g., coupling modes)
Is defined by
https://w3id.org/tvbo/struct
has super-classes
DimensionType c

Model featurec back to ToC or Class ToC

IRI: https://w3id.org/tvbo/ModelFeature

Intrinsic structural trait of a Dynamics model (e.g. sigmoid activation, fast-slow decomposition, E/I subpopulations). Distinct from BackendCapability: a feature is what the model has, a capability is what a backend provides.
has super-classes
Thing c
is in range of
has model feature op
has members
Excitatory/inhibitory subpopulations ni, Fast-slow decomposition ni, Sigmoid activation ni

model_description (ModelParadigm)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/ModelParadigm#model_description

Declarative model specification language.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
ModelParadigm c

model_repositoryc back to ToC or Class ToC

IRI: http://www.wikidata.org/entity/Q7397

Database or repository of published models.
has super-classes
ToolRole c

ModelTypec back to ToC or Class ToC

IRI: https://w3id.org/tvbo/ModelType

Coarse classification of a Dynamics model by its mathematical/biological origin. Used for filtering and display in list_db().
Is defined by
https://w3id.org/tvbo/struct
is equivalent to
field (ModelType) c or generic (ModelType) c or mean_field (ModelType) c or neural_mass (ModelType) c or phase_oscillator (ModelType) c or phenomenological (ModelType) c or spiking (ModelType) c
has super-classes
Thing c
has sub-classes
field (ModelType) c, generic (ModelType) c, mean_field (ModelType) c, neural_mass (ModelType) c, phase_oscillator (ModelType) c, phenomenological (ModelType) c, spiking (ModelType) c

Mohm (UnitEnum)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/UnitEnum#Mohm

Megaohm (MΩ)
Is defined by
https://w3id.org/tvbo/struct
has super-classes
UnitEnum c

mol_per_cm3 (UnitEnum)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/UnitEnum#mol_per_cm3

Mole per cubic centimetre (mol/cm³)
Is defined by
https://w3id.org/tvbo/struct
has super-classes
UnitEnum c

mol_per_m3c back to ToC or Class ToC

IRI: http://qudt.org/vocab/unit/MOL-PER-M3

Mole per cubic metre (mol/m³)
has super-classes
UnitEnum c

mol_per_m_per_A_per_s (UnitEnum)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/UnitEnum#mol_per_m_per_A_per_s

Mole per metre per ampere per second (concentration-current coupling)
Is defined by
https://w3id.org/tvbo/struct
has super-classes
UnitEnum c

MoorePenrose (ContinuationAlgorithm)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/ContinuationAlgorithm#MoorePenrose

Moore-Penrose continuation.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
ContinuationAlgorithm c

moved (DevelopmentStatus)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/DevelopmentStatus#moved

Project has been moved to a different location.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
DevelopmentStatus c

msc back to ToC or Class ToC

IRI: http://qudt.org/vocab/unit/MilliSEC

Millisecond
has super-classes
UnitEnum c

mS_per_cm2 (UnitEnum)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/UnitEnum#mS_per_cm2

Millisiemens per square centimetre (conductance density)
Is defined by
https://w3id.org/tvbo/struct
has super-classes
UnitEnum c

Multiplicative noisec back to ToC or Class ToC

IRI: https://w3id.org/tvbo/MultiplicativeNoise

has super-classes
Stochasticity character c

multiscalec back to ToC or Class ToC

IRI: http://www.wikidata.org/entity/Q1948412

Bridging multiple spatial/temporal scales.
has super-classes
ModelParadigm c

Multistablec back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Multistable

has super-classes
Dynamical regime c
is also defined as
named individual

mVc back to ToC or Class ToC

IRI: http://qudt.org/vocab/unit/MilliV

Millivolt
has super-classes
UnitEnum c

mV_per_msc back to ToC or Class ToC

IRI: http://qudt.org/vocab/unit/MilliV-PER-MilliSEC

Millivolt per millisecond
has super-classes
UnitEnum c

mV_per_sc back to ToC or Class ToC

IRI: http://qudt.org/vocab/unit/MilliV-PER-SEC

Millivolt per second
has super-classes
UnitEnum c

N_per_mc back to ToC or Class ToC

IRI: http://qudt.org/vocab/unit/N-PER-M

Newton per metre (spring constant)
has super-classes
UnitEnum c

nAc back to ToC or Class ToC

IRI: http://qudt.org/vocab/unit/NanoA

Nanoampere
has super-classes
UnitEnum c

Natural (ContinuationAlgorithm)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/ContinuationAlgorithm#Natural

Natural parameter continuation. Simple parameter stepping, no arc-length constraint.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
ContinuationAlgorithm c

NDArrayc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/NDArray

Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

Networkc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Network

Network specification with nodes, edges, and reusable coupling configurations. Supports both explicit node/edge representation and matrix-based connectivity (Connectome compatibility).
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c
has members
SmileyNetwork ni, acq-EEGBrainstorm65_sensors ni, acq-MEGBrainstorm276_sensors ni, acq-SEEG588_sensors ni, example_3node_network ni, sensors_eeg_standard1005_fsaverage_aparc_projection ni, tpl-FSLMNI152_cohort-HCPYA_rec-Hansen2022_atlas-Schaefer2018_seg-7Networks_scale-100_desc-SCFC_relmat ni, tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_scale-1000_desc-SC_relmat ni, tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-1000_desc-SC_relmat ni, tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-100_desc-SC_relmat ni, tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-200_desc-SC_relmat ni, tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-300_desc-SC_relmat ni, tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-400_desc-SC_relmat ni, tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-500_desc-SC_relmat ni, tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-600_desc-SC_relmat ni, tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-700_desc-SC_relmat ni, tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-800_desc-SC_relmat ni, tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-900_desc-SC_relmat ni, tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-1000_desc-SC_relmat ni, tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-100_desc-SC_relmat ni, tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-200_desc-SC_relmat ni, tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-300_desc-SC_relmat ni, tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-400_desc-SC_relmat ni, tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-500_desc-SC_relmat ni, tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-600_desc-SC_relmat ni, tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-700_desc-SC_relmat ni, tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-800_desc-SC_relmat ni, tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-900_desc-SC_relmat ni, tpl-FSLMNI152_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-Schaefer2018_scale-1000_desc-SC_relmat ni, tpl-FSLMNI152_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-Schaefer2018_seg-17Networks_scale-1000_desc-SC_relmat ni, tpl-FSLMNI152_cohort-PPMI85_rec-PPMI85_atlas-Schaefer2018_scale-1000_desc-SC_relmat ni, tpl-FSLMNI152_cohort-PPMI85_rec-PPMI85_atlas-Schaefer2018_seg-17Networks_scale-1000_desc-SC_relmat ni, tpl-MNI152NLin2009bAsym_cohort-HCPYA_rec-dTOR_atlas-HCPMMP1_desc-SC_relmat ni, tpl-MNI152NLin2009bAsym_cohort-HCPYA_rec-dTOR_atlas-HCPMMP1_seg-ordered_desc-SC_relmat ni, tpl-MNI152NLin2009bAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-HCPMMP1_desc-SC_relmat ni, tpl-MNI152NLin2009bAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-HCPMMP1_seg-ordered_desc-SC_relmat ni, tpl-MNI152NLin2009bAsym_cohort-PPMI85_rec-PPMI85_atlas-HCPMMP1_desc-SC_relmat ni, tpl-MNI152NLin2009bAsym_cohort-PPMI85_rec-PPMI85_atlas-HCPMMP1_seg-ordered_desc-SC_relmat ni, tpl-MNI152NLin2009cAsym_cohort-HCPYA_atlas-Lobar8_desc-surf_relmat ni, tpl-MNI152NLin2009cAsym_cohort-HCPYA_atlas-Lobar8_hemi-L_desc-surf_relmat ni, tpl-MNI152NLin2009cAsym_cohort-HCPYA_atlas-Lobar8_hemi-R_desc-surf_relmat ni, tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-DesikanKilliany_desc-SC_relmat ni, tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Destrieux_desc-SC_relmat ni, tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-HCPex_desc-SC_relmat ni, tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Lobar8_desc-SCFC_relmat ni, tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Lobar_desc-SC_relmat ni, tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Lobar_desc-surf_relmat ni, tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Yeo17_desc-SC_relmat ni, tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-virtualdbs_desc-SC_relmat ni, tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-DesikanKilliany_desc-SC_relmat ni, tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-Destrieux_desc-SC_relmat ni, tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-HOCPA_desc-SC_relmat ni, tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-Yeo17_desc-SC_relmat ni, tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-virtualdbs_desc-SC_relmat ni, tpl-MNI152NLin2009cAsym_cohort-PPMI85_rec-PPMI85_atlas-DesikanKilliany_desc-SC_relmat ni, tpl-MNI152NLin2009cAsym_cohort-PPMI85_rec-PPMI85_atlas-Destrieux_desc-SC_relmat ni, tpl-MNI152NLin2009cAsym_cohort-PPMI85_rec-PPMI85_atlas-Yeo17_desc-SC_relmat ni, tpl-MNI152NLin2009cAsym_cohort-PPMI85_rec-PPMI85_atlas-virtualdbs_desc-SC_relmat ni, tpl-MNI152NLin2009cAsym_rec-avgMatrix_atlas-DesikanKilliany_desc-SCFC_relmat ni, tpl-MNI152NLin2009cAsym_rec-avgMatrix_atlas-Lobar8_desc-SCFC_relmat ni, tpl-fsaverage_acq-EEGstandard1005_atlas-DesikanKilliany_desc-projection_sensors ni

network_systemc back to ToC or Class ToC

IRI: http://www.wikidata.org/entity/Q1073340

Whole-brain or large-scale network of regions.
has super-classes
SimulationScale c

Neumann (BoundaryConditionType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/BoundaryConditionType#Neumann

Is defined by
https://w3id.org/tvbo/struct
has super-classes
BoundaryConditionType c

neural_massc back to ToC or Class ToC

IRI: http://www.wikidata.org/entity/Q7003015

Phenomenological population-rate / neural-mass models.
has super-classes
ModelParadigm c, SimulationScale c

neural_mass (ModelType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/ModelType#neural_mass

Phenomenological population-rate / neural-mass models that describe synaptic and firing-rate dynamics without an explicit derivation from single-neuron statistics. Examples: JansenRit, WilsonCowan, LarterBreakspear, TsodyksMarkram.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
ModelType c

neural_networkc back to ToC or Class ToC

IRI: http://www.wikidata.org/entity/Q484761

Microcircuit / local network of neurons.
has super-classes
SimulationScale c

neuronc back to ToC or Class ToC

IRI: http://www.wikidata.org/entity/Q43054

Single neuron (compartmental or point).
has super-classes
SimulationScale c

newton (InitialStateMethod)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/InitialStateMethod#newton

Use Newton's method to find the nearest fixed point.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
InitialStateMethod c

nFc back to ToC or Class ToC

IRI: http://qudt.org/vocab/unit/NanoFARAD

Nanofarad
has super-classes
UnitEnum c

Nodec back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Node

A node in a network with its own dynamics and properties
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

node (DimensionType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/DimensionType#node

Network node dimension (general graph term)
Is defined by
https://w3id.org/tvbo/struct
has super-classes
DimensionType c

Noisec back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Noise

Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

NoiseTypec back to ToC or Class ToC

IRI: https://w3id.org/tvbo/NoiseType

Is defined by
https://w3id.org/tvbo/struct
is equivalent to
brown (NoiseType) c or gaussian (NoiseType) c or pink (NoiseType) c or white (NoiseType) c
has super-classes
Thing c
has sub-classes
brown (NoiseType) c, gaussian (NoiseType) c, pink (NoiseType) c, white (NoiseType) c

none (AggregationType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/AggregationType#none

No aggregation
Is defined by
https://w3id.org/tvbo/struct
has super-classes
AggregationType c

none (PhysicalDimension)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/PhysicalDimension#none

Dimensionless
Is defined by
https://w3id.org/tvbo/struct
has super-classes
PhysicalDimension c

none (ReductionType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/ReductionType#none

No reduction (return per-element values)
Is defined by
https://w3id.org/tvbo/struct
has super-classes
ReductionType c

npmc back to ToC or Class ToC

IRI: http://www.wikidata.org/entity/Q7067518

Node Package Manager registry.
has super-classes
EcosystemEnum c

nSc back to ToC or Class ToC

IRI: http://qudt.org/vocab/unit/NanoS

Nanosiemens
has super-classes
UnitEnum c

nS_per_mV (UnitEnum)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/UnitEnum#nS_per_mV

Nanosiemens per millivolt
Is defined by
https://w3id.org/tvbo/struct
has super-classes
UnitEnum c

NumericalDiscretizationMethodc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/NumericalDiscretizationMethod

Numerical discretization method for boundary value problems (periodic orbits, connecting orbits, quasi-periodic tori).
Is defined by
https://w3id.org/tvbo/struct
is equivalent to
collocation (NumericalDiscretizationMethod) c or poincare (NumericalDiscretizationMethod) c or shooting (NumericalDiscretizationMethod) c or trapezoid (NumericalDiscretizationMethod) c
has super-classes
Thing c
has sub-classes
collocation (NumericalDiscretizationMethod) c, poincare (NumericalDiscretizationMethod) c, shooting (NumericalDiscretizationMethod) c, trapezoid (NumericalDiscretizationMethod) c

Observationc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Observation

Unified class for all observation/measurement specifications. Covers monitors (BOLD, EEG), tuning observables, and derived quantities. Pipeline is a sequence of Functions with input -> output flow.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c
has sub-classes
DerivedObservation c
has members
AfferentCoupling ni, AfferentCouplingTemporalAverage ni, BOLD_DoubleExponential ni, BOLD_Gamma ni, BOLD_MixtureOfGammas ni, BOLD_RegionROI ni, BOLD_TVB ni, EEG ni, FunctionalConnectivity ni, GlobalAverage ni, MEG ni, Raw ni, SpatialAverage ni, SubSample ni, TemporalAverage ni, iEEG ni

ohmc back to ToC or Class ToC

IRI: http://qudt.org/vocab/unit/OHM

Ohm (Ω)
has super-classes
UnitEnum c

OperatorTypec back to ToC or Class ToC

IRI: https://w3id.org/tvbo/OperatorType

Is defined by
https://w3id.org/tvbo/struct
is equivalent to
curl (OperatorType) c or divergence (OperatorType) c or gradient (OperatorType) c or laplacian (OperatorType) c
has super-classes
Thing c
has sub-classes
curl (OperatorType) c, divergence (OperatorType) c, gradient (OperatorType) c, laplacian (OperatorType) c

Optimizationc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Optimization

Configuration for parameter optimization. Inherits single-stage fields from OptimizationStage. For multi-stage workflows, use 'stages' (ignores inherited single-stage fields). Loss equation references observations directly by name.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
OptimizationStage c

optimization_frameworkc back to ToC or Class ToC

IRI: http://www.wikidata.org/entity/Q816286

Parameter optimization / fitting tool.
has super-classes
ToolRole c

OptimizationStagec back to ToC or Class ToC

IRI: https://w3id.org/tvbo/OptimizationStage

A single stage in a multi-stage optimization workflow. Stages run sequentially, with each stage potentially using different parameters, shapes, learning rates, and algorithms.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c
has sub-classes
Optimization c

Optionc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Option

A toolkit-specific key-value option (string name + string value). Used for backend settings that are not universal numeric parameters (e.g., solver name, tangent method, jacobian type).
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

optional (RequirementRole)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/RequirementRole#optional

Optional or extra feature dependency.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
RequirementRole c

Oscillatoryc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Oscillatory

has super-classes
Dynamical regime c
is also defined as
named individual

other (SexEnum)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/SexEnum#other

Other or not reported
Is defined by
https://w3id.org/tvbo/struct
has super-classes
SexEnum c

pAc back to ToC or Class ToC

IRI: http://qudt.org/vocab/unit/PicoA

Picoampere
has super-classes
UnitEnum c

PALC (ContinuationAlgorithm)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/ContinuationAlgorithm#PALC

Pseudo-arclength continuation (default). Uses weighted dot product constraint.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
ContinuationAlgorithm c

Parameterc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Parameter

Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c
has sub-classes
DerivedParameter c
is in range of
parameters (slot) op
has members
A (JansenRit parameter) ni, A (JansenRit1995 parameter) ni, A (ModelJansen1995 parameter) ni, B (JansenRit parameter) ni, B (JansenRit1995 parameter) ni, B (ModelJansen1995 parameter) ni, C (CakanObermayer parameter) ni, C (JansenRit1995 parameter) ni, C (LarterBreakspear parameter) ni, C (ModelJansen1995 parameter) ni, C_m (ZerlautAdaptationFirstOrder parameter) ni, Chn (KIonEx parameter) ni, Ckp (KIonEx parameter) ni, Cl_i0 (KIonEx parameter) ni, Cl_o0 (KIonEx parameter) ni, Cm (KIonEx parameter) ni, Cmna (KIonEx parameter) ni, Cnap (KIonEx parameter) ni, Cnk (KIonEx parameter) ni, DChn (KIonEx parameter) ni, DCkp (KIonEx parameter) ni, DCmna (KIonEx parameter) ni, DCnap (KIonEx parameter) ni, DCnk (KIonEx parameter) ni, DTvN0 (ZerlautAdaptationFirstOrder parameter) ni, Delta (CoombesByrne parameter) ni, Delta (CoombesByrne2D parameter) ni, Delta (GastSchmidtKnosche_SD parameter) ni, Delta (GastSchmidtKnosche_SF parameter) ni, Delta (KIonEx parameter) ni, Delta (MontbrioPazoRoxin parameter) ni, Delta_e (DumontGutkin parameter) ni, Delta_i (DumontGutkin parameter) ni, DmuV0 (ZerlautAdaptationFirstOrder parameter) ni, DsV0 (ZerlautAdaptationFirstOrder parameter) ni, E (KIonEx parameter) ni, E0 (TsodyksMarkram parameter) ni, E_A (CakanObermayer parameter) ni, E_L (CakanObermayer parameter) ni, E_L_e (ZerlautAdaptationFirstOrder parameter) ni, E_L_i (ZerlautAdaptationFirstOrder parameter) ni, E_e (ZerlautAdaptationFirstOrder parameter) ni, E_i (ZerlautAdaptationFirstOrder parameter) ni, G (FastLinearCoupling parameter) ni, G (PreSigmoidal parameter) ni, G (ReducedWongWangExcInh parameter) ni, G (example_3node_network parameter) ni, Gamma (DumontGutkin parameter) ni, H (PreSigmoidal parameter) ni, He (ZetterbergJansen parameter) ni, Hi (ZetterbergJansen parameter) ni, I (GastSchmidtKnosche_SD parameter) ni, I (GastSchmidtKnosche_SF parameter) ni, I (Generic2dOscillator parameter) ni, I (MontbrioPazoRoxin parameter) ni, I_A (CakanObermayer parameter) ni, I_e (DumontGutkin parameter) ni, I_ext (LarterBreakspear parameter) ni, I_ext (ReducedWongWangExcInh parameter) ni, I_i (DumontGutkin parameter) ni, I_o (ReducedWongWang parameter) ni, I_o (ReducedWongWangExcInh parameter) ni, I_o (ReducedWongWangTvboptim parameter) ni, I_rs (EpileptorRestingState parameter) ni, Iext (Epileptor2D parameter) ni, Iext (Epileptor5D parameter) ni, Iext (EpileptorRestingState parameter) ni, Iext2 (Epileptor5D parameter) ni, Iext2 (EpileptorRestingState parameter) ni, J (GastSchmidtKnosche_SD parameter) ni, J (GastSchmidtKnosche_SF parameter) ni, J (JansenRit parameter) ni, J (KIonEx parameter) ni, J (MontbrioPazoRoxin parameter) ni, J (TsodyksMarkram parameter) ni, J_EE (CakanObermayer parameter) ni, J_EI (CakanObermayer parameter) ni, J_IE (CakanObermayer parameter) ni, J_II (CakanObermayer parameter) ni, J_N (ReducedWongWang parameter) ni, J_N (ReducedWongWangExcInh parameter) ni, J_N (ReducedWongWangTvboptim parameter) ni, J_ee (DumontGutkin parameter) ni, J_ei (DumontGutkin parameter) ni, J_i (ReducedWongWangExcInh parameter) ni, J_ie (DumontGutkin parameter) ni, J_ii (DumontGutkin parameter) ni, K11 (StefanescuJirsa2D parameter) ni, K12 (StefanescuJirsa2D parameter) ni, K21 (StefanescuJirsa2D parameter) ni, K_11 (StefanescuJirsa3D parameter) ni, K_12 (StefanescuJirsa3D parameter) ni, K_21 (StefanescuJirsa3D parameter) ni, K_bath (KIonEx parameter) ni, K_ext_e (ZerlautAdaptationFirstOrder parameter) ni, K_ext_i (ZerlautAdaptationFirstOrder parameter) ni, K_i0 (KIonEx parameter) ni, K_o0 (KIonEx parameter) ni, K_rs (EpileptorRestingState parameter) ni, Kf (Epileptor5D parameter) ni, Kf (EpileptorRestingState parameter) ni, Ks (Epileptor2D parameter) ni, Ks (Epileptor5D parameter) ni, Ks (EpileptorRestingState parameter) ni, Kvf (Epileptor2D parameter) ni, Kvf (Epileptor5D parameter) ni, Kvf (EpileptorRestingState parameter) ni, N (Epileptor3DStefanescuMcDonald parameter) ni, N (KuramotoCoupling parameter) ni, N_tot (ZerlautAdaptationFirstOrder parameter) ni, Na_i0 (KIonEx parameter) ni, Na_o0 (KIonEx parameter) ni, P (PreSigmoidal parameter) ni, P (WilsonCowan parameter) ni, P (ZetterbergJansen parameter) ni, P0_e (ZerlautAdaptationFirstOrder parameter) ni, P0_i (ZerlautAdaptationFirstOrder parameter) ni, P1_e (ZerlautAdaptationFirstOrder parameter) ni, P1_i (ZerlautAdaptationFirstOrder parameter) ni, P2_e (ZerlautAdaptationFirstOrder parameter) ni, P2_i (ZerlautAdaptationFirstOrder parameter) ni, P3_e (ZerlautAdaptationFirstOrder parameter) ni, P3_i (ZerlautAdaptationFirstOrder parameter) ni, P4_e (ZerlautAdaptationFirstOrder parameter) ni, P4_i (ZerlautAdaptationFirstOrder parameter) ni, P5_e (ZerlautAdaptationFirstOrder parameter) ni, P5_i (ZerlautAdaptationFirstOrder parameter) ni, P6_e (ZerlautAdaptationFirstOrder parameter) ni, P6_i (ZerlautAdaptationFirstOrder parameter) ni, P7_e (ZerlautAdaptationFirstOrder parameter) ni, P7_i (ZerlautAdaptationFirstOrder parameter) ni, P8_e (ZerlautAdaptationFirstOrder parameter) ni, P8_i (ZerlautAdaptationFirstOrder parameter) ni, P9_e (ZerlautAdaptationFirstOrder parameter) ni, P9_i (ZerlautAdaptationFirstOrder parameter) ni, P_e (ZerlautAdaptationFirstOrder parameter) ni, P_i (ZerlautAdaptationFirstOrder parameter) ni, Q (PreSigmoidal parameter) ni, Q (WilsonCowan parameter) ni, Q (ZetterbergJansen parameter) ni, Q_Vmax (LarterBreakspear parameter) ni, Q_Zmax (LarterBreakspear parameter) ni, Q_e (ZerlautAdaptationFirstOrder parameter) ni, Q_i (ZerlautAdaptationFirstOrder parameter) ni, R_minus (KIonEx parameter) ni, R_plus (KIonEx parameter) ni, S_i (ZerlautAdaptationFirstOrder parameter) ni, T (ZerlautAdaptationFirstOrder parameter) ni, TR (FC parameter) ni, TR (bold_double_exponential parameter) ni, TR (bold_gamma parameter) ni, TR (bold_mixture_of_gammas parameter) ni, TR (bold_tvb parameter) ni, T_Ca (LarterBreakspear parameter) ni, T_K (LarterBreakspear parameter) ni, T_Na (LarterBreakspear parameter) ni, TvN0 (ZerlautAdaptationFirstOrder parameter) ni, U (ZetterbergJansen parameter) ni, U0 (TsodyksMarkram parameter) ni, V_Ca (LarterBreakspear parameter) ni, V_K (LarterBreakspear parameter) ni, V_L (LarterBreakspear parameter) ni, V_Na (LarterBreakspear parameter) ni, V_T (LarterBreakspear parameter) ni, Vstar (KIonEx parameter) ni, W_e (ReducedWongWangExcInh parameter) ni, W_i (ReducedWongWangExcInh parameter) ni, Z_T (LarterBreakspear parameter) ni, a (Difference parameter) ni, a (Epileptor2D parameter) ni, a (Epileptor5D parameter) ni, a (EpileptorRestingState parameter) ni, a (Generic2dOscillator parameter) ni, a (HyperbolicTangent parameter) ni, a (JansenRit parameter) ni, a (JansenRit1995 parameter) ni, a (KuramotoCoupling parameter) ni, a (Linear parameter) ni, a (ModelJansen1995 parameter) ni, a (ReducedWongWang parameter) ni, a (ReducedWongWangTvboptim parameter) ni, a (Scaling parameter) ni, a (Sigmoidal parameter) ni, a (SigmoidalJansenRit parameter) ni, a (StefanescuJirsa2D parameter) ni, a (StefanescuJirsa3D parameter) ni, a (SupHopf parameter) ni, a_1 (JansenRit parameter) ni, a_2 (JansenRit parameter) ni, a_3 (JansenRit parameter) ni, a_4 (JansenRit parameter) ni, a_e (ReducedWongWangExcInh parameter) ni, a_e (WilsonCowan parameter) ni, a_e (ZerlautAdaptationFirstOrder parameter) ni, a_ee (LarterBreakspear parameter) ni, a_ei (LarterBreakspear parameter) ni, a_i (ReducedWongWangExcInh parameter) ni, a_i (WilsonCowan parameter) ni, a_i (ZerlautAdaptationFirstOrder parameter) ni, a_ie (LarterBreakspear parameter) ni, a_ne (LarterBreakspear parameter) ni, a_ni (LarterBreakspear parameter) ni, a_rs (EpileptorRestingState parameter) ni, aa (Epileptor5D parameter) ni, aa (EpileptorRestingState parameter) ni, alpha (CoombesByrne parameter) ni, alpha (GastSchmidtKnosche_SD parameter) ni, alpha (GastSchmidtKnosche_SF parameter) ni, alpha (Generic2dOscillator parameter) ni, alpha (TsodyksMarkram parameter) ni, alpha_e (WilsonCowan parameter) ni, alpha_i (WilsonCowan parameter) ni, alpha_rs (EpileptorRestingState parameter) ni, b (Epileptor2D parameter) ni, b (Epileptor5D parameter) ni, b (EpileptorRestingState parameter) ni, b (FastLinearCoupling parameter) ni, b (Generic2dOscillator parameter) ni, b (HyperbolicTangent parameter) ni, b (JansenRit parameter) ni, b (JansenRit1995 parameter) ni, b (LarterBreakspear parameter) ni, b (Linear parameter) ni, b (ModelJansen1995 parameter) ni, b (ReducedWongWang parameter) ni, b (ReducedWongWangTvboptim parameter) ni, b (StefanescuJirsa2D parameter) ni, b (StefanescuJirsa3D parameter) ni, b_e (ReducedWongWangExcInh parameter) ni, b_e (WilsonCowan parameter) ni, b_e (ZerlautAdaptationFirstOrder parameter) ni, b_i (ReducedWongWangExcInh parameter) ni, b_i (WilsonCowan parameter) ni, b_i (ZerlautAdaptationFirstOrder parameter) ni, b_rs (EpileptorRestingState parameter) ni, bb (Epileptor5D parameter) ni, bb (EpileptorRestingState parameter) ni, beta (Generic2dOscillator parameter) ni, beta_rs (EpileptorRestingState parameter) ni, c (Epileptor2D parameter) ni, c (Epileptor5D parameter) ni, c (EpileptorRestingState parameter) ni, c (Generic2dOscillator parameter) ni, c (StefanescuJirsa3D parameter) ni, c_e (WilsonCowan parameter) ni, c_ee (WilsonCowan parameter) ni, c_ei (WilsonCowan parameter) ni, c_i (WilsonCowan parameter) ni, c_ie (WilsonCowan parameter) ni, c_ii (WilsonCowan parameter) ni, c_minus (KIonEx parameter) ni, c_plus (KIonEx parameter) ni, cmax (Sigmoidal parameter) ni, cmax (SigmoidalJansenRit parameter) ni, cmin (Sigmoidal parameter) ni, cmin (SigmoidalJansenRit parameter) ni, conduction_speed (SmileyNetwork parameter) ni, conduction_speed (acq-EEGBrainstorm65_sensors parameter) ni, conduction_speed (acq-MEGBrainstorm276_sensors parameter) ni, conduction_speed (acq-SEEG588_sensors parameter) ni, conduction_speed (example_3node_network parameter) ni, conduction_speed (sensors_eeg_standard1005_fsaverage_aparc_projection parameter) ni, conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-Hansen2022_atlas-Schaefer2018_seg-7Networks_scale-100_desc-SCFC_relmat parameter) ni, conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_scale-1000_desc-SC_relmat parameter) ni, conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-1000_desc-SC_relmat parameter) ni, conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-100_desc-SC_relmat parameter) ni, conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-200_desc-SC_relmat parameter) ni, conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-300_desc-SC_relmat parameter) ni, conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-400_desc-SC_relmat parameter) ni, conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-500_desc-SC_relmat parameter) ni, conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-600_desc-SC_relmat parameter) ni, conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-700_desc-SC_relmat parameter) ni, conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-800_desc-SC_relmat parameter) ni, conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-900_desc-SC_relmat parameter) ni, conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-1000_desc-SC_relmat parameter) ni, conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-100_desc-SC_relmat parameter) ni, conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-200_desc-SC_relmat parameter) ni, conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-300_desc-SC_relmat parameter) ni, conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-400_desc-SC_relmat parameter) ni, conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-500_desc-SC_relmat parameter) ni, conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-600_desc-SC_relmat parameter) ni, conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-700_desc-SC_relmat parameter) ni, conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-800_desc-SC_relmat parameter) ni, conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-900_desc-SC_relmat parameter) ni, conduction_speed (tpl-FSLMNI152_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-Schaefer2018_scale-1000_desc-SC_relmat parameter) ni, conduction_speed (tpl-FSLMNI152_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-Schaefer2018_seg-17Networks_scale-1000_desc-SC_relmat parameter) ni, conduction_speed (tpl-FSLMNI152_cohort-PPMI85_rec-PPMI85_atlas-Schaefer2018_scale-1000_desc-SC_relmat parameter) ni, conduction_speed (tpl-FSLMNI152_cohort-PPMI85_rec-PPMI85_atlas-Schaefer2018_seg-17Networks_scale-1000_desc-SC_relmat parameter) ni, conduction_speed (tpl-MNI152NLin2009bAsym_cohort-HCPYA_rec-dTOR_atlas-HCPMMP1_desc-SC_relmat parameter) ni, conduction_speed (tpl-MNI152NLin2009bAsym_cohort-HCPYA_rec-dTOR_atlas-HCPMMP1_seg-ordered_desc-SC_relmat parameter) ni, conduction_speed (tpl-MNI152NLin2009bAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-HCPMMP1_desc-SC_relmat parameter) ni, conduction_speed (tpl-MNI152NLin2009bAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-HCPMMP1_seg-ordered_desc-SC_relmat parameter) ni, conduction_speed (tpl-MNI152NLin2009bAsym_cohort-PPMI85_rec-PPMI85_atlas-HCPMMP1_desc-SC_relmat parameter) ni, conduction_speed (tpl-MNI152NLin2009bAsym_cohort-PPMI85_rec-PPMI85_atlas-HCPMMP1_seg-ordered_desc-SC_relmat parameter) ni, conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_atlas-Lobar8_desc-surf_relmat parameter) ni, conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_atlas-Lobar8_hemi-L_desc-surf_relmat parameter) ni, conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_atlas-Lobar8_hemi-R_desc-surf_relmat parameter) ni, conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-DesikanKilliany_desc-SC_relmat parameter) ni, conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Destrieux_desc-SC_relmat parameter) ni, conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-HCPex_desc-SC_relmat parameter) ni, conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Lobar8_desc-SCFC_relmat parameter) ni, conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Lobar_desc-SC_relmat parameter) ni, conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Lobar_desc-surf_relmat parameter) ni, conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Yeo17_desc-SC_relmat parameter) ni, conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-virtualdbs_desc-SC_relmat parameter) ni, conduction_speed (tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-DesikanKilliany_desc-SC_relmat parameter) ni, conduction_speed (tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-Destrieux_desc-SC_relmat parameter) ni, conduction_speed (tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-HOCPA_desc-SC_relmat parameter) ni, conduction_speed (tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-Yeo17_desc-SC_relmat parameter) ni, conduction_speed (tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-virtualdbs_desc-SC_relmat parameter) ni, conduction_speed (tpl-MNI152NLin2009cAsym_cohort-PPMI85_rec-PPMI85_atlas-DesikanKilliany_desc-SC_relmat parameter) ni, conduction_speed (tpl-MNI152NLin2009cAsym_cohort-PPMI85_rec-PPMI85_atlas-Destrieux_desc-SC_relmat parameter) ni, conduction_speed (tpl-MNI152NLin2009cAsym_cohort-PPMI85_rec-PPMI85_atlas-Yeo17_desc-SC_relmat parameter) ni, conduction_speed (tpl-MNI152NLin2009cAsym_cohort-PPMI85_rec-PPMI85_atlas-virtualdbs_desc-SC_relmat parameter) ni, conduction_speed (tpl-MNI152NLin2009cAsym_rec-avgMatrix_atlas-DesikanKilliany_desc-SCFC_relmat parameter) ni, conduction_speed (tpl-MNI152NLin2009cAsym_rec-avgMatrix_atlas-Lobar8_desc-SCFC_relmat parameter) ni, conduction_speed (tpl-fsaverage_acq-EEGstandard1005_atlas-DesikanKilliany_desc-projection_sensors parameter) ni, conductivity (eeg parameter) ni, conductivity (ieeg parameter) ni, cr (GastSchmidtKnosche_SD parameter) ni, cr (GastSchmidtKnosche_SF parameter) ni, cr (MontbrioPazoRoxin parameter) ni, cv (GastSchmidtKnosche_SD parameter) ni, cv (GastSchmidtKnosche_SF parameter) ni, cv (MontbrioPazoRoxin parameter) ni, d (Epileptor2D parameter) ni, d (Epileptor5D parameter) ni, d (EpileptorRestingState parameter) ni, d (Generic2dOscillator parameter) ni, d (ReducedWongWang parameter) ni, d (ReducedWongWangTvboptim parameter) ni, d (StefanescuJirsa3D parameter) ni, d_e (ReducedWongWangExcInh parameter) ni, d_i (ReducedWongWangExcInh parameter) ni, d_rs (EpileptorRestingState parameter) ni, delta_Ca (LarterBreakspear parameter) ni, delta_K (LarterBreakspear parameter) ni, delta_Na (LarterBreakspear parameter) ni, delta_V (LarterBreakspear parameter) ni, delta_Z (LarterBreakspear parameter) ni, e (Generic2dOscillator parameter) ni, e0 (JansenRit1995 parameter) ni, e0 (ModelJansen1995 parameter) ni, e0 (ZetterbergJansen parameter) ni, e_rs (EpileptorRestingState parameter) ni, epsilon (KIonEx parameter) ni, eta (CoombesByrne parameter) ni, eta (CoombesByrne2D parameter) ni, eta (GastSchmidtKnosche_SD parameter) ni, eta (GastSchmidtKnosche_SF parameter) ni, eta (KIonEx parameter) ni, eta (MontbrioPazoRoxin parameter) ni, eta_e (DumontGutkin parameter) ni, eta_i (DumontGutkin parameter) ni, external_input_ex_ex (ZerlautAdaptationFirstOrder parameter) ni, external_input_ex_in (ZerlautAdaptationFirstOrder parameter) ni, external_input_in_ex (ZerlautAdaptationFirstOrder parameter) ni, external_input_in_in (ZerlautAdaptationFirstOrder parameter) ni, f (Generic2dOscillator parameter) ni, f_rs (EpileptorRestingState parameter) ni, fisher_z (FC parameter) ni, g (Generic2dOscillator parameter) ni, g (ZerlautAdaptationFirstOrder parameter) ni, g_Ca (LarterBreakspear parameter) ni, g_Cl (KIonEx parameter) ni, g_K (KIonEx parameter) ni, g_K (LarterBreakspear parameter) ni, g_Kl (KIonEx parameter) ni, g_L (LarterBreakspear parameter) ni, g_L (ZerlautAdaptationFirstOrder parameter) ni, g_Na (KIonEx parameter) ni, g_Na (LarterBreakspear parameter) ni, g_Nal (KIonEx parameter) ni, gamma (Generic2dOscillator parameter) ni, gamma (GenericLinear parameter) ni, gamma (KIonEx parameter) ni, gamma (ReducedWongWang parameter) ni, gamma (ReducedWongWangTvboptim parameter) ni, gamma_1 (ZetterbergJansen parameter) ni, gamma_1T (ZetterbergJansen parameter) ni, gamma_2 (ZetterbergJansen parameter) ni, gamma_2T (ZetterbergJansen parameter) ni, gamma_3 (ZetterbergJansen parameter) ni, gamma_3T (ZetterbergJansen parameter) ni, gamma_4 (ZetterbergJansen parameter) ni, gamma_5 (ZetterbergJansen parameter) ni, gamma_e (ReducedWongWangExcInh parameter) ni, gamma_i (ReducedWongWangExcInh parameter) ni, gamma_rs (EpileptorRestingState parameter) ni, hrf_length (bold_region_roi parameter) ni, k (CoombesByrne parameter) ni, k (CoombesByrne2D parameter) ni, k_e (WilsonCowan parameter) ni, k_i (WilsonCowan parameter) ni, k_phi (CakanObermayer parameter) ni, ke (ZetterbergJansen parameter) ni, ki (ZetterbergJansen parameter) ni, lamda (ReducedWongWangExcInh parameter) ni, midpoint (HyperbolicTangent parameter) ni, midpoint (Sigmoidal parameter) ni, midpoint (SigmoidalJansenRit parameter) ni, modification (Epileptor2D parameter) ni, modification (Epileptor5D parameter) ni, mu (JansenRit parameter) ni, mu (StefanescuJirsa2D parameter) ni, mu (StefanescuJirsa3D parameter) ni, muV0 (ZerlautAdaptationFirstOrder parameter) ni, mu_E (CakanObermayer parameter) ni, mu_I (CakanObermayer parameter) ni, mu_th (CakanObermayer parameter) ni, nu_max (JansenRit parameter) ni, omega (Kuramoto parameter) ni, omega (KuramotoModel2 parameter) ni, omega (SupHopf parameter) ni, p (EpileptorRestingState parameter) ni, p (JansenRit1995 parameter) ni, p (ModelJansen1995 parameter) ni, p_connect_e (ZerlautAdaptationFirstOrder parameter) ni, p_connect_i (ZerlautAdaptationFirstOrder parameter) ni, permeability (meg parameter) ni, phi (LarterBreakspear parameter) ni, r (Epileptor2D parameter) ni, r (Epileptor5D parameter) ni, r (EpileptorRestingState parameter) ni, r (JansenRit parameter) ni, r (JansenRit1995 parameter) ni, r (ModelJansen1995 parameter) ni, r (SigmoidalJansenRit parameter) ni, r (StefanescuJirsa3D parameter) ni, r_NMDA (LarterBreakspear parameter) ni, r_e (WilsonCowan parameter) ni, r_i (WilsonCowan parameter) ni, r_max (CakanObermayer parameter) ni, reference_electrode (eeg parameter) ni, rho (KIonEx parameter) ni, rho_1 (ZetterbergJansen parameter) ni, rho_2 (ZetterbergJansen parameter) ni, s (Epileptor5D parameter) ni, s (StefanescuJirsa3D parameter) ni, sV0 (ZerlautAdaptationFirstOrder parameter) ni, s_EE (CakanObermayer parameter) ni, s_EI (CakanObermayer parameter) ni, s_IE (CakanObermayer parameter) ni, s_II (CakanObermayer parameter) ni, shift_sigmoid (WilsonCowan parameter) ni, sigma (HyperbolicTangent parameter) ni, sigma (Sigmoidal parameter) ni, sigma (StefanescuJirsa2D parameter) ni, sigma (StefanescuJirsa3D parameter) ni, slope (Epileptor2D parameter) ni, slope (Epileptor5D parameter) ni, slope (EpileptorRestingState parameter) ni, spatial_mask (spatial_average parameter) ni, t_scale (LarterBreakspear parameter) ni, tau (Epileptor5D parameter) ni, tau (EpileptorRestingState parameter) ni, tau (GastSchmidtKnosche_SD parameter) ni, tau (GastSchmidtKnosche_SF parameter) ni, tau (Generic2dOscillator parameter) ni, tau (MontbrioPazoRoxin parameter) ni, tau (StefanescuJirsa2D parameter) ni, tau (TsodyksMarkram parameter) ni, tauD (TsodyksMarkram parameter) ni, tauF (TsodyksMarkram parameter) ni, tauT (Hopfield parameter) ni, tau_A (CakanObermayer parameter) ni, tau_A (GastSchmidtKnosche_SD parameter) ni, tau_A (GastSchmidtKnosche_SF parameter) ni, tau_K (LarterBreakspear parameter) ni, tau_OU (ZerlautAdaptationFirstOrder parameter) ni, tau_e (DumontGutkin parameter) ni, tau_e (ReducedWongWangExcInh parameter) ni, tau_e (WilsonCowan parameter) ni, tau_e (ZerlautAdaptationFirstOrder parameter) ni, tau_i (DumontGutkin parameter) ni, tau_i (ReducedWongWangExcInh parameter) ni, tau_i (WilsonCowan parameter) ni, tau_i (ZerlautAdaptationFirstOrder parameter) ni, tau_n (KIonEx parameter) ni, tau_rs (EpileptorRestingState parameter) ni, tau_s (DumontGutkin parameter) ni, tau_s (ReducedWongWang parameter) ni, tau_s (ReducedWongWangTvboptim parameter) ni, tau_se (CakanObermayer parameter) ni, tau_si (CakanObermayer parameter) ni, tau_w_e (ZerlautAdaptationFirstOrder parameter) ni, tau_w_i (ZerlautAdaptationFirstOrder parameter) ni, tau_z (Epileptor3DStefanescuMcDonald parameter) ni, taux (Hopfield parameter) ni, theta (PreSigmoidal parameter) ni, theta_e (WilsonCowan parameter) ni, theta_i (WilsonCowan parameter) ni, tt (Epileptor2D parameter) ni, tt (Epileptor5D parameter) ni, tt (EpileptorRestingState parameter) ni, v0 (JansenRit parameter) ni, v0 (JansenRit1995 parameter) ni, v0 (ModelJansen1995 parameter) ni, v_syn (CoombesByrne parameter) ni, v_syn (CoombesByrne2D parameter) ni, w (ReducedWongWang parameter) ni, w (ReducedWongWangTvboptim parameter) ni, w_i (KIonEx parameter) ni, w_o (KIonEx parameter) ni, w_p (ReducedWongWangExcInh parameter) ni, weight_noise (ZerlautAdaptationFirstOrder parameter) ni, x0 (Epileptor2D parameter) ni, x0 (Epileptor5D parameter) ni, x0 (EpileptorRestingState parameter) ni, x_0 (Epileptor3DStefanescuMcDonald parameter) ni, x_0 (StefanescuJirsa3D parameter) ni

Parcellationc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Parcellation

Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

ParcellationEntityc back to ToC or Class ToC

IRI: http://uri.interlex.org/tgbugs/uris/readable/ParcellationEntity

A schema for representing a parcellation entity, which is an anatomical location or study target.
has super-classes
Thing c
is in range of
hasParent op

ParcellationTerminologyc back to ToC or Class ToC

IRI: http://uri.interlex.org/tgbugs/uris/readable/ParcellationTerminology

A schema for representing a parcellation terminology, which consists of parcellation entities.
has super-classes
Thing c

PDEc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/PDE

Partial differential equation problem definition.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

PDESolverc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/PDESolver

Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

per_msc back to ToC or Class ToC

IRI: http://qudt.org/vocab/unit/PER-MilliSEC

Per millisecond (ms⁻¹)
has super-classes
UnitEnum c

per_mVc back to ToC or Class ToC

IRI: http://qudt.org/vocab/unit/PER-MilliV

Reciprocal millivolt (mV⁻¹)
has super-classes
UnitEnum c

per_nCc back to ToC or Class ToC

IRI: http://qudt.org/vocab/unit/PER-NanoC

Reciprocal nanocoulomb (nC⁻¹)
has super-classes
UnitEnum c

per_pCc back to ToC or Class ToC

IRI: http://qudt.org/vocab/unit/PER-PicoC

Reciprocal picocoulomb (pC⁻¹)
has super-classes
UnitEnum c

per_sc back to ToC or Class ToC

IRI: http://qudt.org/vocab/unit/PER-SEC

Per second (s⁻¹)
has super-classes
UnitEnum c

per_time (PhysicalDimension)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/PhysicalDimension#per_time

Inverse time [T⁻¹]
Is defined by
https://w3id.org/tvbo/struct
has super-classes
PhysicalDimension c

per_unit (UnitEnum)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/UnitEnum#per_unit

Per-unit (dimensionless power-systems convention)
Is defined by
https://w3id.org/tvbo/struct
has super-classes
UnitEnum c

percentc back to ToC or Class ToC

IRI: http://qudt.org/vocab/unit/PERCENT

Percent (%)
has super-classes
UnitEnum c

Period doublingc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/PeriodDoubling

has super-classes
Bifurcation c

Periodic (BoundaryConditionType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/BoundaryConditionType#Periodic

Is defined by
https://w3id.org/tvbo/struct
has super-classes
BoundaryConditionType c

pFc back to ToC or Class ToC

IRI: http://qudt.org/vocab/unit/PicoFARAD

Picofarad
has super-classes
UnitEnum c

phase_oscillatorc back to ToC or Class ToC

IRI: http://www.wikidata.org/entity/Q634884

Phase-reduced or Kuramoto-type oscillator models.
has super-classes
ModelParadigm c

phase_oscillator (ModelType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/ModelType#phase_oscillator

Phase-reduced or Kuramoto-type oscillator models. Examples: Kuramoto, SupHopf.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
ModelType c

phenomenological (ModelType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/ModelType#phenomenological

Empirical / phenomenological models that capture macroscopic dynamics without direct biophysical derivation. Examples: Epileptor2D, Epileptor5D.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
ModelType c

pink (NoiseType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/NoiseType#pink

Is defined by
https://w3id.org/tvbo/struct
has super-classes
NoiseType c

Pitchforkc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Pitchfork

has super-classes
Bifurcation c

plasticityc back to ToC or Class ToC

IRI: http://www.wikidata.org/entity/Q747830

Synaptic plasticity (STDP, homeostatic, etc.).
has super-classes
ModelParadigm c

poincare (NumericalDiscretizationMethod)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/NumericalDiscretizationMethod#poincare

Poincaré shooting.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
NumericalDiscretizationMethod c

preset_time (EventType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/EventType#preset_time

Triggered at predetermined time points. Maps to PresetTimeCallback / PresetTimeComponentCallback.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
EventType c

ProgrammingLanguageEnumc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/ProgrammingLanguageEnum

Programming languages relevant to computational neuroscience tools. Mapped to Wikidata identifiers.
Is defined by
https://w3id.org/tvbo/struct
is equivalent to
C c or MATLAB c or JavaScript c or R c or XML c or C# c or C++ c or Java c or Python c or Haskell c or Julia c or Rust c or HOC c or Fortran c
has super-classes
Thing c
has sub-classes
C c, C# c, C++ c, Fortran c, HOC c, Haskell c, Java c, JavaScript c, Julia c, MATLAB c, Python c, R c, Rust c, XML c

Provenancec back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Provenance

W3C PROV-O aligned provenance. Reusable on any entity (Network, TimeSeries, Dynamics, etc.).
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

pSc back to ToC or Class ToC

IRI: http://qudt.org/vocab/unit/PicoS

Picosiemens
has super-classes
UnitEnum c

pypic back to ToC or Class ToC

IRI: http://www.wikidata.org/entity/Q2984888

Python Package Index.
has super-classes
EcosystemEnum c

Pythonc back to ToC or Class ToC

IRI: http://www.wikidata.org/entity/Q28865

has super-classes
ProgrammingLanguageEnum c

quad (ElementType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/ElementType#quad

Is defined by
https://w3id.org/tvbo/struct
has super-classes
ElementType c

Quiescentc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Quiescent

has super-classes
Dynamical regime c
is also defined as
named individual

Rc back to ToC or Class ToC

IRI: http://www.wikidata.org/entity/Q206904

has super-classes
ProgrammingLanguageEnum c

radc back to ToC or Class ToC

IRI: http://qudt.org/vocab/unit/RAD

Radian
has super-classes
UnitEnum c

rad_per_ms (UnitEnum)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/UnitEnum#rad_per_ms

Radian per millisecond
Is defined by
https://w3id.org/tvbo/struct
has super-classes
UnitEnum c

rad_per_sc back to ToC or Class ToC

IRI: http://qudt.org/vocab/unit/RAD-PER-SEC

Radian per second (angular velocity)
has super-classes
UnitEnum c

RandomRegular (StandardGraphType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/StandardGraphType#RandomRegular

Random regular graph (params: k)
Is defined by
https://w3id.org/tvbo/struct
has super-classes
StandardGraphType c

RandomStreamc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/RandomStream

Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

Rangec back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Range

Specifies a range for array generation, parameter bounds, or grid exploration.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c
is in range of
domain (slot) op

rate_basedc back to ToC or Class ToC

IRI: http://www.wikidata.org/entity/Q3685405

Firing-rate models.
has super-classes
ModelParadigm c

reaction_diffusionc back to ToC or Class ToC

IRI: http://www.wikidata.org/entity/Q851270

Stochastic or deterministic reaction-diffusion.
has super-classes
ModelParadigm c

ReductionTypec back to ToC or Class ToC

IRI: https://w3id.org/tvbo/ReductionType

Operations for reducing/aggregating values across dimensions
Is defined by
https://w3id.org/tvbo/struct
is equivalent to
max (ReductionType) c or mean (ReductionType) c or min (ReductionType) c or none (ReductionType) c or sum (ReductionType) c
has super-classes
Thing c
has sub-classes
max (ReductionType) c, mean (ReductionType) c, min (ReductionType) c, none (ReductionType) c, sum (ReductionType) c

region (DimensionType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/DimensionType#region

Spatial/regional dimension (alias for node in brain networks)
Is defined by
https://w3id.org/tvbo/struct
has super-classes
DimensionType c

RegionMappingc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/RegionMapping

Maps vertices to parent regions for hierarchical/aggregated coupling
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

Reportc back to ToC or Class ToC

IRI: http://schema.org/Report

has super-classes
Thing c
has members
Chirikov1969 ni

resistance (PhysicalDimension)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/PhysicalDimension#resistance

Resistance [M L² T⁻³ I⁻²]
Is defined by
https://w3id.org/tvbo/struct
has super-classes
PhysicalDimension c

right (Hemisphere)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Hemisphere#right

Is defined by
https://w3id.org/tvbo/struct
has super-classes
Hemisphere c

Robin (BoundaryConditionType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/BoundaryConditionType#Robin

Is defined by
https://w3id.org/tvbo/struct
has super-classes
BoundaryConditionType c

runtime (RequirementRole)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/RequirementRole#runtime

General runtime dependency.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
RequirementRole c

Rustc back to ToC or Class ToC

IRI: http://www.wikidata.org/entity/Q575650

has super-classes
ProgrammingLanguageEnum c

sc back to ToC or Class ToC

IRI: http://qudt.org/vocab/unit/SEC

Second
has super-classes
UnitEnum c

s2c back to ToC or Class ToC

IRI: http://qudt.org/vocab/unit/SEC2

Second squared (inertia constant)
has super-classes
UnitEnum c

S_per_cm2 (UnitEnum)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/UnitEnum#S_per_cm2

Siemens per square centimetre (conductance density)
Is defined by
https://w3id.org/tvbo/struct
has super-classes
UnitEnum c

S_per_mc back to ToC or Class ToC

IRI: http://qudt.org/vocab/unit/S-PER-M

Siemens per metre (conductivity)
has super-classes
UnitEnum c

S_per_m2 (UnitEnum)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/UnitEnum#S_per_m2

Siemens per square metre (conductance density, SI)
Is defined by
https://w3id.org/tvbo/struct
has super-classes
UnitEnum c

Saddle-nodec back to ToC or Class ToC

IRI: https://w3id.org/tvbo/SaddleNode

has super-classes
Bifurcation c
is also defined as
named individual

Samplec back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Sample

Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

sample (DimensionType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/DimensionType#sample

Sample/trial/realization dimension
Is defined by
https://w3id.org/tvbo/struct
has super-classes
DimensionType c

SamplingAxisc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/SamplingAxis

Dimension along which a distribution is sampled.
Is defined by
https://w3id.org/tvbo/struct
is equivalent to
space (SamplingAxis) c or time (SamplingAxis) c
has super-classes
Thing c
has sub-classes
space (SamplingAxis) c, time (SamplingAxis) c

ScalarValuec back to ToC or Class ToC

IRI: https://w3id.org/tvbo/ScalarValue

A scalar value: float, integer, string, or boolean. Used for slots that accept literals of any primitive type, such as argument values which may be numbers, strings, references, or booleans.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c
is in range of
value (slot) op

Scholarly articlec back to ToC or Class ToC

IRI: http://schema.org/ScholarlyArticle

has super-classes
Thing c
has members
Bandyopadhyay2021 ni, Baran1998 ni, Bo-Cheng2008 ni, BoCheng2008 ni, Byrne2020 ni, Cabral2011 ni, Cai2007 ni, Cao2013 ni, Chen2006 ni, Chua1992 ni, Chua2007 ni, Courtiol2020 ni, Datseris2019 ni, Deco2013 ni, Deco2014 ni, Deco2017 ni, Depannemaecker2023 ni, Dumont2019 ni, Feigenbaum1978 ni, FitzHugh1961 ni, Freire2008 ni, Galan2008 ni, Gast2020 ni, Gissinger2012 ni, Grebogi1983 ni, Greene1979 ni, GuckenheimerHolmes1983Alias ni, Henon1964 ni, Henon1976 ni, HenonHeiles1964 ni, Hindmarsh1984 ni, HindmarshRose1984 ni, Hodgkin1952 ni, HodgkinHuxley1952 ni, Hoover1995 ni, Hopfield1982 ni, Hopfield1984 ni, Hoppensteadt2006 ni, Huisman2001 ni, Hussain2015 ni, Jansen1993 ni, Jansen1995 ni, Jirsa2014 ni, Kanamaru2007 ni, KantzGrassberger1988 ni, Kuramoto1975 ni, Landau1944 ni, Letellier2007 ni, Li2015 ni, Lorenz1963 ni, Lorenz1996 ni, Manneville1980 ni, MannevillePomeau1980 ni, May1976 ni, Meyer2019 ni, Micluta-Campeanu2018 ni, MiclutaCampeanu2018 ni, Mirshra2018 ni, Mishra2018 ni, Mishra2018a ni, Montbrio2015 ni, MorrisLecar1981 ni, Nagumo1962 ni, Pang2011 ni, Proix2014 ni, Proix2017 ni, Qi2008 ni, R_ossler1976 ni, Rikitake1958 ni, Roessler1976 ni, Roessler1979 ni, Roessler1979Alias ni, Rossler1976 ni, Rossler1979 ni, Ruelle1980 ni, Rulkov2001 ni, Rulkov2002 ni, Sprott2014 ni, Sprott2014b ni, Sprott2020 ni, SprottXiong2015 ni, Stommel1961 ni, Strogatz2000 ni, Thomas1999 ni, Tufillaro1984 ni, Ueda1961 ni, Volo2019 ni, Volo2019a ni, Wang2008 ni, Wang2009 ni, Wilson1972 ni, Wilson1973 ni, Wong2006 ni, Zaslavskii1978 ni, Zerlaut2018 ni, Zetterberg1978 ni, vanderpol1926 ni

SEEG (ImagingModality)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/ImagingModality#SEEG

Stereoelectroencephalography.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
ImagingModality c

Session (study)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/study/Session

A data collection session for a subject. Corresponds to a BIDS 'ses-' entity. Sessions capture longitudinal timepoints (baseline, follow-up), different experimental conditions, or repeated measures.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

SexEnumc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/SexEnum

Is defined by
https://w3id.org/tvbo/struct
is equivalent to
female (SexEnum) c or male (SexEnum) c or other (SexEnum) c
has super-classes
Thing c
has sub-classes
female (SexEnum) c, male (SexEnum) c, other (SexEnum) c

shooting (NumericalDiscretizationMethod)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/NumericalDiscretizationMethod#shooting

Standard multiple shooting.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
NumericalDiscretizationMethod c

Simulation taskc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/SimulationTask

A computational task: forward integration in some formalism, parameter exploration, gradient-based optimisation, numerical continuation, or bifurcation analysis.
has super-classes
Thing c
is in range of
supports task op
has members
Bifurcation analysis ni, DDE integration ni, Event-driven integration ni, Gradient-based optimisation ni, Numerical continuation ni, ODE integration ni, Parameter exploration ni, RDE integration ni, SDDE integration ni, SDE integration ni

SimulationScalec back to ToC or Class ToC

IRI: https://w3id.org/tvbo/SimulationScale

Spatial / organizational scale at which a tool operates. Multi-valued: a tool can span multiple scales. Mapped to SIO and Wikidata where possible.
Is defined by
https://w3id.org/tvbo/struct
is equivalent to
network_system c or neuron c or neural_network c or neural_mass c or channel c
has super-classes
Thing c
has sub-classes
channel c, network_system c, neural_mass c, neural_network c, neuron c

SimulationStudyc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/SimulationStudy

Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

SimulationTool (software)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/software/SimulationTool

A software tool for computational neuroscience simulation, analysis, or model specification. Extends SoftwarePackage with neuroscience-specific controlled vocabularies for scale, paradigm, role, and interoperability. Aligned with CodeMeta v3 and DOAP.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
SoftwarePackage (software) c

simulatorc back to ToC or Class ToC

IRI: http://www.wikidata.org/entity/Q1569346

Core numerical simulator.
has super-classes
ToolRole c

singularity (EnvironmentType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/EnvironmentType#singularity

Singularity/Apptainer container.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
EnvironmentType c

SKOS Conceptc back to ToC or Class ToC

IRI: http://www.w3.org/2004/02/skos/core#Concept

has super-classes
Thing c
has members
CouplingInput ni, E/I balance ni, Excitation ni, FeedbackScaling ni, Inhibition ni, InternalCoupling ni, TimeScaling ni

Software packagec back to ToC or Class ToC

IRI: https://w3id.org/tvbo/SoftwarePackage

has super-classes
Thing c
has members
AUTO-07p ni, Arbor ni, BSB ni, BifurcationKit.jl ni, BluePyOpt ni, BrainBrowser ni, BrainPy ni, BrainSimII ni, Brainstorm ni, Brian2 ni, CARLsim ni, CoreNEURON ni, CxSystem2 ni, DifferentialEquations.jl ni, EEGLAB ni, Elephant ni, FastDMF ni, FieldTrip ni, GENESIS ni, GeNN ni, HNN-core ni, LEMS ni, LFPy ni, MCell ni, MNE-Python ni, MOOSE ni, MatCont ni, ModelDB ni, NEST ni, NEURON ni, NWB ni, Nengo ni, Neo ni, NetPyNE ni, NetworkDynamics.jl ni, NeuroML ni, Neuroblox.jl ni, Neurofitter ni, NineML ni, Open Source Brain ni, OpenWorm ni, PSICS ni, PyNN ni, PyRates ni, PyRhO ni, SONATA ni, SPM ni, STEPS ni, Snudda ni, SpikeInterface ni, SpineCreator ni, SpineML ni, TVB ni, TVB-O ni, TVB-Optim ni, jNeuroML ni, jaxley ni, neuroConstruct ni, neurolib ni, pyNeuroML ni, pynn_genn ni, sPyNNaker ni

SoftwareEnvironment (software)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/software/SoftwareEnvironment

A reproducible software environment aggregating one or more SoftwareRequirement entries. Used by SimulationExperiment to specify the execution context.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c
is in range of
environment (slot) op

SoftwarePackage (software)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/software/SoftwarePackage

Identity and metadata for a software package, aligned with schema.org/SoftwareApplication and CodeMeta v3.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c
has sub-classes
SimulationTool (software) c

SoftwareRequirement (software)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/software/SoftwareRequirement

An individual software requirement binding a package to a version constraint and a role within an environment.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c
is in range of
requirements (slot) op

Solverc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Solver

Lightweight specification of a numerical ODE solver / integrator. Covers adaptive solvers (Vern9, Rodas5, Tsit5, etc.) used in shooting methods, initial-state integration, and other contexts where only the algorithm and tolerances matter.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c
has sub-classes
Integrator c

space (SamplingAxis)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/SamplingAxis#space

Sample once per node (heterogeneous parameter or spatially varying IC).
Is defined by
https://w3id.org/tvbo/struct
has super-classes
SamplingAxis c

SparseFormatc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/SparseFormat

Is defined by
https://w3id.org/tvbo/struct
is equivalent to
coo (SparseFormat) c or csr (SparseFormat) c or dense (SparseFormat) c
has super-classes
Thing c
has sub-classes
coo (SparseFormat) c, csr (SparseFormat) c, dense (SparseFormat) c

SpatialDomainc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/SpatialDomain

Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

SpatialFieldc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/SpatialField

Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

specification_languagec back to ToC or Class ToC

IRI: http://www.wikidata.org/entity/Q2661442

Model description language or data standard.
has super-classes
ToolRole c

SpecimenEnumc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/SpecimenEnum

A set of permissible types for specimens used in brain atlas creation.
Is defined by
https://w3id.org/tvbo/struct
is equivalent to
Subject (SpecimenEnum) c or SubjectGroup (SpecimenEnum) c or TissueSample (SpecimenEnum) c or TissueSampleCollection (SpecimenEnum) c
has super-classes
Thing c
has sub-classes
Subject (SpecimenEnum) c, SubjectGroup (SpecimenEnum) c, TissueSample (SpecimenEnum) c, TissueSampleCollection (SpecimenEnum) c

Spectral (DiscretizationMethod)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/DiscretizationMethod#Spectral

Is defined by
https://w3id.org/tvbo/struct
has super-classes
DiscretizationMethod c

spikingc back to ToC or Class ToC

IRI: http://www.wikidata.org/entity/Q7579783

Spiking neuron models (LIF, AdEx, Izhikevich, etc.).
has super-classes
ModelParadigm c

spiking (ModelType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/ModelType#spiking

Single-neuron or conductance-based spiking models (HH, AdEx, LIF, Izhikevich, etc.). These can be used as nodes in a network alongside mean-field models.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
ModelType c

StandardGraphTypec back to ToC or Class ToC

IRI: https://w3id.org/tvbo/StandardGraphType

Well-known graph generator families with automatic backend mapping. The type field on GraphGenerator is a free string; this enum lists common types that get automatic code generation for Julia (Graphs.jl) and Python (NetworkX).
Is defined by
https://w3id.org/tvbo/struct
is equivalent to
BarabasiAlbert (StandardGraphType) c or Complete (StandardGraphType) c or Cycle (StandardGraphType) c or ErdosRenyi (StandardGraphType) c or Grid (StandardGraphType) c or RandomRegular (StandardGraphType) c or Star (StandardGraphType) c or WattsStrogatz (StandardGraphType) c
has super-classes
Thing c
has sub-classes
BarabasiAlbert (StandardGraphType) c, Complete (StandardGraphType) c, Cycle (StandardGraphType) c, ErdosRenyi (StandardGraphType) c, Grid (StandardGraphType) c, RandomRegular (StandardGraphType) c, Star (StandardGraphType) c, WattsStrogatz (StandardGraphType) c

Star (StandardGraphType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/StandardGraphType#Star

Star graph
Is defined by
https://w3id.org/tvbo/struct
has super-classes
StandardGraphType c

state (DimensionType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/DimensionType#state

State variable dimension
Is defined by
https://w3id.org/tvbo/struct
has super-classes
DimensionType c

StateValuec back to ToC or Class ToC

IRI: https://w3id.org/tvbo/StateValue

A named state variable value for per-node initialization.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

StateVariablec back to ToC or Class ToC

IRI: https://w3id.org/tvbo/StateVariable

Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c
has sub-classes
FieldStateVariable c
has members
A (GastSchmidtKnosche_SD state variable) ni, A (GastSchmidtKnosche_SF state variable) ni, B (GastSchmidtKnosche_SD state variable) ni, B (GastSchmidtKnosche_SF state variable) ni, DKi (KIonEx state variable) ni, E (TsodyksMarkram state variable) ni, E (WilsonCowan state variable) ni, E (ZerlautAdaptationFirstOrder state variable) ni, I (WilsonCowan state variable) ni, I (ZerlautAdaptationFirstOrder state variable) ni, I_A_var (CakanObermayer state variable) ni, Kg (KIonEx state variable) ni, S (ReducedWongWang state variable) ni, S (ReducedWongWangTvboptim state variable) ni, S_e (ReducedWongWangExcInh state variable) ni, S_i (ReducedWongWangExcInh state variable) ni, V (CoombesByrne state variable) ni, V (CoombesByrne2D state variable) ni, V (GastSchmidtKnosche_SD state variable) ni, V (GastSchmidtKnosche_SF state variable) ni, V (Generic2dOscillator state variable) ni, V (KIonEx state variable) ni, V (LarterBreakspear state variable) ni, V (MontbrioPazoRoxin state variable) ni, V_e (DumontGutkin state variable) ni, V_i (DumontGutkin state variable) ni, W (Generic2dOscillator state variable) ni, W (LarterBreakspear state variable) ni, W_e (ZerlautAdaptationFirstOrder state variable) ni, W_i (ZerlautAdaptationFirstOrder state variable) ni, Z (LarterBreakspear state variable) ni, alpha (StefanescuJirsa2D state variable) ni, alpha (StefanescuJirsa3D state variable) ni, beta (StefanescuJirsa2D state variable) ni, beta (StefanescuJirsa3D state variable) ni, eta (StefanescuJirsa2D state variable) ni, eta (StefanescuJirsa3D state variable) ni, g (CoombesByrne state variable) ni, g (Epileptor5D state variable) ni, g (EpileptorRestingState state variable) ni, gamma (StefanescuJirsa3D state variable) ni, mu_se (CakanObermayer state variable) ni, mu_si (CakanObermayer state variable) ni, n (KIonEx state variable) ni, ou_drift (ZerlautAdaptationFirstOrder state variable) ni, q (CoombesByrne state variable) ni, r (CoombesByrne state variable) ni, r (CoombesByrne2D state variable) ni, r (GastSchmidtKnosche_SD state variable) ni, r (GastSchmidtKnosche_SF state variable) ni, r (MontbrioPazoRoxin state variable) ni, r_e (DumontGutkin state variable) ni, r_i (DumontGutkin state variable) ni, s_ee (DumontGutkin state variable) ni, s_ei (DumontGutkin state variable) ni, s_ie (DumontGutkin state variable) ni, s_ii (DumontGutkin state variable) ni, tau (StefanescuJirsa3D state variable) ni, theta (Hopfield state variable) ni, theta (Kuramoto state variable) ni, theta (KuramotoModel2 state variable) ni, u (TsodyksMarkram state variable) ni, v1 (ZetterbergJansen state variable) ni, v2 (ZetterbergJansen state variable) ni, v3 (ZetterbergJansen state variable) ni, v4 (ZetterbergJansen state variable) ni, v5 (ZetterbergJansen state variable) ni, v6 (ZetterbergJansen state variable) ni, v7 (ZetterbergJansen state variable) ni, x (GenericLinear state variable) ni, x (Hopfield state variable) ni, x (KIonEx state variable) ni, x (SupHopf state variable) ni, x (TsodyksMarkram state variable) ni, x1 (Epileptor2D state variable) ni, x1 (Epileptor3DStefanescuMcDonald state variable) ni, x1 (Epileptor5D state variable) ni, x1 (EpileptorRestingState state variable) ni, x2 (Epileptor5D state variable) ni, x2 (EpileptorRestingState state variable) ni, x_rs (EpileptorRestingState state variable) ni, xi (StefanescuJirsa2D state variable) ni, xi (StefanescuJirsa3D state variable) ni, y (SupHopf state variable) ni, y0 (JansenRit state variable) ni, y0 (JansenRit1995 state variable) ni, y0 (ModelJansen1995 state variable) ni, y1 (Epileptor5D state variable) ni, y1 (EpileptorRestingState state variable) ni, y1 (JansenRit state variable) ni, y1 (JansenRit1995 state variable) ni, y1 (ModelJansen1995 state variable) ni, y1 (ZetterbergJansen state variable) ni, y2 (Epileptor5D state variable) ni, y2 (EpileptorRestingState state variable) ni, y2 (JansenRit state variable) ni, y2 (JansenRit1995 state variable) ni, y2 (ModelJansen1995 state variable) ni, y2 (ZetterbergJansen state variable) ni, y3 (JansenRit state variable) ni, y3 (JansenRit1995 state variable) ni, y3 (ModelJansen1995 state variable) ni, y3 (ZetterbergJansen state variable) ni, y4 (JansenRit state variable) ni, y4 (JansenRit1995 state variable) ni, y4 (ModelJansen1995 state variable) ni, y4 (ZetterbergJansen state variable) ni, y5 (JansenRit state variable) ni, y5 (JansenRit1995 state variable) ni, y5 (ModelJansen1995 state variable) ni, y5 (ZetterbergJansen state variable) ni, y_rs (EpileptorRestingState state variable) ni, z (Epileptor2D state variable) ni, z (Epileptor3DStefanescuMcDonald state variable) ni, z (Epileptor5D state variable) ni, z (EpileptorRestingState state variable) ni

StimulationSetting (dbs)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/dbs/StimulationSetting

DBS parameters for a specific session.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

Stimulusc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Stimulus

Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

stimulus (EventType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/EventType#stimulus

Continuous time-dependent input signal (e.g., external current). Legacy Stimulus behavior.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
EventType c

Stochasticity characterc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Stochasticity

Stochasticity character of the model definition itself, independent of any optional integrator-level noise injection.
has super-classes
Dynamical property c
has sub-classes
Additive noise c, Coloured noise c, Deterministic c, Multiplicative noise c

Strange attractorc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/StrangeAttractor

has super-classes
Attractor c
is also defined as
named individual

Subcritical Hopfc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/SubcriticalHopf

has super-classes
Hopf c

Subject (SpecimenEnum)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/SpecimenEnum#Subject

Is defined by
https://w3id.org/tvbo/struct
has super-classes
SpecimenEnum c

Subject (study)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/study/Subject

A participant in a study. Each subject typically has their own brain network (connectome) and empirical recordings. Corresponds to a BIDS 'sub-' entity.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c
has sub-classes
DBSSubject (dbs) c
is in range of
subjects (study) op

SubjectGroup (SpecimenEnum)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/SpecimenEnum#SubjectGroup

Is defined by
https://w3id.org/tvbo/struct
has super-classes
SpecimenEnum c

substance (PhysicalDimension)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/PhysicalDimension#substance

Amount of substance [N]
Is defined by
https://w3id.org/tvbo/struct
has super-classes
PhysicalDimension c

sum (ReductionType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/ReductionType#sum

Sum of values
Is defined by
https://w3id.org/tvbo/struct
has super-classes
ReductionType c

Supercritical Hopfc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/SupercriticalHopf

has super-classes
Hopf c
is also defined as
named individual

suspended (DevelopmentStatus)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/DevelopmentStatus#suspended

Development paused; may resume in future.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
DevelopmentStatus c

SystemTypec back to ToC or Class ToC

IRI: https://w3id.org/tvbo/SystemType

Is defined by
https://w3id.org/tvbo/struct
is equivalent to
continuous (SystemType) c or discrete (SystemType) c
has super-classes
Thing c
has sub-classes
continuous (SystemType) c, discrete (SystemType) c

temperature (PhysicalDimension)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/PhysicalDimension#temperature

Temperature [K]
Is defined by
https://w3id.org/tvbo/struct
has super-classes
PhysicalDimension c

TemporalApplicableEquationc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/TemporalApplicableEquation

Is defined by
https://w3id.org/tvbo/struct
has super-classes
Equation c

tetrahedron (ElementType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/ElementType#tetrahedron

Is defined by
https://w3id.org/tvbo/struct
has super-classes
ElementType c

time (DimensionType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/DimensionType#time

Temporal dimension
Is defined by
https://w3id.org/tvbo/struct
has super-classes
DimensionType c

time (PhysicalDimension)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/PhysicalDimension#time

Time [T]
Is defined by
https://w3id.org/tvbo/struct
has super-classes
PhysicalDimension c

time (SamplingAxis)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/SamplingAxis#time

Resample every integration timestep (stochastic time-varying input).
Is defined by
https://w3id.org/tvbo/struct
has super-classes
SamplingAxis c

time_integration (InitialStateMethod)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/InitialStateMethod#time_integration

Integrate the ODE forward until convergence (robust, default).
Is defined by
https://w3id.org/tvbo/struct
has super-classes
InitialStateMethod c

TimeSeriesc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/TimeSeries

Time series data from simulations or measurements. Supports BIDS-compatible export for computational modeling (BEP034).
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

TissueSample (SpecimenEnum)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/SpecimenEnum#TissueSample

Is defined by
https://w3id.org/tvbo/struct
has super-classes
SpecimenEnum c

TissueSampleCollection (SpecimenEnum)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/SpecimenEnum#TissueSampleCollection

Is defined by
https://w3id.org/tvbo/struct
has super-classes
SpecimenEnum c

ToolRolec back to ToC or Class ToC

IRI: https://w3id.org/tvbo/ToolRole

Primary function of the tool in a simulation workflow.
Is defined by
https://w3id.org/tvbo/struct
is equivalent to
simulator c or specification_language c or framework c or model_repository c or optimization_framework c or bifurcation_analysis c or visualization_tool c or analysis_tool c or backend_runtime (ToolRole) c or workflow_framework (ToolRole) c
has super-classes
Thing c
has sub-classes
analysis_tool c, backend_runtime (ToolRole) c, bifurcation_analysis c, framework c, model_repository c, optimization_framework c, simulator c, specification_language c, visualization_tool c, workflow_framework (ToolRole) c

Torusc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Torus

has super-classes
Attractor c
is also defined as
named individual

Tractogramc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Tractogram

Reference to tractography/diffusion MRI data used to derive structural connectivity
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

Transcriticalc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/Transcritical

has super-classes
Bifurcation c

trapezoid (NumericalDiscretizationMethod)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/NumericalDiscretizationMethod#trapezoid

Trapezoidal rule discretization.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
NumericalDiscretizationMethod c

triangle (ElementType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/ElementType#triangle

Is defined by
https://w3id.org/tvbo/struct
has super-classes
ElementType c

TuningObjectivec back to ToC or Class ToC

IRI: https://w3id.org/tvbo/TuningObjective

Defines what the tuning algorithm optimizes for. Can be an activity target (FIC) or a connectivity target (EIB).
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

uA_per_cm2 (UnitEnum)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/UnitEnum#uA_per_cm2

Microampere per square centimetre (current density)
Is defined by
https://w3id.org/tvbo/struct
has super-classes
UnitEnum c

uF_per_cm2 (UnitEnum)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/UnitEnum#uF_per_cm2

Microfarad per square centimetre (specific capacitance)
Is defined by
https://w3id.org/tvbo/struct
has super-classes
UnitEnum c

um3c back to ToC or Class ToC

IRI: http://qudt.org/vocab/unit/MicroM3

Cubic micrometre (µm³)
has super-classes
UnitEnum c

UnitEnumc back to ToC or Class ToC

IRI: https://w3id.org/tvbo/UnitEnum

Physical units of measurement for model parameters, state variables, and integration settings. Uses conventional abbreviations as values, mapped to the QUDT ontology (http://qudt.org/vocab/unit/) with UO cross-references where available.
Is defined by
https://w3id.org/tvbo/struct
is equivalent to
A c or cm c or degC c or H_per_m c or Hz c or kg c or kHz c or m c or m_per_s c or m_per_s2 c or mol_per_m3 c or um3 c or uS c or us c or mm c or mm_per_ms c or mmol_per_m3 c or ms c or mV c or mV_per_ms c or mV_per_s c or N_per_m c or nA c or nF c or nS c or ohm c or per_ms c or per_mV c or per_nC c or per_pC c or per_s c or percent c or pA c or pF c or pS c or rad c or rad_per_s c or S_per_m c or s c or s2 c or dimensionless c or V c or Hz_per_nA (UnitEnum) c or Mohm (UnitEnum) c or S_per_cm2 (UnitEnum) c or S_per_m2 (UnitEnum) c or arbitrary_unit (UnitEnum) c or kg_per_s (UnitEnum) c or kohm_cm (UnitEnum) c or mS_per_cm2 (UnitEnum) c or mol_per_cm3 (UnitEnum) c or mol_per_m_per_A_per_s (UnitEnum) c or nS_per_mV (UnitEnum) c or per_unit (UnitEnum) c or rad_per_ms (UnitEnum) c or uA_per_cm2 (UnitEnum) c or uF_per_cm2 (UnitEnum) c
has super-classes
Thing c
has sub-classes
A c, H_per_m c, Hz c, Hz_per_nA (UnitEnum) c, Mohm (UnitEnum) c, N_per_m c, S_per_cm2 (UnitEnum) c, S_per_m c, S_per_m2 (UnitEnum) c, V c, arbitrary_unit (UnitEnum) c, cm c, degC c, dimensionless c, kHz c, kg c, kg_per_s (UnitEnum) c, kohm_cm (UnitEnum) c, m c, mS_per_cm2 (UnitEnum) c, mV c, mV_per_ms c, mV_per_s c, m_per_s c, m_per_s2 c, mm c, mm_per_ms c, mmol_per_m3 c, mol_per_cm3 (UnitEnum) c, mol_per_m3 c, mol_per_m_per_A_per_s (UnitEnum) c, ms c, nA c, nF c, nS c, nS_per_mV (UnitEnum) c, ohm c, pA c, pF c, pS c, per_mV c, per_ms c, per_nC c, per_pC c, per_s c, per_unit (UnitEnum) c, percent c, rad c, rad_per_ms (UnitEnum) c, rad_per_s c, s c, s2 c, uA_per_cm2 (UnitEnum) c, uF_per_cm2 (UnitEnum) c, uS c, um3 c, us c
is in range of
time_scale (slot) op, unit (slot) dp

unsupported (DevelopmentStatus)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/DevelopmentStatus#unsupported

Released but no longer supported.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
DevelopmentStatus c

UpdateRulec back to ToC or Class ToC

IRI: https://w3id.org/tvbo/UpdateRule

Defines how a parameter is updated based on observables. Represents iterative learning rules like FIC or EIB updates. Functions from experiment.functions are available in the equation.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
Thing c

uSc back to ToC or Class ToC

IRI: http://qudt.org/vocab/unit/MicroS

Microsiemens
has super-classes
UnitEnum c

usc back to ToC or Class ToC

IRI: http://qudt.org/vocab/unit/MicroSEC

Microsecond
has super-classes
UnitEnum c

Vc back to ToC or Class ToC

IRI: http://qudt.org/vocab/unit/V

Volt
has super-classes
UnitEnum c

venv (EnvironmentType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/EnvironmentType#venv

Python virtual environment.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
EnvironmentType c

visualization_toolc back to ToC or Class ToC

IRI: https://bio.tools/ontology/operation_0337

Visualization or graphical user interface.
has super-classes
ToolRole c

voltage (PhysicalDimension)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/PhysicalDimension#voltage

Voltage [M L² T⁻³ I⁻¹]
Is defined by
https://w3id.org/tvbo/struct
has super-classes
PhysicalDimension c

volume (PhysicalDimension)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/PhysicalDimension#volume

Volume [L³]
Is defined by
https://w3id.org/tvbo/struct
has super-classes
PhysicalDimension c

WattsStrogatz (StandardGraphType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/StandardGraphType#WattsStrogatz

Watts-Strogatz small-world (params: k, p)
Is defined by
https://w3id.org/tvbo/struct
has super-classes
StandardGraphType c

white (NoiseType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/NoiseType#white

Is defined by
https://w3id.org/tvbo/struct
has super-classes
NoiseType c

window (AggregationType)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/AggregationType#window

Sliding window aggregation
Is defined by
https://w3id.org/tvbo/struct
has super-classes
AggregationType c

wip (DevelopmentStatus)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/DevelopmentStatus#wip

Work in progress; not yet feature-complete.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
DevelopmentStatus c

workflow_framework (ToolRole)c back to ToC or Class ToC

IRI: https://w3id.org/tvbo/ToolRole#workflow_framework

Orchestration, model-building, or pipeline tool.
Is defined by
https://w3id.org/tvbo/struct
has super-classes
ToolRole c

XMLc back to ToC or Class ToC

IRI: http://www.wikidata.org/entity/Q2115

has super-classes
ProgrammingLanguageEnum c

Object Properties

additional_equations (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/additional_equations

affect (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/affect

Affect function: what happens when the event triggers. Can modify state variables and/or parameters. For stimulus type, this is the stimulus equation.

affect_negative (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/affect_negative

Affect on downcrossing (continuous events only). If not specified, uses the same affect for both crossings.

algorithms (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/algorithms

Iterative parameter tuning algorithms (FIC, EIB, etc.)

amplitude (dbs)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/dbs/amplitude

axis (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/axis

Dimension along which the distribution is sampled. 'space' = per-node (default), 'time' = per-timestep (stochastic input).

bc_type (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/bc_type

bids (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/bids

BIDS filename entities for this dataset

bifurcation parameterop back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/bifurcationParameter

Parameter (CURIE into the per-model parameter namespace) along which the bifurcation is observed.
has domain
Bifurcation event c

bifurcation typeop back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/bifurcationType

Object is a Bifurcation class (e.g. tvbo:Hopf). Encoded as a class so DL reasoners can use the subClassOf hierarchy on the Bifurcation tree.
has domain
Bifurcation event c

boundaries (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/boundaries

bounds (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/bounds

Constraints on parameter values after update

branches (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/branches

Child branches to continue from detected bifurcation points (PO from Hopf, fold continuation, etc.).

call_args (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/call_args

Arguments passed when calling the instance (__call__). Usually the input data from simulation result. Example: result (simulation output array).

cases (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/cases

centerop back to ToC or Object Property ToC

IRI: http://uri.interlex.org/tgbugs/uris/readable/center

Add the center coordinate of this entity.

class_call (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/class_call

Class instantiation and call (alternative to callable/function). Use for external library classes that need __init__ then __call__. Example: Bold monitor from tvboptim.

class_reference (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/class_reference

Direct class reference (alternative to pipeline). Use for external library classes like tvboptim.Bold, custom monitors, or any callable class. The class is instantiated with constructor_args and called with call_args. Example: {name: Bold, module: tvboptim.observations.tvb_monitors.bold, constructor_args: [{name: period, value: 1000.0}]}

clinical_improvement (dbs)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/dbs/clinical_improvement

Observed improvement relative to baseline based on a defined score.

clinical_scores (dbs)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/dbs/clinical_scores

coefficient (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/coefficient

conditionals (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/conditionals

Conditional logic for piecewise equations.

connectivity (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/connectivity

constructor_args (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/constructor_args

Arguments passed to __init__ when instantiating the class. Example: period=1000.0, downsample_period=4.0 for Bold monitor.

contacts (dbs)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/dbs/contacts

List of physical contacts along the electrode

continuation (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/continuation

Override solver settings for this branch. Uses the same Continuation type — only explicitly set attributes override the parent's values.

continuations (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/continuations

Numerical continuation and bifurcation analysis specifications. Each entry defines a continuation experiment (equilibrium branch, codim-2 curve, periodic orbit family, etc.). # Either reference a full reusable environment (preferred) or, for

coordinate (dbs)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/dbs/coordinate

3D coordinate of the contact center in the defined coordinate space

coordinates (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/coordinates

Node coordinates (x,y,z) in the given coordinate space.

coordinateSpaceop back to ToC or Object Property ToC

IRI: http://uri.interlex.org/tgbugs/uris/readable/coordinateSpace

Common coordinate space (e.g. FSLMNI152, MNI152NLin2009cAsym). Reference by name; the CommonCoordinateSpace must be defined in tvbo/database/coordinate_spaces/ (or future equivalent location).
has range
CommonCoordinateSpace c

correlation (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/correlation

coupling_function (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/coupling_function

Mathematical function defining the coupling

coupling_inputs (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/coupling_inputs

coupling_terms (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/coupling_terms

data (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/data

dataset (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/dataset

Multi-subject dataset for workflow rendering. When set, render_workflow() uses dataset.subjects/sessions to generate per-subject parallel jobs.

derived_from_model (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/derived_from_model

derived_observations (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/derived_observations

Observations derived from combining other observations. Computed after all regular observations are available. Examples: fc_corr (from fc, fc_target), rmse, etc.

description (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/description

has range
string c
is also defined as
data property

development_status (software)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/software/development_status

Development status (repostatus.org aligned).

distance_unit (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/distance_unit

Unit for distances/lengths in the network

domain (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/domain

has range
Range c

ecosystem (software)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/software/ecosystem

Package ecosystem(s) through which the software is distributed.

edge_matrix_files (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/edge_matrix_files

edges (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/edges

List of directed edges with coupling references (optional, for explicit edge definition)

efield (dbs)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/dbs/efield

Metadata about the E-field result for this setting

electrode_reference (dbs)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/dbs/electrode_reference

electrodes (dbs)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/dbs/electrodes

element_type (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/element_type

engine (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/engine

Primary engine (must appear in environment.requirements; migration target replacing deprecated 'software').

entitiesop back to ToC or Object Property ToC

IRI: http://uri.interlex.org/tgbugs/uris/readable/entities

environment (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/environment

Execution environment (collection of requirements).
has range
SoftwareEnvironment (software) c

environment_type (software)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/software/environment_type

Category: conda, venv, docker, etc.

equation (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/equation

has range
Equation c

event_type (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/event_type

Type of event trigger mechanism.

executable onop back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/executableOn

has range
Backend c

exhibits bifurcationop back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/exhibitsBifurcation

Range is a reified BifurcationEvent that records the bifurcation type, the locus parameter, and (optionally) the critical value.
has range
Bifurcation event c

exhibits regimeop back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/exhibitsRegime

Object is a Regime class (open-world: model may admit additional regimes for parameter values not yet catalogued).

explorations (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/explorations

Parameter exploration/grid search specifications

field (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/field

Primary field being solved for (deprecated; use state_variables).

field_dynamics (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/field_dynamics

freeze_parameters (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/freeze_parameters

Parameters from previous stages to freeze (keep at optimized value but not update)

frequency (dbs)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/dbs/frequency

graph_generator (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/graph_generator

Graph generator specification. When set, overrides explicit edges/nodes for graph construction. The type field is a free string; StandardGraphType lists well-known types that get automatic code generation across backends.

has attractorop back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/hasAttractor

has model featureop back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/hasModelFeature

has range
Model feature c

has stochasticity characterop back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/hasStochasticityCharacter

Intrinsic stochasticity of the model definition itself. A model whose equations are deterministic but is integrated with additive noise via the Integrator is still tvbo:Deterministic here.

hasParentop back to ToC or Object Property ToC

IRI: http://uri.interlex.org/tgbugs/uris/readable/hasParent

Add all anatomical parent structures for this entity as defined within the corresponding brain atlas.
has range
ParcellationEntity c

head (dbs)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/dbs/head

hemisphereop back to ToC or Object Property ToC

IRI: http://uri.interlex.org/tgbugs/uris/readable/hemisphere

Add the hemisphere of this entity.

hi (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/hi

Upper bound or stopping value. Can be a number or argument name.

history (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/history

imaging_modality (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/imaging_modality

Type of imaging modality (BOLD, EEG, MEG, etc.)

includes (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/includes

Include update rules from other algorithms with optional argument overrides. Unlike depends_on (sequential), includes means combined execution. Example: includes: [{algorithm: fic, arguments: [{name: eta, value: 0.1}]}]

incoming_states (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/incoming_states

References to state variables from connected (source) nodes. Auto-populated from state_variables with coupling_variable=true when omitted. Used by name in pre_expression.

initial_expression (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/initial_expression

Analytic initial condition for the field.

initial_state (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/initial_state

How to obtain the initial equilibrium. Default: time integration to steady state.

inner_coupling (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/inner_coupling

For hierarchical coupling: inner coupling applied at regional level

intensity (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/intensity

Optional scalar or vector intensity parameter for noise.

intermediate_expressions (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/intermediate_expressions

interoperates_with (software)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/software/interoperates_with

Tools this tool can exchange data with or delegate to.

label (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/label

has range
string c
is also defined as
data property

linear_solver (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/linear_solver

Linear solver for the Newton bordered system. E.g. COPBLS (collocation), MatrixBLS (shooting/poincaré).

lo (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/lo

Lower bound or starting value. Can be a number or argument name.

loader (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/loader

Callable that loads the data (e.g., load_functional_connectivity)

local_coupling_term (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/local_coupling_term

local_states (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/local_states

References to state variables from the local (target) node. Used by name in pre_expression.

loss (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/loss

Loss function call. Uses FunctionCall to either: 1. Reference existing function: function: rmse 2. Inline callable: callable: {module: ..., name: ...} Arguments specify inputs (simulated_fc, empirical_fc, etc.)

metric (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/metric

Metric equation for matching (e.g., correlation, rmse)

modality (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/modality

Imaging modality or simulation output type.

model (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/model

has range
Dynamics c

model_paradigm (software)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/software/model_paradigm

Computational paradigms supported.

models anatomical regionop back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/modelsAnatomicalRegion

Anatomical region(s) the Dynamics model is intended to represent. Range: UBERON terms.

models cell typeop back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/modelsCellType

Cell type(s) whose collective dynamics the model represents. Range: CL terms.

models neurotransmitter systemop back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/modelsNeurotransmitterSystem

Neurotransmitter system(s) whose synaptic dynamics the model represents. Range: GO biological-process terms.

modes (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/modes

name (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/name

has range
string c
is also defined as
data property

network (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/network

nodes (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/nodes

List of nodes with individual dynamics (optional, for heterogeneous networks)

objective (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/objective

What the algorithm optimizes for

observable (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/observable

Observable to compute at each point. Use function: obs_name for simple observation, or function: func_name + arguments for FunctionCall.

ode_solver (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/ode_solver

ODE solver for flow-based methods (shooting, poincaré). Specifies algorithm (e.g. Vern9, Rodas5) and tolerances. Not needed for collocation or trapezoid.

operator_type (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/operator_type

operators (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/operators

optimizations (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/optimizations

Parameter optimization configurations

output_equation (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/output_equation

Output transformation equation (if equation-based)

over (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/over

Dimension to aggregate over (e.g., node, time, state)

package (software)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/software/package

Reference to the software package identity.

parameters (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/parameters

has range
Parameter c

parcellation (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/parcellation

Brain parcellation/atlas reference

parent_score (dbs)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/dbs/parent_score

If this score is a subscore of a broader composite

pipeline (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/pipeline

Ordered sequence of Functions. Each step has a unique `name` (used to key step outputs) and transforms input -> output. List form preserves execution order.

position (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/position

Spatial coordinates (x, y, z) of the node

post_expression (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/post_expression

Post-processing expression applied after coupling

pre_expression (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/pre_expression

Pre-processing expression applied before coupling

preprocessing (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/preprocessing

Optional preprocessing to apply after loading

programming_language (software)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/software/programming_language

Implementation languages.

protocols (dbs)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/dbs/protocols

All DBS protocols assigned to this subject.

provenance (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/provenance

W3C PROV-O aligned provenance

provides capabilityop back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/providesCapability

has domain
Backend c
has range
Backend capability c

pulse_width (dbs)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/dbs/pulse_width

random_state (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/random_state

region_mapping (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/region_mapping

For hierarchical coupling: vertex-to-region mapping for aggregation

regional_connectivity (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/regional_connectivity

For hierarchical coupling: region-to-region connectivity with weights and delays

requirements (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/requirements

has range
SoftwareRequirement (software) c

requirements (software)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/software/requirements

Constituent software requirements.

requires (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/requires

Observables required by this update rule

role (software)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/software/role

sample (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/sample

scale (dbs)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/dbs/scale

The scale this score belongs to, if applicable

scale (software)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/software/scale

Spatial/organizational scales the tool operates at.

score (dbs)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/dbs/score

sessions (study)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/study/sessions

Data collection sessions for this subject. Each session can have its own network, empirical data, and conditions.

settings (dbs)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/dbs/settings

sex (study)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/study/sex

Biological sex.

simulation_experiments (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/simulation_experiments

software_environment (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/software_environment

Software environment used to generate this data.

source (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/source

has range
string c
is also defined as
data property

source_experiment (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/source_experiment

Reference to the SimulationExperiment that generated this TimeSeries.

source_observations (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/source_observations

One or more observations to derive from. For transformations (e.g., fc from bold), use single source. For comparisons (e.g., fc_corr from fc and fc_target), use multiple sources. Order may matter for asymmetric operations.

sources (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/sources

space (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/space

Ordered list of exploration axes spanning the search space. Each axis references an existing Parameter (by dotted name, e.g. "ReducedWongWang.w" or "FastLinearCoupling.G") and supplies the Range to sweep. No new Parameter is created here.

stages (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/stages

Ordered list of optimization stages. Stages run sequentially. Stage n+1 starts from optimized values of stage n. When defined, inherited single-stage fields are ignored.

state (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/state

Per-node initial state variable values, keyed by state variable name.

step (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/step

Step size. Can be: number, argument name, or expression.

stimulation (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/stimulation

stimulus (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/stimulus

subjects (study)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/study/subjects

Subjects in a dataset.
has range
Subject (study) c

supports taskop back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/supportsTask

has domain
Backend c
has range
Simulation task c

system_type (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/system_type

tail (dbs)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/dbs/tail

target_data (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/target_data

Reference to empirical data observation for matching objectives

target_parameter (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/target_parameter

The parameter to update (e.g., J_i, wLRE)

target_structure (dbs)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/dbs/target_structure

Anatomical target structure from a brain atlas

target_variable (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/target_variable

State variable for activity targets (e.g., S_e)

targets (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/targets

State variables this noise applies to; if omitted, applies globally.

tensor_coefficient (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/tensor_coefficient

Optional anisotropic tensor (e.g., diffusion).

terminologyop back to ToC or Object Property ToC

IRI: http://uri.interlex.org/tgbugs/uris/readable/terminology

Add the parcellation terminology version used for this brain atlas version.

time (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/time

time_scale (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/time_scale

Time unit for the integration / simulation. Determines the physical time meaning of one model time-step.
has range
UnitEnum c

time_unit (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/time_unit

Default time unit for the network

tool_role (software)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/software/tool_role

Primary function(s) in a simulation workflow.

tractogram (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/tractogram

Reference to tractography data

trajectory (dbs)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/dbs/trajectory

The planned trajectory for electrode implantation

transforms (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/transforms

Ordered list of transforms applied to edge property matrices. Each Function's name identifies the target edge property (e.g. 'weight', 'length'). Supports equation-based (symbolic) or callable-based (software) transforms. Multiple transforms on the same target are applied sequentially.

update_expression (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/update_expression

update_rules (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/update_rules

How parameters are updated each iteration. When using 'includes', update_rules are inherited from included algorithms.

value (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/value

has range
ScalarValue c
is also defined as
data property

warmup_from (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/warmup_from

Previous stage to initialize from. Final values from that stage become initial values for this stage.

x (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/x

y (slot)op back to ToC or Object Property ToC

IRI: https://w3id.org/tvbo/y

Data Properties

abbreviationdp back to ToC or Data Property ToC

IRI: http://uri.interlex.org/tgbugs/uris/readable/abbreviation

has range
string c

absolute_value (dbs)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/dbs/absolute_value

Absolute value of the score at the time of assessment

acronym (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/acronym

has range
string c

active_contacts (dbs)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/dbs/active_contacts

additive (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/additive

Indicates whether the noise is additive

age (study)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/study/age

Age at time of study (years).

alternateNamedp back to ToC or Data Property ToC

IRI: http://uri.interlex.org/tgbugs/uris/readable/alternateName

has range
string c

apply_every (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/apply_every

Apply update every N iterations

authordp back to ToC or Data Property ToC

IRI: http://uri.interlex.org/tgbugs/uris/readable/author

has range
string c

autonomous (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/autonomous

Whether the system is autonomous (equations do not depend explicitly on time t). Non-autonomous systems have explicit time dependence, e.g. f*cos(omega*t).

baseline_value (dbs)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/dbs/baseline_value

Preoperative baseline value of the score

batch_size (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/batch_size

Batch size for vectorized operations (None = auto)

conditional (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/conditional

contact_id (dbs)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/dbs/contact_id

Identifier (e.g., 0, 1, 2)

correlated (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/correlated

coupling_variable (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/coupling_variable

Whether this state variable is transmitted to connected nodes through the coupling function. In TVB terms, this determines the cvar indices (state variables extracted from history and fed into the coupling function). The coupling function may override this via its incoming_states attribute.

critical valuedp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/criticalValue

has characteristics: functional

has domain
Bifurcation event c
has range
double

dataLocationdp back to ToC or Data Property ToC

IRI: http://uri.interlex.org/tgbugs/uris/readable/dataLocation

has range
string c

dataset_id (study)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/study/dataset_id

has range
string c

dataset_path (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/dataset_path

has range
string c

date_created (software)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/software/date_created

Date the software was first released (YYYY-MM-DD).

date_modified (software)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/software/date_modified

Date of the most recent release or significant update.

default (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/default

has range
string c

definition (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/definition

has range
string c

degree (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/degree

Polynomial degree per mesh interval for collocation. The m in PeriodicOrbitOCollProblem(N, m).

delay (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/delay

Conduction delay (explicit edges, ms)

delta_p (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/delta_p

Initial parameter offset from the bifurcation point.

derivative_initial_value (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/derivative_initial_value

Initial value for the first time derivative, used when equation_order > 1. For a second-order ODE d²x/dt² = f, this sets dx/dt(0). Required by ModelingToolkit.jl to fully specify higher-order initial value problems.

detect_bifurcation (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/detect_bifurcation

Bifurcation detection level. 0 = off, 1 = eigenvalues only, 2 = detect, 3 = locate precisely.

detect_fold (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/detect_fold

Enable fold (limit point) detection.

digitalIdentifierdp back to ToC or Data Property ToC

IRI: http://uri.interlex.org/tgbugs/uris/readable/digitalIdentifier

Add the digital identifier of this brain atlas or coordinate space version.
has range
string c

dimension (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/dimension

Dimensionality of the coupling input (number of coupled values)

distance (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/distance

Edge length / tract distance (explicit edges, mm)

downsample_period (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/downsample_period

Intermediate downsampling period (ms). For BOLD: typically matches dt.

ds (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/ds

Initial arc-length step size.

ds_max (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/ds_max

Maximum adaptive step size.

ds_min (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/ds_min

Minimum adaptive step size.

dt (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/dt

Time step (s).

duration (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/duration

has range
float

element (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/element

Element/node index this range applies to. Used in element_domains to explicitly link a domain to a specific element of a heterogeneous parameter (e.g., element: 0 for node 0). Required when used in element_domains to avoid ambiguous positional indexing.

equation_order (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/equation_order

Order of the time derivative on the LHS. Default 1 means dx/dt = rhs (first-order ODE). Order 2 means d²x/dt² = rhs (second-order ODE), etc. Higher-order ODEs are automatically lowered to coupled first-order systems by backends like ModelingToolkit.jl via mtkcompile.

file (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/file

has range
string c

find_fixpoint (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/find_fixpoint

Whether to find a fixed point (steady state) before time integration. Used as initial condition for ODEProblem. Maps to NLsolve.fixpoint! in ND.jl or similar in other backends.

free (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/free

gaussian (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/gaussian

Indicates whether the noise is Gaussian

generated_at (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/generated_at

Timestamp when this TimeSeries was generated.

grounding (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/grounding

External ontology IRIs (typically GO, ChEBI, UBERON, CL, MeSH) that this entity is a surrogate / abstraction / model of. Replaces the legacy OWL pattern `tvbo:surrogate_of` by carrying the link inline with the YAML data instance. Multiple IRIs allowed: a single parameter may abstract several biological processes (e.g. a synaptic conductance grounding both GO:0060079 (excitatory PSP) and GO:0007268 (chemical synaptic transmission)).
has range
any U R I

has conserved quantitydp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/hasConservedQuantity

has range
boolean

has timescale separationdp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/hasTimescaleSeparation

has range
boolean

has_reference (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/has_reference

has range
string c

homepage (software)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/software/homepage

Project homepage URL.

id (dbs)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/dbs/id

Surrogate integer key.
has range
integer

id (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/id

Unique node identifier

iri (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/iri

Optional stable IRI (or compact URI) for this entity in an external ontology or knowledge base. Used to load metadata from an external source; not required when the entity is fully self-contained (equations, parameters, etc. defined in the file itself).
has range
any U R I

is_accessible_for_free (software)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/software/is_accessible_for_free

Whether the tool is free/open-source.

issue_tracker (software)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/software/issue_tracker

URL of the bug tracker or issue board.

latex (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/latex

learning_rate_warmup (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/learning_rate_warmup

Linear warmup of learning rate from 0 to learning_rate over n_iterations. eta_effective = eta * (i+1) / n_iterations

log_scale (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/log_scale

Whether to use logarithmic spacing.

lookupLabeldp back to ToC or Data Property ToC

IRI: http://uri.interlex.org/tgbugs/uris/readable/lookupLabel

Enter the label used for looking up this entity in the parcellation terminology.
has range
integer

max_bisection_steps (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/max_bisection_steps

Maximum bisection steps for bifurcation point localization.

max_iterations (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/max_iterations

max_steps (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/max_steps

Maximum continuation steps.

mesh_intervals (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/mesh_intervals

Number of mesh intervals (time slices) for collocation or trapezoid methods. Collocation: N in PeriodicOrbitOCollProblem(N, m). Trapezoid: M in PeriodicOrbitTrapProblem(M=...).

modified (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/modified

n (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/n

Number of points (alternative to step for grid exploration).

n_inversion (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/n_inversion

Number of eigenvalue sign inversions to flag a bifurcation. Must be even. Higher = fewer false positives.

n_iterations (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/n_iterations

Number of iterations to run

n_parallel (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/n_parallel

Parallel evaluations

n_regions (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/n_regions

Total number of regions

n_sections (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/n_sections

Number of shooting sections for shooting or Poincaré methods.

n_threads (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/n_threads

Number of CPU threads per worker (-1 = auto-detect)

n_trials (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/n_trials

Number of independent trials per grid point. Each trial uses a different noise seed. Used for averaging stochastic simulations (e.g., VEP = average of 20 trials).

n_vertices (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/n_vertices

Total number of vertices

n_workers (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/n_workers

Number of parallel workers (maps to pmap devices in JAX, processes in multiprocessing)

nev (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/nev

Number of eigenvalues to compute. Must be >= number of state variables for reliable Hopf detection.

newton_max_iterations (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/newton_max_iterations

Maximum Newton corrector iterations per step.

newton_tol (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/newton_tol

Absolute tolerance for Newton corrector convergence.

non_negative (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/non_negative

All values >= 0

number_of_elements (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/number_of_elements

Number of elements (triangles, quads, tetrahedra, etc.).

number_of_modes (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/number_of_modes

number_of_nodes (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/number_of_nodes

Number of nodes in the network (derived from nodes if not set)

number_of_stages (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/number_of_stages

number_of_subjects (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/number_of_subjects

Number of subjects in the tractography dataset

number_of_vertices (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/number_of_vertices

Number of vertices in the mesh.

ontologyIdentifierdp back to ToC or Data Property ToC

IRI: http://uri.interlex.org/tgbugs/uris/readable/ontologyIdentifier

has range
string c

optional (software)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/software/optional

originalLookupLabeldp back to ToC or Data Property ToC

IRI: http://uri.interlex.org/tgbugs/uris/readable/originalLookupLabel

Add the original label of this entity as defined in the parcellation terminology.

percent_change (dbs)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/dbs/percent_change

Percent change compared to preoperative baseline (positive = improvement)

period (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/period

Sampling period for monitors (ms). For BOLD: TR in ms.

phase-space dimensiondp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/phaseSpaceDimension

has characteristics: functional

has range
positive Integer

random_seed (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/random_seed

Base random seed for reproducibility

record (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/record

Whether to include this element in simulation output files. Applicable to state variables (default true), derived variables (default false), and network nodes (default true). Set false to suppress recording.
has range
boolean

references (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/references

has range
string c

reported_optimum (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/reported_optimum

has range
float

repository (software)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/software/repository

Source code repository URL.

run_id (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/run_id

BIDS run number.

same_as (software)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/software/same_as

URIs that unambiguously identify this tool (Wikidata, bio.tools, RRID, SciCrunch).

sampling_period (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/sampling_period

Time between samples (inverse of sampling_rate).

sampling_rate (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/sampling_rate

Sampling rate in Hz.

scipy_ode_base (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/scipy_ode_base

session_id (study)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/study/session_id

has range
string c

simulation_period (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/simulation_period

Duration of each simulation step (e.g., one BOLD TR)

size (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/size

skip_t (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/skip_t

Number of samples to skip at the start (transient removal). For FC: typically 10-20 TRs.

sparse (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/sparse

Whether the coupling uses sparse representations

state_wise_sigma (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/state_wise_sigma

step_size (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/step_size

steps (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/steps

stimulation_variable (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/stimulation_variable

subject_id (study)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/study/subject_id

has range
string c

symbol (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/symbol

has range
string c

tail_samples (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/tail_samples

Number of samples from the end to use. Takes the last N samples before aggregation. E.g., tail_samples: 500 means use data[-500:].

target (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/target

Target node ID (set for explicit edges, absent for template edges)

target_value (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/target_value

Target value for activity objectives

threshold_applied (dbs)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/dbs/threshold_applied

Threshold value applied to the E-field simulation

time_post_surgery (dbs)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/dbs/time_post_surgery

Timepoint of assessment in days or months after implantation

tol_stability (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/tol_stability

Tolerance on real part of eigenvalue for stability boundary.

transient_time (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/transient_time

trigger_times (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/trigger_times

Predetermined trigger times for preset_time events. The solver will step exactly to these times.

valid_diagonal (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/valid_diagonal

Self-connections are meaningful

variable_of_interest (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/variable_of_interest

versionIdentifierdp back to ToC or Data Property ToC

IRI: http://uri.interlex.org/tgbugs/uris/readable/versionIdentifier

has range
string c

vertex_to_region (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/vertex_to_region

Array mapping each vertex index to its parent region index. Can use dataLocation instead for large arrays.

voi (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/voi

Variable of interest index (which state variable to monitor). Default: 0.

warmup (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/warmup

Whether to apply learning rate warmup to this update rule. When true, the learning rate (eta) is scaled by (i+1)/n_iterations.

weight (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/weight

Connection weight (explicit edges)

weighted (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/weighted

Matrix entries carry weights (not just 0/1)

window_size (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/window_size

Number of samples for windowed aggregation

xdp back to ToC or Data Property ToC

IRI: http://uri.interlex.org/tgbugs/uris/readable/x

X coordinate

ydp back to ToC or Data Property ToC

IRI: http://uri.interlex.org/tgbugs/uris/readable/y

Y coordinate

year (slot)dp back to ToC or Data Property ToC

IRI: https://w3id.org/tvbo/year

zdp back to ToC or Data Property ToC

IRI: http://uri.interlex.org/tgbugs/uris/readable/z

Z coordinate

Annotation Properties

alt Labelap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/2004/02/skos/core#altLabel

anatomical Axes Orientationap back to ToC or Annotation Property ToC

IRI: https://w3id.org/tvbo/anatomicalAxesOrientation

authorap back to ToC or Annotation Property ToC

IRI: http://schema.org/author

axes Originap back to ToC or Annotation Property ToC

IRI: https://w3id.org/tvbo/axesOrigin

broad Matchap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/2004/02/skos/core#broadMatch

code Repositoryap back to ToC or Annotation Property ToC

IRI: http://schema.org/codeRepository

contributorap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/contributor

createdap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/created

creatorap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/creator

default Valueap back to ToC or Annotation Property ToC

IRI: http://schema.org/defaultValue

definitionap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/2004/02/skos/core#definition

descriptionap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/description

exact Matchap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/2004/02/skos/core#exactMatch

has Db Xrefap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#hasDbXref

has Derived Variableap back to ToC or Annotation Property ToC

IRI: https://w3id.org/tvbo/hasDerivedVariable

has Parameterap back to ToC or Annotation Property ToC

IRI: https://w3id.org/tvbo/hasParameter

has State Variableap back to ToC or Annotation Property ToC

IRI: https://w3id.org/tvbo/hasStateVariable

identifierap back to ToC or Annotation Property ToC

IRI: http://schema.org/identifier

in Schemeap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/2004/02/skos/core#inScheme

is Part Ofap back to ToC or Annotation Property ToC

IRI: http://schema.org/isPartOf

issue Numberap back to ToC or Annotation Property ToC

IRI: http://schema.org/issueNumber

issuedap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/issued

lhsap back to ToC or Annotation Property ToC

IRI: https://w3id.org/tvbo/lhs

licenseap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/license

model_type (slot)ap back to ToC or Annotation Property ToC

IRI: https://w3id.org/tvbo/model_type

Coarse classification of this model (mean_field, neural_mass, phase_oscillator, phenomenological, spiking, generic, field). Used for filtering in Dynamics.list_db(model_type=...).

modifiedap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/modified

notationap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/2004/02/skos/core#notation

noteap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/2004/02/skos/core#note

paginationap back to ToC or Annotation Property ToC

IRI: http://schema.org/pagination

permissible valuesap back to ToC or Annotation Property ToC

IRI: https://w3id.org/linkml/permissible_values

pref Labelap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/2004/02/skos/core#prefLabel

publisherap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/publisher

publisherap back to ToC or Annotation Property ToC

IRI: http://schema.org/publisher

referencesap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/references

rhsap back to ToC or Annotation Property ToC

IRI: https://w3id.org/tvbo/rhs

subjectap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/subject

titleap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/title

unit (slot)ap back to ToC or Annotation Property ToC

IRI: https://w3id.org/tvbo/unit

has range
UnitEnum c
is also defined as
data property

urlap back to ToC or Annotation Property ToC

IRI: http://schema.org/url

versionap back to ToC or Annotation Property ToC

IRI: http://purl.org/pav/version

volume Numberap back to ToC or Annotation Property ToC

IRI: http://schema.org/volumeNumber

Named Individuals

a (Difference parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/coupling_functions/Difference/parameters/a

belongs to
Parameter c
has facts
default Value ap "0.1"^^double
notation ap "a"

a (Epileptor2D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor2D/parameters/a

Coefficient of the cubic term in the first state-variable x_E2D via the function f(x)_E2D, in Epileptor2D Proix et al.,2014).
belongs to
Parameter c
has facts
description ap "Coefficient of the cubic term in the first state-variable x_E2D via the function f(x)_E2D, in Epileptor2D Proix et al"
default Value ap "1.0"^^double
definition ap "Coefficient of the cubic term in the first state-variable x_E2D via the function f(x)_E2D, in Epileptor2D Proix et al.,2014)."
notation ap "a"

a (Epileptor5D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor5D/parameters/a

Coefficient of the cubic term in the first state variable
belongs to
Parameter c
has facts
description ap "Coefficient of the cubic term in the first state variable"
default Value ap "1.0"^^double
definition ap "Coefficient of the cubic term in the first state variable"
notation ap "a"

a (EpileptorRestingState parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/EpileptorRestingState/parameters/a

Coefficient of the cubic term in the first state-variable x1.
belongs to
Parameter c
has facts
description ap "Coefficient of the cubic term in the first state-variable x1"
default Value ap "1.0"^^double
definition ap "Coefficient of the cubic term in the first state-variable x1."
notation ap "a"

A (GastSchmidtKnosche_SD state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/GastSchmidtKnosche_SD/state_variables/A

belongs to
StateVariable c
has facts
notation ap "A"
lhs ap "Derivative(A, t)"
rhs ap "B/tau_A"

A (GastSchmidtKnosche_SF state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/GastSchmidtKnosche_SF/state_variables/A

belongs to
StateVariable c
has facts
notation ap "A"
lhs ap "Derivative(A, t)"
rhs ap "B/tau_A"

a (Generic2dOscillator parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Generic2dOscillator/parameters/a

Vertical shift of the configurable nullcline
belongs to
Parameter c
has facts
description ap "Vertical shift of the configurable nullcline"
default Value ap "-2.0"^^double
definition ap "Vertical shift of the configurable nullcline"
notation ap "a"

a (HyperbolicTangent parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/coupling_functions/HyperbolicTangent/parameters/a

belongs to
Parameter c
has facts
description ap "Minimum of the sigmoid function"
default Value ap "1.0"^^double
notation ap "a"

A (JansenRit parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/JansenRit/parameters/A

Maximum amplitude of EPSP [mV]. Also called average synaptic gain.
belongs to
Parameter c
has facts
description ap "Maximum amplitude of EPSP [mV]"
default Value ap "3.25"^^double
has Db Xref ap G O 0060079 ep
definition ap "Maximum amplitude of EPSP [mV]. Also called average synaptic gain."
notation ap "A"
unit (slot) dp "mV"

a (JansenRit parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/JansenRit/parameters/a

Rate constant of the excitatory post-synaptic potential (EPSP). It is interpreted as being the lumped representation of the sum of the reciprocal of the time constant of passive membrane and all other spatially distributed delays, including temporal dispersion in the afferent tract, synaptic diffusion, and resistive-capacitive delay in the dendritic network.
belongs to
Parameter c
has facts
description ap "Reciprocal of the time constant of passive membrane and all other spatially distributed delays in the dendritic network. Also called average synaptic time constant."
default Value ap "0.1"^^double
has Db Xref ap G O 0099605 ep
definition ap "Rate constant of the excitatory post-synaptic potential (EPSP). It is interpreted as being the lumped representation of the sum of the reciprocal of the time constant of passive membrane and all other spatially distributed delays, including temporal dispersion in the afferent tract, synaptic diffusion, and resistive-capacitive delay in the dendritic network."
notation ap "a"
unit (slot) dp "per_ms"

A (JansenRit1995 parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/JansenRit1995/parameters/A

belongs to
Parameter c
has facts
description ap "Maximum amplitude of excitatory PSP (EPSP)"
default Value ap "3.25"^^double
notation ap "A"
unit (slot) dp "mV"

a (JansenRit1995 parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/JansenRit1995/parameters/a

belongs to
Parameter c
has facts
description ap "Reciprocal of EPSP time constant"
default Value ap "100"^^integer
notation ap "a"
unit (slot) dp "per_s"

a (KuramotoCoupling parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/coupling_functions/KuramotoCoupling/parameters/a

belongs to
Parameter c
has facts
description ap "Rescales the connection strength."
default Value ap "1.0"^^double
notation ap "a"

a (Linear parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/coupling_functions/Linear/parameters/a

belongs to
Parameter c
has facts
description ap "Linear scaling factor of the coupled (delayed) input."
default Value ap "0.00390625"^^double
notation ap "a"

A (ModelJansen1995 parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ModelJansen1995/parameters/A

belongs to
Parameter c
has facts
default Value ap "3.25"^^double
notation ap "A"
unit (slot) dp "mV"

a (ModelJansen1995 parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ModelJansen1995/parameters/a

belongs to
Parameter c
has facts
default Value ap "0.1"^^double
notation ap "a"
unit (slot) dp "per_ms"

a (ReducedWongWang parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWang/parameters/a

Slope (or gain) parameter of the sigmoid input-output function H_RWW (Deco et al., 2013). Note: ----- In the original publication, the parameter 'a' is set in (nC)^-1 (i.e., equivalent to (nA.s)^-1). In TVB, the parameter has been converted in (pC)^-1 for setting the system in millisecond.
belongs to
Parameter c
has facts
description ap "Slope (or gain) parameter of the sigmoid input-output function H_RWW (Deco et al"
default Value ap "0.27"^^double
definition ap "Slope (or gain) parameter of the sigmoid input-output function H_RWW (Deco et al., 2013). Note: ----- In the original publication, the parameter 'a' is set in (nC)^-1 (i.e., equivalent to (nA.s)^-1). In TVB, the parameter has been converted in (pC)^-1 for setting the system in millisecond."
notation ap "a"
unit (slot) dp "per_pC"

a (ReducedWongWangTvboptim parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWangTvboptim/parameters/a

Input gain parameter of the sigmoid transfer function H(x).
belongs to
Parameter c
has facts
description ap "Input gain parameter"
default Value ap "0.27"^^double
definition ap "Input gain parameter of the sigmoid transfer function H(x)."
notation ap "a"
unit (slot) dp "per_pC"

a (Scaling parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/coupling_functions/Scaling/parameters/a

belongs to
Parameter c
has facts
description ap "Linear scaling factor of the coupled (delayed) input."
default Value ap "0.00390625"^^double
notation ap "a"

a (Sigmoidal parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/coupling_functions/Sigmoidal/parameters/a

belongs to
Parameter c
has facts
description ap "Scaling of sigmoidal"
default Value ap "1.0"^^double
notation ap "a"

a (SigmoidalJansenRit parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/coupling_functions/SigmoidalJansenRit/parameters/a

belongs to
Parameter c
has facts
description ap "Scaling of the coupling term"
default Value ap "1.0"^^double
notation ap "a"

a (StefanescuJirsa2D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa2D/parameters/a

Heterogeneity scale parameter entering the m_i, n_i offsets.
belongs to
Parameter c
has facts
default Value ap "0.45"^^double
definition ap "Heterogeneity scale parameter entering the m_i, n_i offsets."
notation ap "a"

a (StefanescuJirsa3D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa3D/parameters/a

Hindmarsh-Rose dimensionless coefficient a.
belongs to
Parameter c
has facts
default Value ap "1.0"^^double
definition ap "Hindmarsh-Rose dimensionless coefficient a."
notation ap "a"

a (SupHopf parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/SupHopf/parameters/a

Local bifurcation parameter.
belongs to
Parameter c
has facts
description ap "Local bifurcation parameter"
default Value ap "-0.5"^^double
definition ap "Local bifurcation parameter."
notation ap "a"

a_1 (JansenRit parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/JansenRit/parameters/a_1

Average probability constant of the number of synapses made by the pyramidal cells to the dendrites of the excitatory interneurons (feedback excitatory loop). It characterizes the connectivity between the PCs and EINs.
belongs to
Parameter c
has facts
description ap "Average probability constant of the number of synapses made by the pyramidal cells to the dendrites of the excitatory interneurons (feedback excitatory loop)"
default Value ap "1.0"^^double
has Db Xref ap G O 0099536 ep
definition ap "Average probability constant of the number of synapses made by the pyramidal cells to the dendrites of the excitatory interneurons (feedback excitatory loop). It characterizes the connectivity between the PCs and EINs."
notation ap "a_1"

a_2 (JansenRit parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/JansenRit/parameters/a_2

Average probability constant of the number of synapses made by the EINs to the dendrites of the PCs. It characterizes the excitatory connectivity between the EINs and PCs.
belongs to
Parameter c
has facts
description ap "Average probability constant of the number of synapses made by the EINs to the dendrites of the PCs"
default Value ap "0.8"^^double
has Db Xref ap G O 0099536 ep
definition ap "Average probability constant of the number of synapses made by the EINs to the dendrites of the PCs. It characterizes the excitatory connectivity between the EINs and PCs."
notation ap "a_2"

a_3 (JansenRit parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/JansenRit/parameters/a_3

Average probability constant of the number of synapses made by the PCs to the dendrites of the IINs. It characterizes the connectivity between the PCs and inhibitory IINs.
belongs to
Parameter c
has facts
description ap "Average probability constant of the number of synapses made by the PCs to the dendrites of the IINs"
default Value ap "0.25"^^double
has Db Xref ap G O 0099536 ep
definition ap "Average probability constant of the number of synapses made by the PCs to the dendrites of the IINs. It characterizes the connectivity between the PCs and inhibitory IINs."
notation ap "a_3"

a_4 (JansenRit parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/JansenRit/parameters/a_4

Average probability constant of the number of synapses made by the IINs to the dendrites of the PCs. It characterizes the connectivity between the IINs and PCs.
belongs to
Parameter c
has facts
description ap "Average probability constant of the number of synapses made by the IINs to the dendrites of the PCs"
default Value ap "0.25"^^double
has Db Xref ap G O 0060077 ep
has Db Xref ap G O 0099536 ep
definition ap "Average probability constant of the number of synapses made by the IINs to the dendrites of the PCs. It characterizes the connectivity between the IINs and PCs."
notation ap "a_4"

a_e (ReducedWongWangExcInh parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWangExcInh/parameters/a_e

Slope (or gain) parameter of the sigmoid function HE_RWW_EI (Deco et al., 2014).
belongs to
Parameter c
has facts
description ap "Slope (or gain) parameter of the sigmoid function HE_RWW_EI (Deco et al"
default Value ap "310.0"^^double
definition ap "Slope (or gain) parameter of the sigmoid function HE_RWW_EI (Deco et al., 2014)."
notation ap "a_e"
unit (slot) dp "per_nC"

a_e (WilsonCowan parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/WilsonCowan/parameters/a_e

Steepness of the excitatory response function S_e_WC (Wilson and Cowan, 1972).
belongs to
Parameter c
has facts
description ap "Steepness of the excitatory response function S_e_WC (Wilson and Cowan, 1972)"
default Value ap "1.2"^^double
has Db Xref ap G O 0060079 ep
definition ap "Steepness of the excitatory response function S_e_WC (Wilson and Cowan, 1972)."
notation ap "a_e"

a_e (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/a_e

Excitatory adaptation conductance [nS]
belongs to
Parameter c
has facts
description ap "Excitatory adaptation conductance [nS]"
default Value ap "4.0"^^double
has Db Xref ap G O 0060079 ep
definition ap "Excitatory adaptation conductance [nS]"
notation ap "a_e"

a_ee (LarterBreakspear parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/LarterBreakspear/parameters/a_ee

Excitatory-to-excitatory synaptic strength.
belongs to
Parameter c
has facts
description ap "Excitatory-to-excitatory synaptic strength"
default Value ap "0.4"^^double
has Db Xref ap G O 0060079 ep
definition ap "Excitatory-to-excitatory synaptic strength."
notation ap "a_ee"

a_ei (LarterBreakspear parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/LarterBreakspear/parameters/a_ei

Excitatory-to-inhibitory synaptic strength.
belongs to
Parameter c
has facts
description ap "Excitatory-to-inhibitory synaptic strength"
default Value ap "2.0"^^double
has Db Xref ap G O 0060079 ep
definition ap "Excitatory-to-inhibitory synaptic strength."
notation ap "a_ei"

a_i (ReducedWongWangExcInh parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWangExcInh/parameters/a_i

Slope (or gain) parameter of the sigmoid function HI_RWW_EI of the inhibitory population (Deco et al., 2014).
belongs to
Parameter c
has facts
description ap "Slope (or gain) parameter of the sigmoid function HI_RWW_EI of the inhibitory population (Deco et al"
default Value ap "615.0"^^double
definition ap "Slope (or gain) parameter of the sigmoid function HI_RWW_EI of the inhibitory population (Deco et al., 2014)."
notation ap "a_i"
unit (slot) dp "per_nC"

a_i (StefanescuJirsa3D derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa3D/derived_variables/a_i

belongs to
DerivedVariable c
has facts
description ap "Per-mode cubic coefficient for the excitatory xi dynamics (a * <V|V^3>)."
notation ap "a_i"
lhs ap "a_i"
rhs ap "a"

a_i (WilsonCowan parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/WilsonCowan/parameters/a_i

Steepness of the excitatory response function S_i_WC (Wilson and Cowan, 1972).
belongs to
Parameter c
has facts
description ap "Steepness of the excitatory response function S_i_WC (Wilson and Cowan, 1972)"
default Value ap "1.0"^^double
has Db Xref ap G O 0060080 ep
definition ap "Steepness of the excitatory response function S_i_WC (Wilson and Cowan, 1972)."
notation ap "a_i"

a_i (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/a_i

Inhibitory adaptation conductance [nS]
belongs to
Parameter c
has facts
description ap "Inhibitory adaptation conductance [nS]"
default Value ap "0.0"^^double
has Db Xref ap G O 0060080 ep
definition ap "Inhibitory adaptation conductance [nS]"
notation ap "a_i"

a_ie (LarterBreakspear parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/LarterBreakspear/parameters/a_ie

Inhibitory-to-excitatory synaptic strength.
belongs to
Parameter c
has facts
description ap "Inhibitory-to-excitatory synaptic strength"
default Value ap "2.0"^^double
has Db Xref ap G O 0060080 ep
definition ap "Inhibitory-to-excitatory synaptic strength."
notation ap "a_ie"

A_ik (StefanescuJirsa3D derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa3D/derived_variables/A_ik

belongs to
DerivedVariable c
has facts
description ap "Excitatory-to-excitatory mode-coupling matrix from Gaussian quadrature."
has Db Xref ap G O 0060079 ep
notation ap "A_ik"
lhs ap "A_ik"
rhs ap "0.5"

a_ne (LarterBreakspear parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/LarterBreakspear/parameters/a_ne

Non-specific-to-excitatory synaptic strength.
belongs to
Parameter c
has facts
description ap "Non-specific-to-excitatory synaptic strength"
default Value ap "1.0"^^double
has Db Xref ap G O 0060079 ep
definition ap "Non-specific-to-excitatory synaptic strength."
notation ap "a_ne"

a_ni (LarterBreakspear parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/LarterBreakspear/parameters/a_ni

Non-specific-to-inhibitory synaptic strength.
belongs to
Parameter c
has facts
description ap "Non-specific-to-inhibitory synaptic strength"
default Value ap "0.4"^^double
has Db Xref ap G O 0060080 ep
definition ap "Non-specific-to-inhibitory synaptic strength."
notation ap "a_ni"

a_rs (EpileptorRestingState parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/EpileptorRestingState/parameters/a_rs

Vertical shift of the configurable nullcline in the state-variable y_rs.
belongs to
Parameter c
has facts
description ap "Vertical shift of the configurable nullcline in the state-variable y_rs"
default Value ap "-2.0"^^double
definition ap "Vertical shift of the configurable nullcline in the state-variable y_rs."
notation ap "a_rs"

aa (Epileptor5D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor5D/parameters/aa

Linear coefficient in fifth state variable
belongs to
Parameter c
has facts
description ap "Linear coefficient in fifth state variable"
default Value ap "6.0"^^double
definition ap "Linear coefficient in fifth state variable"
notation ap "aa"

aa (EpileptorRestingState parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/EpileptorRestingState/parameters/aa

Linear coefficient in the fifth state-variable y2.
belongs to
Parameter c
has facts
description ap "Linear coefficient in the fifth state-variable y2"
default Value ap "6.0"^^double
definition ap "Linear coefficient in the fifth state-variable y2."
notation ap "aa"

Abbott2005ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Abbott2005

belongs to
Book c
has facts
issued ap "2005"
title ap "Theoretical Neuroscience: Computational and Mathematical Modeling of Neural Systems"
author ap "Abbott, L. F."
author ap "Dayan, Peter"
publisher ap "MIT Press"

acq-EEGBrainstorm65_sensorsni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/acq-EEGBrainstorm65_sensors

belongs to
Network c
has facts
description ap "65-channel EEG sensor array (Brainstorm default). Positions in mm, Brainstorm coordinate space."
alt Label ap "EEG Brainstorm 65"
has Parameter ap conduction_speed (acq-EEGBrainstorm65_sensors parameter) ni

acq-MEGBrainstorm276_sensorsni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/acq-MEGBrainstorm276_sensors

belongs to
Network c
has facts
description ap "276-channel MEG sensor array (Brainstorm default). Positions and orientations in mm."
alt Label ap "MEG Brainstorm 276"
has Parameter ap conduction_speed (acq-MEGBrainstorm276_sensors parameter) ni

acq-SEEG588_sensorsni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/acq-SEEG588_sensors

belongs to
Network c
has facts
description ap "588-contact stereo-EEG array (TVB default). Intracranial depth electrodes. No precomputed projection — gain is computed analytically."
alt Label ap "SEEG 588 contacts"
has Parameter ap conduction_speed (acq-SEEG588_sensors parameter) ni

AfferentCouplingni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/observation_models/afferent_coupling

belongs to
Observation c
has facts
description ap "Records the afferent (incoming) coupling term at each network node at every integration step. Records the coupling input that drives the dynamics rather than the model state itself."

AfferentCouplingTemporalAverageni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/observation_models/afferent_coupling_temporal_average

belongs to
Observation c
has facts
description ap "Temporally averaged afferent coupling input at each node. Combines coupling input recording with temporal averaging."

Aik (StefanescuJirsa2D derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa2D/derived_variables/Aik

belongs to
DerivedVariable c
has facts
description ap "Excitatory-to-excitatory mode-coupling matrix derived from Gaussian quadrature over N(mu, sigma); computed offline at `update_derived_parameters`."
has Db Xref ap G O 0060079 ep
notation ap "Aik"
lhs ap "Aik"
rhs ap "0.5"

alpha (CoombesByrne parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/CoombesByrne/parameters/alpha

Parameter of the alpha-function
belongs to
Parameter c
has facts
description ap "Parameter of the alpha-function"
default Value ap "0.95"^^double
definition ap "Parameter of the alpha-function"
notation ap "alpha"

alpha (GastSchmidtKnosche_SD parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/GastSchmidtKnosche_SD/parameters/alpha

adaptation rate
belongs to
Parameter c
has facts
description ap "adaptation rate"
default Value ap "0.5"^^double
definition ap "adaptation rate"
notation ap "alpha"

alpha (GastSchmidtKnosche_SF parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/GastSchmidtKnosche_SF/parameters/alpha

adaptation rate
belongs to
Parameter c
has facts
description ap "adaptation rate"
default Value ap "10.0"^^double
has Db Xref ap G O 0042391 ep
definition ap "adaptation rate"
notation ap "alpha"

alpha (Generic2dOscillator parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Generic2dOscillator/parameters/alpha

alpha_G2D is the coefficient of the linear feedback coupling term of the state-variable W_G2D to the first state-equation Vdot_G2D. Constant parameter to scale the rate of feedback from the slow variable to the fast variable.
belongs to
Parameter c
has facts
description ap "Constant parameter to scale the rate of feedback from the slow variable to the fast variable."
default Value ap "1.0"^^double
definition ap "alpha_G2D is the coefficient of the linear feedback coupling term of the state-variable W_G2D to the first state-equation Vdot_G2D. Constant parameter to scale the rate of feedback from the slow variable to the fast variable."
notation ap "alpha"

alpha (StefanescuJirsa2D state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa2D/state_variables/alpha

belongs to
StateVariable c
has facts
description ap "Inhibitory fast variable (per mode)."
has Db Xref ap G O 0060080 ep
notation ap "alpha"
lhs ap "Derivative(alpha, t)"
rhs ap "tau*(alpha - f_i*alpha**3/3 - beta) + K21*(Cik*xi - alpha) + tau*(II_i + c_pop0 + local_coupling*xi)"

alpha (StefanescuJirsa3D state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa3D/state_variables/alpha

belongs to
StateVariable c
has facts
description ap "Inhibitory fast variable (per mode)."
has Db Xref ap G O 0060080 ep
notation ap "alpha"
lhs ap "Derivative(alpha, t)"
rhs ap "beta - e_i*alpha**3 + f_i*alpha**2 - gamma + K_21*(C_ik*xi - alpha) + II_i + c_pop0 + local_coupling*xi"

alpha (TsodyksMarkram parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/TsodyksMarkram/parameters/alpha

belongs to
Parameter c
has facts
description ap "Softplus nonlinearity steepness (smoothed threshold gain)"
default Value ap "1.5"^^double
notation ap "alpha"

alpha_e (WilsonCowan parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/WilsonCowan/parameters/alpha_e

Balance parameter between excitatory and inhibitory masses (Sanz-Leon et al., 2015).
belongs to
Parameter c
has facts
description ap "Balance parameter between excitatory and inhibitory masses (Sanz-Leon et al"
default Value ap "1.0"^^double
definition ap "Balance parameter between excitatory and inhibitory masses (Sanz-Leon et al., 2015)."
notation ap "alpha_e"

alpha_i (WilsonCowan parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/WilsonCowan/parameters/alpha_i

Balance parameter between excitatory and inhibitory masses (Sanz-Leon et al., 2015).
belongs to
Parameter c
has facts
description ap "Balance parameter between excitatory and inhibitory masses (Sanz-Leon et al"
default Value ap "1.0"^^double
definition ap "Balance parameter between excitatory and inhibitory masses (Sanz-Leon et al., 2015)."
notation ap "alpha_i"

alpha_rs (EpileptorRestingState parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/EpileptorRestingState/parameters/alpha_rs

Constant parameter to scale the rate of feedback from the slow variable y_rs to the fast variable x_rs.
belongs to
Parameter c
has facts
description ap "Constant parameter to scale the rate of feedback from the slow variable y_rs to the fast variable x_rs"
default Value ap "1.0"^^double
definition ap "Constant parameter to scale the rate of feedback from the slow variable y_rs to the fast variable x_rs."
notation ap "alpha_rs"

Arborni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/Arbor

belongs to
Software package c
has facts
description ap "A high-performance library for computational neuroscience simulation with native support for morphologically detailed neuron models on modern hardware including GPUs and many-core CPUs."
license ap "BSD-2-Clause"
code Repository ap "https://github.com/arbor-sim/arbor"
identifier ap "10.5281/zenodo.1459679"
url ap "https://arbor-sim.org"

Arnold1968ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Arnold1968

belongs to
Book c
has facts
issued ap "1968"
title ap "Ergodic Problems of Classical Mechanics"
author ap "Arnol'd, V. I."
author ap "Avez, A."
publisher ap "W. A. Benjamin"

Arnold1968ani back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Arnold1968a

belongs to
Book c
has facts
issued ap "1968"
title ap "Ergodic Problems of Classical Mechanics"
author ap "Arnol'd, V. I."
author ap "Avez, A."
publisher ap "W. A. Benjamin"

AUTO-07pni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/AUTO-07p

belongs to
Software package c
has facts
description ap "A software package for continuation and bifurcation problems in ordinary differential equations. The standard tool for numerical continuation in dynamical systems since 1980."
license ap "BSD-2-Clause"
code Repository ap "https://github.com/auto-07p/auto-07p"
identifier ap "10.1007/978-1-4614-6141-2_3"
url ap "https://github.com/auto-07p/auto-07p"

Automatic differentiationni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Autodiff

belongs to
Backend capability c

b (Epileptor2D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor2D/parameters/b

Coefficient of the squared term in the first state-variable x_E2D via the function f_E2D, in Epileptor2D (Proix et al.,2014).
belongs to
Parameter c
has facts
description ap "Coefficient of the squared term in the first state-variable x_E2D via the function f_E2D, in Epileptor2D (Proix et al"
default Value ap "3.0"^^double
definition ap "Coefficient of the squared term in the first state-variable x_E2D via the function f_E2D, in Epileptor2D (Proix et al.,2014)."
notation ap "b"

b (Epileptor5D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor5D/parameters/b

Coefficient of the squared term in the first state variabel
belongs to
Parameter c
has facts
description ap "Coefficient of the squared term in the first state variabel"
default Value ap "3.0"^^double
definition ap "Coefficient of the squared term in the first state variabel"
notation ap "b"

b (EpileptorRestingState parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/EpileptorRestingState/parameters/b

Coefficient of the squared term in the first state-variable x1.
belongs to
Parameter c
has facts
description ap "Coefficient of the squared term in the first state-variable x1"
default Value ap "3.0"^^double
definition ap "Coefficient of the squared term in the first state-variable x1."
notation ap "b"

b (FastLinearCoupling parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/coupling_functions/FastLinearCoupling/parameters/b

belongs to
Parameter c
has facts
description ap "Offset/bias added to coupling signal"
default Value ap "0.0"^^double
notation ap "b"

B (GastSchmidtKnosche_SD state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/GastSchmidtKnosche_SD/state_variables/B

belongs to
StateVariable c
has facts
notation ap "B"
lhs ap "Derivative(B, t)"
rhs ap "(-A - 2*B + alpha*r)/tau_A"

B (GastSchmidtKnosche_SF state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/GastSchmidtKnosche_SF/state_variables/B

belongs to
StateVariable c
has facts
notation ap "B"
lhs ap "Derivative(B, t)"
rhs ap "(-A - 2*B + alpha*r)/tau_A"

b (Generic2dOscillator parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Generic2dOscillator/parameters/b

Linear slope of the configurable nullcline
belongs to
Parameter c
has facts
description ap "Linear slope of the configurable nullcline"
default Value ap "-10.0"^^double
has Db Xref ap G O 0098873 ep
has Db Xref ap G O 0099178 ep
definition ap "Linear slope of the configurable nullcline"
notation ap "b"

b (HyperbolicTangent parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/coupling_functions/HyperbolicTangent/parameters/b

belongs to
Parameter c
has facts
description ap "Scaling factor for the variable"
default Value ap "1.0"^^double
notation ap "b"

B (JansenRit parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/JansenRit/parameters/B

Maximum amplitude of IPSP [mV]. Also called average synaptic gain.
belongs to
Parameter c
has facts
description ap "Maximum amplitude of IPSP [mV]"
default Value ap "22.0"^^double
has Db Xref ap G O 0060080 ep
definition ap "Maximum amplitude of IPSP [mV]. Also called average synaptic gain."
notation ap "B"
unit (slot) dp "mV"

b (JansenRit parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/JansenRit/parameters/b

Rate constant of the inhibitory post-synaptic potential (IPSP). It is interpreted as being the lumped representation of the sum of the reciprocal of the time constant of passive membrane and all other spatially distributed delays, including temporal dispersion in the afferent tract, synaptic diffusion, and resistive-capacitive delay in the dendritic network (Freeman 1975).
belongs to
Parameter c
has facts
description ap "Rate constant of the inhibitory post-synaptic potential (IPSP)"
default Value ap "0.05"^^double
has Db Xref ap G O 0060080 ep
definition ap "Rate constant of the inhibitory post-synaptic potential (IPSP). It is interpreted as being the lumped representation of the sum of the reciprocal of the time constant of passive membrane and all other spatially distributed delays, including temporal dispersion in the afferent tract, synaptic diffusion, and resistive-capacitive delay in the dendritic network (Freeman 1975)."
notation ap "b"
unit (slot) dp "per_ms"

B (JansenRit1995 parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/JansenRit1995/parameters/B

belongs to
Parameter c
has facts
description ap "Maximum amplitude of inhibitory PSP (IPSP)"
default Value ap "22"^^integer
notation ap "B"
unit (slot) dp "mV"

b (JansenRit1995 parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/JansenRit1995/parameters/b

belongs to
Parameter c
has facts
description ap "Reciprocal of IPSP time constant"
default Value ap "50"^^integer
notation ap "b"
unit (slot) dp "per_s"

b (LarterBreakspear parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/LarterBreakspear/parameters/b

Time constant scaling factor.
belongs to
Parameter c
has facts
description ap "Time constant scaling factor"
default Value ap "0.1"^^double
definition ap "Time constant scaling factor."
notation ap "b"

b (Linear parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/coupling_functions/Linear/parameters/b

belongs to
Parameter c
has facts
description ap "Shifts the base of the connection strength while maintaining the absolute difference between different values."
default Value ap "0.0"^^double
notation ap "b"

B (ModelJansen1995 parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ModelJansen1995/parameters/B

belongs to
Parameter c
has facts
default Value ap "22"^^integer
notation ap "B"
unit (slot) dp "mV"

b (ModelJansen1995 parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ModelJansen1995/parameters/b

belongs to
Parameter c
has facts
default Value ap "0.05"^^double
notation ap "b"
unit (slot) dp "per_ms"

b (ReducedWongWang parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWang/parameters/b

Shift parameter of the sigmoid input-output function H_RWW (Deco et al., 2013). Note: ------ In the original publication, the parameter 'b' is set in Hz. In TVB, the parameter has been converted in kHz for setting the system in millisecond.
belongs to
Parameter c
has facts
description ap "Shift parameter of the sigmoid input-output function H_RWW (Deco et al"
default Value ap "0.108"^^double
definition ap "Shift parameter of the sigmoid input-output function H_RWW (Deco et al., 2013). Note: ------ In the original publication, the parameter 'b' is set in Hz. In TVB, the parameter has been converted in kHz for setting the system in millisecond."
notation ap "b"
unit (slot) dp "kHz"

b (ReducedWongWangTvboptim parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWangTvboptim/parameters/b

Input shift parameter of the sigmoid transfer function H(x).
belongs to
Parameter c
has facts
description ap "Input shift parameter"
default Value ap "0.108"^^double
definition ap "Input shift parameter of the sigmoid transfer function H(x)."
notation ap "b"
unit (slot) dp "kHz"

b (StefanescuJirsa2D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa2D/parameters/b

FitzHugh-Nagumo recovery decay rate.
belongs to
Parameter c
has facts
default Value ap "0.9"^^double
definition ap "FitzHugh-Nagumo recovery decay rate."
notation ap "b"

b (StefanescuJirsa3D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa3D/parameters/b

Hindmarsh-Rose dimensionless coefficient b.
belongs to
Parameter c
has facts
default Value ap "3.0"^^double
definition ap "Hindmarsh-Rose dimensionless coefficient b."
notation ap "b"

b_e (ReducedWongWangExcInh parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWangExcInh/parameters/b_e

Shift parameter of the sigmoid function HE_RWW_EI of the excitatory population (Deco et al., 2014).
belongs to
Parameter c
has facts
description ap "Shift parameter of the sigmoid function HE_RWW_EI of the excitatory population (Deco et al"
default Value ap "125.0"^^double
definition ap "Shift parameter of the sigmoid function HE_RWW_EI of the excitatory population (Deco et al., 2014)."
notation ap "b_e"
unit (slot) dp "Hz"

b_e (WilsonCowan parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/WilsonCowan/parameters/b_e

Position of the maximum slope of the excitatory response function S_e_WC (Sanz-Leon et al., 2015).
belongs to
Parameter c
has facts
description ap "Position of the maximum slope of the excitatory response function S_e_WC (Sanz-Leon et al"
default Value ap "2.8"^^double
has Db Xref ap G O 0060079 ep
definition ap "Position of the maximum slope of the excitatory response function S_e_WC (Sanz-Leon et al., 2015)."
notation ap "b_e"

b_e (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/b_e

Excitatory adaptation current increment [pA]
belongs to
Parameter c
has facts
description ap "Excitatory adaptation current increment [pA]"
default Value ap "60.0"^^double
has Db Xref ap G O 0060079 ep
definition ap "Excitatory adaptation current increment [pA]"
notation ap "b_e"

b_i (ReducedWongWangExcInh parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWangExcInh/parameters/b_i

Shift parameter of the sigmoid function HI_RWW_EI of the inhibitory population (Deco et al., 2014).
belongs to
Parameter c
has facts
description ap "Shift parameter of the sigmoid function HI_RWW_EI of the inhibitory population (Deco et al"
default Value ap "177.0"^^double
definition ap "Shift parameter of the sigmoid function HI_RWW_EI of the inhibitory population (Deco et al., 2014)."
notation ap "b_i"
unit (slot) dp "Hz"

b_i (StefanescuJirsa3D derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa3D/derived_variables/b_i

belongs to
DerivedVariable c
has facts
description ap "Per-mode quadratic coefficient for the excitatory xi dynamics."
notation ap "b_i"
lhs ap "b_i"
rhs ap "b"

b_i (WilsonCowan parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/WilsonCowan/parameters/b_i

Position of the maximum slope of a sigmoid function [in threshold units]
belongs to
Parameter c
has facts
description ap "Position of the maximum slope of a sigmoid function [in threshold units]"
default Value ap "4.0"^^double
has Db Xref ap G O 0060080 ep
definition ap "Position of the maximum slope of a sigmoid function [in threshold units]"
notation ap "b_i"

b_i (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/b_i

Inhibitory adaptation current increment [pA]
belongs to
Parameter c
has facts
description ap "Inhibitory adaptation current increment [pA]"
default Value ap "0.0"^^double
has Db Xref ap G O 0060080 ep
definition ap "Inhibitory adaptation current increment [pA]"
notation ap "b_i"

B_ik (StefanescuJirsa3D derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa3D/derived_variables/B_ik

belongs to
DerivedVariable c
has facts
description ap "Inhibitory-to-excitatory mode-coupling matrix."
has Db Xref ap G O 0060080 ep
notation ap "B_ik"
lhs ap "B_ik"
rhs ap "0.5"

b_rs (EpileptorRestingState parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/EpileptorRestingState/parameters/b_rs

Linear coefficient of the state-variable y_rs.
belongs to
Parameter c
has facts
description ap "Linear coefficient of the state-variable y_rs"
default Value ap "-10.0"^^double
definition ap "Linear coefficient of the state-variable y_rs."
notation ap "b_rs"

Bandyopadhyay2021ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Bandyopadhyay2021

belongs to
Scholarly article c
has facts
issued ap "2021"
title ap "K Ion Exchange model reference"
author ap "Bandyopadhyay, S."
author ap "others"
is Part Of ap "Preprint"

Baran1998ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Baran1998

belongs to
Scholarly article c
has facts
issued ap "1998"
title ap "Chaotic Dynamics in a Quartic Nuclear Collective Hamiltonian"
author ap "Baran, V."
author ap "Raduta, A. A."
is Part Of ap "International Journal of Modern Physics E"
pagination ap "527--551"
volume Number ap "7"

bb (Epileptor5D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor5D/parameters/bb

Linear coefficient of lowpass excitatory coupling in fourth state variable
belongs to
Parameter c
has facts
description ap "Linear coefficient of lowpass excitatory coupling in fourth state variable"
default Value ap "2.0"^^double
definition ap "Linear coefficient of lowpass excitatory coupling in fourth state variable"
notation ap "bb"

bb (EpileptorRestingState parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/EpileptorRestingState/parameters/bb

Linear coefficient of lowpass excitatory coupling in the fourth state-variable x2.
belongs to
Parameter c
has facts
description ap "Linear coefficient of lowpass excitatory coupling in the fourth state-variable x2"
default Value ap "2.0"^^double
definition ap "Linear coefficient of lowpass excitatory coupling in the fourth state-variable x2."
notation ap "bb"

beta (Generic2dOscillator parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Generic2dOscillator/parameters/beta

Constant parameter to scale the rate of feedback from the slow variable to itself
belongs to
Parameter c
has facts
description ap "Constant parameter to scale the rate of feedback from the slow variable to itself"
default Value ap "1.0"^^double
definition ap "Constant parameter to scale the rate of feedback from the slow variable to itself"
notation ap "beta"

beta (KIonEx derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/derived_variables/beta

belongs to
DerivedVariable c
has facts
notation ap "beta"
lhs ap "beta"
rhs ap "w_i/w_o"

beta (StefanescuJirsa2D state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa2D/state_variables/beta

belongs to
StateVariable c
has facts
description ap "Inhibitory slow recovery variable (per mode)."
has Db Xref ap G O 0060080 ep
notation ap "beta"
lhs ap "Derivative(beta, t)"
rhs ap "(alpha - b*beta + n_i)/tau"

beta (StefanescuJirsa3D state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa3D/state_variables/beta

belongs to
StateVariable c
has facts
description ap "Inhibitory recovery variable (per mode)."
has Db Xref ap G O 0042391 ep
notation ap "beta"
lhs ap "Derivative(beta, t)"
rhs ap "h_i - p_i*alpha**2 - beta"

beta_rs (EpileptorRestingState parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/EpileptorRestingState/parameters/beta_rs

Constant parameter to scale the rate of feedback from the slow variable y_rs to itself.
belongs to
Parameter c
has facts
description ap "Constant parameter to scale the rate of feedback from the slow variable y_rs to itself"
default Value ap "1.0"^^double
definition ap "Constant parameter to scale the rate of feedback from the slow variable y_rs to itself."
notation ap "beta_rs"

Bifurcation analysisni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/BifurcationAnalysis

Detection and classification of bifurcations along a continuation branch.
belongs to
Simulation task c

BifurcationKit.jlni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/BifurcationKit

belongs to
Backend c
has facts
provides capability op Continuation solver ni
provides capability op Julia JIT ni
supports task op Bifurcation analysis ni
supports task op Numerical continuation ni

BifurcationKit.jlni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/BifurcationKit.jl

belongs to
Software package c
has facts
description ap "A Julia package for bifurcation analysis of large-dimensional equations. Supports continuation of equilibria, periodic orbits, and detection of bifurcation points for ODE and PDE systems."
license ap "MIT"
code Repository ap "https://github.com/bifurcationkit/BifurcationKit.jl"
identifier ap "10.21105/joss.06316"
url ap "https://bifurcationkit.github.io/BifurcationKitDocs.jl/stable/"

Bik (StefanescuJirsa2D derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa2D/derived_variables/Bik

belongs to
DerivedVariable c
has facts
description ap "Inhibitory-to-excitatory mode-coupling matrix."
has Db Xref ap G O 0060079 ep
notation ap "Bik"
lhs ap "Bik"
rhs ap "0.5"

BluePyOptni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/BluePyOpt

belongs to
Software package c
has facts
description ap "Blue Brain Python Optimisation Library — a framework for data-driven model parameter optimisation using multi-objective evolutionary algorithms on NEURON models."
license ap "LGPL-3.0-only"
code Repository ap "https://github.com/BlueBrain/BluePyOpt"
identifier ap "10.3389/fninf.2016.00017"
url ap "https://bluepyopt.readthedocs.io"

Bo-Cheng2008ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Bo-Cheng2008

belongs to
Scholarly article c
has facts
issued ap "2008"
title ap "A hyperchaotic attractor coined from chaotic L"u system"
author ap "Bo-Cheng, B."
author ap "Zhong, L."
is Part Of ap "Chinese Physics Letters"
issue Number ap "7"
pagination ap "2396"
volume Number ap "25"

BoCheng2008ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/BoCheng2008

belongs to
Scholarly article c
has facts
issued ap "2008"
title ap "A hyperchaotic attractor coined from chaotic L"u system"
author ap "Bo-Cheng, B."
author ap "Zhong, L."
identifier ap "10.1088/0256-307x/25/7/018"
is Part Of ap "Chinese Physics Letters"
issue Number ap "7"
pagination ap "2396"
volume Number ap "25"

BOLD_DoubleExponentialni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/observation_models/bold_double_exponential

belongs to
Observation c
has facts
description ap "BOLD fMRI observation model using a Double Exponential hemodynamic response function."
has Parameter ap TR (bold_double_exponential parameter) ni

BOLD_Gammani back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/observation_models/bold_gamma

belongs to
Observation c
has facts
description ap "BOLD fMRI observation model using a Gamma-shaped hemodynamic response function. Provides a simpler, unimodal HRF shape."
has Parameter ap TR (bold_gamma parameter) ni

BOLD_MixtureOfGammasni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/observation_models/bold_mixture_of_gammas

belongs to
Observation c
has facts
description ap "BOLD fMRI observation model using the canonical double-gamma hemodynamic response function (Glover 1999). Standard HRF used in most fMRI analysis packages (SPM, FSL, AFNI)."
has Parameter ap TR (bold_mixture_of_gammas parameter) ni

BOLD_RegionROIni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/observation_models/bold_region_roi

belongs to
Observation c
has facts
description ap "BOLD fMRI observation model that computes the hemodynamic response at each source location and spatially averages within brain regions using a parcellation mapping. Produces per-region BOLD signals suitable for comparison with parcellated empirical data."
has Parameter ap hrf_length (bold_region_roi parameter) ni

BOLD_TVBni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/observation_models/bold_tvb

belongs to
Observation c
has facts
description ap "BOLD fMRI observation model using the Balloon-Windkessel hemodynamic model. Transforms neural activity into simulated BOLD signal via convolution with a hemodynamic response function (First Order Volterra kernel), followed by a nonlinear Volterra transformation."
has Parameter ap TR (bold_tvb parameter) ni

BrainBrowserni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/BrainBrowser

belongs to
Software package c
has facts
description ap "A set of JavaScript visualization tools for rendering brain surfaces, volumes, and connectivity data in the browser using WebGL."
license ap "MIT"
code Repository ap "https://github.com/aces/brainbrowser"
url ap "https://brainbrowser.cbrain.mcgill.ca"

BrainPyni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/BrainPy

belongs to
Software package c
has facts
description ap "A flexible, efficient, and extensible framework for computational neuroscience and brain-inspired computation built on JAX. Supports spiking, rate-based, and mean-field models at all scales."
license ap "Apache-2.0"
code Repository ap "https://github.com/brainpy/BrainPy"
identifier ap "10.7554/eLife.86365"
url ap "https://brainpy.readthedocs.io"

BrainSimIIni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/BrainSimII

belongs to
Software package c
has facts
description ap "A neural simulator exploring AGI-inspired approaches to brain simulation, with a focus on large-scale spiking neuron models and real-time interaction."
license ap "MIT"
code Repository ap "https://github.com/FutureAIGuru/BrainSimII"

Brainstormni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/Brainstorm

belongs to
Software package c
has facts
description ap "A collaborative, open-source application for MEG/EEG/sEEG/ECoG/fNIRS data analysis, visualization, and source localization."
license ap "GPL-3.0-only"
code Repository ap "https://github.com/brainstorm-tools/brainstorm3"
identifier ap "10.1155/2011/879716"
url ap "https://neuroimage.usc.edu/brainstorm/"

Brian2ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/Brian2

belongs to
Software package c
has facts
description ap "A simulator for spiking neural networks. Equations are specified in standard mathematical notation, and Brian2 automatically generates efficient C++ code for numerical integration."
license ap "CeCILL-2.1"
code Repository ap "https://github.com/brian-team/brian2"
identifier ap "10.7554/eLife.47314"
url ap "https://brian2.readthedocs.io"

BSBni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/BSB

belongs to
Software package c
has facts
description ap "Brain Scaffold Builder — a framework for reconstructing and simulating data-driven brain tissue models using morphological and connectivity scaffolds."
license ap "Apache-2.0"
code Repository ap "https://github.com/dbbs-lab/bsb-core"
url ap "https://bsb.readthedocs.io"

Built-in model libraryni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/BuiltinModelLibrary

belongs to
Backend capability c

Byrne2020ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Byrne2020

belongs to
Scholarly article c
has facts
issued ap "2020"
title ap "Next generation neural mass models"
author ap "Byrne, A."
author ap "Coombes, S."
is Part Of ap "Journal of Mathematical Neuroscience"

C (CakanObermayer parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/CakanObermayer/parameters/C

Membrane capacitance of a single AdEx neuron.
belongs to
Parameter c
has facts
default Value ap "200.0"^^double
has Db Xref ap G O 0030322 ep
has Db Xref ap G O 0042391 ep
has Db Xref ap G O 0098696 ep
definition ap "Membrane capacitance of a single AdEx neuron."
notation ap "C"
unit (slot) dp "pF"

c (Epileptor2D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor2D/parameters/c

Additive coefficient for the second state-variable x_{2}, called :math:`y_{0}` in Jirsa paper.
belongs to
Parameter c
has facts
description ap "Additive coefficient for the second state-variable x_{2}, called :math:`y_{0}` in Jirsa paper"
default Value ap "1.0"^^double
definition ap "Additive coefficient for the second state-variable x_{2}, called :math:`y_{0}` in Jirsa paper."
notation ap "c"

c (Epileptor5D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor5D/parameters/c

Additive coefficient for the second state variable, called :math:`y_{0}` in Jirsa paper
belongs to
Parameter c
has facts
description ap "Additive coefficient for the second state variable, called :math:`y_{0}` in Jirsa paper"
default Value ap "1.0"^^double
definition ap "Additive coefficient for the second state variable, called :math:`y_{0}` in Jirsa paper"
notation ap "c"

c (EpileptorRestingState parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/EpileptorRestingState/parameters/c

Additive coefficient for the second state-variable y1, called :math:'y_{0}' in Jirsa et al. (2014).
belongs to
Parameter c
has facts
description ap "Additive coefficient for the second state-variable y1, called :math:'y_{0}' in Jirsa et al"
default Value ap "1.0"^^double
definition ap "Additive coefficient for the second state-variable y1, called :math:'y_{0}' in Jirsa et al. (2014)."
notation ap "c"

c (Generic2dOscillator parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Generic2dOscillator/parameters/c

Parabolic term of the configurable nullcline
belongs to
Parameter c
has facts
description ap "Parabolic term of the configurable nullcline"
default Value ap "0.0"^^double
definition ap "Parabolic term of the configurable nullcline"
notation ap "c"

C (JansenRit1995 parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/JansenRit1995/parameters/C

belongs to
Parameter c
has facts
description ap "Lumped connectivity constant (C = C1)"
default Value ap "135"^^integer
notation ap "C"

C (LarterBreakspear parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/LarterBreakspear/parameters/C

Coupling scaling factor. Strength of excitatory coupling and balance between internal and local/global coupling strength.
belongs to
Parameter c
has facts
description ap "Coupling scaling factor"
default Value ap "0.1"^^double
has Db Xref ap G O 0060079 ep
definition ap "Coupling scaling factor. Strength of excitatory coupling and balance between internal and local/global coupling strength."
notation ap "C"

C (ModelJansen1995 parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ModelJansen1995/parameters/C

belongs to
Parameter c
has facts
default Value ap "135"^^integer
notation ap "C"

c (StefanescuJirsa3D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa3D/parameters/c

Hindmarsh-Rose dimensionless coefficient c.
belongs to
Parameter c
has facts
default Value ap "1.0"^^double
definition ap "Hindmarsh-Rose dimensionless coefficient c."
notation ap "c"

c_e (WilsonCowan parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/WilsonCowan/parameters/c_e

The amplitude parameter for the excitatory response function
belongs to
Parameter c
has facts
description ap "The amplitude parameter for the excitatory response function"
default Value ap "1.0"^^double
has Db Xref ap G O 0060079 ep
definition ap "The amplitude parameter for the excitatory response function"
notation ap "c_e"

c_ee (WilsonCowan parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/WilsonCowan/parameters/c_ee

Excitatory to excitatory coupling coefficient
belongs to
Parameter c
has facts
description ap "Excitatory to excitatory coupling coefficient"
default Value ap "12.0"^^double
has Db Xref ap G O 0060079 ep
definition ap "Excitatory to excitatory coupling coefficient"
notation ap "c_ee"

c_ei (WilsonCowan parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/WilsonCowan/parameters/c_ei

Inhibitory to excitatory coupling coefficient
belongs to
Parameter c
has facts
description ap "Inhibitory to excitatory coupling coefficient"
default Value ap "4.0"^^double
has Db Xref ap G O 0060080 ep
definition ap "Inhibitory to excitatory coupling coefficient"
notation ap "c_ei"

c_i (StefanescuJirsa3D derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa3D/derived_variables/c_i

belongs to
DerivedVariable c
has facts
description ap "Per-mode constant for the excitatory eta dynamics."
notation ap "c_i"
lhs ap "c_i"
rhs ap "c"

c_i (WilsonCowan parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/WilsonCowan/parameters/c_i

The amplitude parameter for the excitatory response function S_i_WC (Sanz-Leon et al., 2015).
belongs to
Parameter c
has facts
description ap "The amplitude parameter for the excitatory response function S_i_WC (Sanz-Leon et al"
default Value ap "1.0"^^double
has Db Xref ap G O 0098815 ep
definition ap "The amplitude parameter for the excitatory response function S_i_WC (Sanz-Leon et al., 2015)."
notation ap "c_i"

c_ie (WilsonCowan parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/WilsonCowan/parameters/c_ie

Excitatory to inhibitory coupling coefficient (Sanz-Leon et al., 2015)
belongs to
Parameter c
has facts
description ap "Excitatory to inhibitory coupling coefficient (Sanz-Leon et al"
default Value ap "13.0"^^double
has Db Xref ap G O 0060079 ep
definition ap "Excitatory to inhibitory coupling coefficient (Sanz-Leon et al., 2015)"
notation ap "c_ie"

c_ii (WilsonCowan parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/WilsonCowan/parameters/c_ii

Inhibitory to inhibitory coupling coefficient (Sanz-Leon et al., 2015)
belongs to
Parameter c
has facts
description ap "Inhibitory to inhibitory coupling coefficient (Sanz-Leon et al"
default Value ap "11.0"^^double
has Db Xref ap G O 0060080 ep
definition ap "Inhibitory to inhibitory coupling coefficient (Sanz-Leon et al., 2015)"
notation ap "c_ii"

C_ik (StefanescuJirsa3D derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa3D/derived_variables/C_ik

belongs to
DerivedVariable c
has facts
description ap "Excitatory-to-inhibitory mode-coupling matrix."
has Db Xref ap G O 0060079 ep
notation ap "C_ik"
lhs ap "C_ik"
rhs ap "0.5"

C_m (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/C_m

membrane capacitance [pF]
belongs to
Parameter c
has facts
description ap "membrane capacitance [pF]"
default Value ap "200.0"^^double
has Db Xref ap G O 0042391 ep
definition ap "membrane capacitance [pF]"
notation ap "C_m"

c_minus (KIonEx parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/parameters/c_minus

x-coordinate left parabola
belongs to
Parameter c
has facts
description ap "x-coordinate left parabola"
default Value ap "-40.0"^^double
definition ap "x-coordinate left parabola"
notation ap "c_minus"

c_plus (KIonEx parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/parameters/c_plus

x-coordinate right parabola
belongs to
Parameter c
has facts
description ap "x-coordinate right parabola"
default Value ap "-20.0"^^double
definition ap "x-coordinate right parabola"
notation ap "c_plus"

Cabral2011ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Cabral2011

belongs to
Scholarly article c
has facts
issued ap "2011"
title ap "Role of local network oscillations in resting-state functional connectivity"
author ap "Cabral, Joana"
author ap "others"
is Part Of ap "NeuroImage"

Cai2007ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Cai2007

belongs to
Scholarly article c
has facts
issued ap "2007"
title ap "A new finance chaotic attractor"
author ap "Cai, G."
author ap "Huang, J."
is Part Of ap "International Journal of Nonlinear Science"
issue Number ap "3"
pagination ap "213--220"
volume Number ap "3"

Cakanni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Cakan

belongs to
Creative work c
has facts
title ap "Reference for network mean-field neural mass model"
author ap "Cakan, C."
author ap "Obermayer, K."

CakanObermayerni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/CakanObermayer

belongs to
Dynamics c
has facts
exhibits bifurcation op ""
exhibits regime op Bistable ni
exhibits regime op Oscillatory ni
exhibits regime op Quiescent ni
has attractor op Fixed point ni
has attractor op Limit cycle ni
has model feature op Excitatory/inhibitory subpopulations ni
has stochasticity character op Deterministic ni
models anatomical region op U B E R O N 0000956 ni
models cell type op C L 0000099 ni
models cell type op C L 0000598 ni
models neurotransmitter system op G O 0007214 ni
models neurotransmitter system op G O 0035249 ni
has timescale separation dp "true"^^boolean
phase-space dimension dp "6"^^integer
description ap "Adaptive linear-nonlinear (aLN) mean-field model of a network of adaptive exponential integrate-and-fire (AdEx) neurons, comprising one excitatory (E) and one inhibitory (I) population. Originally developed by Augustin, Ladenbauer, Liebe & Obermayer (2017) and used as the whole-brain mean-field in neurolib by Cakan, Jajcay & Obermayer (2021). The legacy tvb-o.owl ontology referred to this model by the short name ``Cortical`` (suffix ``_CO``); ``iri`` is preserved for backward ontology mapping while ``name`` reflects the canonical attribution. Defaults are taken verbatim from ``neurolib/models/aln/loadDefaultParams.py``. Note that the full aLN dynamics require a precomputed transfer-function lookup table (``aln-precalc/quantities_cascade.h5``) that maps the filtered mean input ``mu`` and the membrane-potential standard deviation ``sigma`` to a steady-state firing rate. The state-variable equations below are the structural filtered-mean-input scaffold; the nonlinear transfer function ``r_E = Phi(mu_E, sigma_E)`` cannot be expressed in YAML and is therefore approximated as a sigmoid for backend code generation."
pref Label ap "Cakan-Obermayer ALN"@en
has Derived Variable ap r_E (CakanObermayer derived variable) ni
has Derived Variable ap r_I (CakanObermayer derived variable) ni
has Parameter ap C (CakanObermayer parameter) ni
has Parameter ap E_A (CakanObermayer parameter) ni
has Parameter ap E_L (CakanObermayer parameter) ni
has Parameter ap I_A (CakanObermayer parameter) ni
has Parameter ap J_EE (CakanObermayer parameter) ni
has Parameter ap J_EI (CakanObermayer parameter) ni
has Parameter ap J_IE (CakanObermayer parameter) ni
has Parameter ap J_II (CakanObermayer parameter) ni
has Parameter ap k_phi (CakanObermayer parameter) ni
has Parameter ap mu_E (CakanObermayer parameter) ni
has Parameter ap mu_I (CakanObermayer parameter) ni
has Parameter ap mu_th (CakanObermayer parameter) ni
has Parameter ap r_max (CakanObermayer parameter) ni
has Parameter ap s_EE (CakanObermayer parameter) ni
has Parameter ap s_EI (CakanObermayer parameter) ni
has Parameter ap s_IE (CakanObermayer parameter) ni
has Parameter ap s_II (CakanObermayer parameter) ni
has Parameter ap tau_A (CakanObermayer parameter) ni
has Parameter ap tau_se (CakanObermayer parameter) ni
has Parameter ap tau_si (CakanObermayer parameter) ni
has State Variable ap I_A_var (CakanObermayer state variable) ni
has State Variable ap mu_se (CakanObermayer state variable) ni
has State Variable ap mu_si (CakanObermayer state variable) ni
model_type (slot) ap "neural_mass"

Cao2013ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Cao2013

belongs to
Scholarly article c
has facts
issued ap "2013"
title ap "Bursting types and stable domains of Rulkov neuron network with mean field coupling"
author ap "Cao, H."
author ap "Wu, Y."
is Part Of ap "International Journal of Bifurcation and Chaos"
pagination ap "1330041"
volume Number ap "23"

CARLsimni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/CARLsim

belongs to
Software package c
has facts
description ap "An efficient, easy-to-use, GPU-accelerated library for simulating large-scale spiking neural network models with conductance-based synapses, STDP, and neuromodulation."
license ap "MIT"
code Repository ap "https://github.com/UCI-CARL/CARLsim6"
url ap "https://uci-carl.github.io/CARLsim6/"

Chen2006ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Chen2006

belongs to
Scholarly article c
has facts
issued ap "2006"
title ap "Generating hyperchaotic L"u attractor via state feedback control"
author ap "Chen, A."
author ap "L"u, J."
author ap "Lu, J."
author ap "Yu, S."
is Part Of ap "Physica A: Statistical Mechanics and its Applications"
pagination ap "103--110"
volume Number ap "364"

Chirikov1969ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Chirikov1969

belongs to
Report c
has facts
issued ap "1969"
title ap "Research concerning the theory of nonlinear resonance"
author ap "Chirikov, Boris V."
issue Number ap "Preprint 267"

Chn (KIonEx parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/parameters/Chn

belongs to
Parameter c
has facts
default Value ap "0.4"^^double
notation ap "Chn"

Chua1992ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Chua1992

belongs to
Scholarly article c
has facts
issued ap "1992"
title ap "The Genesis of Chua's Circuit"
author ap "Chua, Leon O."
is Part Of ap "Archiv f"ur Elektronik und "Ubertragungstechnik"
pagination ap "250--257"
volume Number ap "46"

Chua2007ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Chua2007

belongs to
Scholarly article c
has facts
issued ap "2007"
title ap "Chua circuit"
author ap "Chua, Leon O."
is Part Of ap "Scholarpedia"
issue Number ap "10"
pagination ap "1488"
url ap "http://www.scholarpedia.org/article/Chua_circuit"
volume Number ap "2"

Cik (StefanescuJirsa2D derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa2D/derived_variables/Cik

belongs to
DerivedVariable c
has facts
description ap "Excitatory-to-inhibitory mode-coupling matrix."
has Db Xref ap G O 0060080 ep
notation ap "Cik"
lhs ap "Cik"
rhs ap "0.5"

Ckp (KIonEx parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/parameters/Ckp

belongs to
Parameter c
has facts
default Value ap "5.5"^^double
notation ap "Ckp"
unit (slot) dp "mol_per_m3"

Cl_i0 (KIonEx parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/parameters/Cl_i0

initial concentration of intracellular Cl
belongs to
Parameter c
has facts
description ap "initial concentration of intracellular Cl"
default Value ap "5.0"^^double
definition ap "initial concentration of intracellular Cl"
notation ap "Cl_i0"
unit (slot) dp "mmol_per_m3"

Cl_o0 (KIonEx parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/parameters/Cl_o0

initial concentration of extracellular Cl
belongs to
Parameter c
has facts
description ap "initial concentration of extracellular Cl"
default Value ap "112.0"^^double
definition ap "initial concentration of extracellular Cl"
notation ap "Cl_o0"
unit (slot) dp "mmol_per_m3"

Cm (KIonEx parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/parameters/Cm

membrane capacitance
belongs to
Parameter c
has facts
description ap "membrane capacitance"
default Value ap "1.0"^^double
has Db Xref ap G O 0042391 ep
definition ap "membrane capacitance"
notation ap "Cm"

cmax (Sigmoidal parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/coupling_functions/Sigmoidal/parameters/cmax

belongs to
Parameter c
has facts
description ap "Maximum of the sigmoid function"
default Value ap "1.0"^^double
notation ap "cmax"

cmax (SigmoidalJansenRit parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/coupling_functions/SigmoidalJansenRit/parameters/cmax

belongs to
Parameter c
has facts
description ap "Maximum of the Sigmoid function"
default Value ap "0.005"^^double
notation ap "cmax"

cmin (Sigmoidal parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/coupling_functions/Sigmoidal/parameters/cmin

belongs to
Parameter c
has facts
description ap "Minimum of sigmoid function"
default Value ap "-1.0"^^double
notation ap "cmin"

cmin (SigmoidalJansenRit parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/coupling_functions/SigmoidalJansenRit/parameters/cmin

belongs to
Parameter c
has facts
description ap "minimum of the Sigmoid function"
default Value ap "0.0"^^double
notation ap "cmin"

Cmna (KIonEx parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/parameters/Cmna

belongs to
Parameter c
has facts
default Value ap "-24.0"^^double
notation ap "Cmna"
unit (slot) dp "mV"

Cnap (KIonEx parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/parameters/Cnap

belongs to
Parameter c
has facts
default Value ap "21.0"^^double
notation ap "Cnap"
unit (slot) dp "mol_per_m3"

Cnk (KIonEx parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/parameters/Cnk

belongs to
Parameter c
has facts
default Value ap "-19.0"^^double
notation ap "Cnk"
unit (slot) dp "mV"

conduction_speed (acq-EEGBrainstorm65_sensors parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/acq-EEGBrainstorm65_sensors/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (acq-MEGBrainstorm276_sensors parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/acq-MEGBrainstorm276_sensors/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (acq-SEEG588_sensors parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/acq-SEEG588_sensors/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (example_3node_network parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/example_3node_network/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (sensors_eeg_standard1005_fsaverage_aparc_projection parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/sensors_eeg_standard1005_fsaverage_aparc_projection/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (SmileyNetwork parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/SmileyNetwork/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-fsaverage_acq-EEGstandard1005_atlas-DesikanKilliany_desc-projection_sensors parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-fsaverage_acq-EEGstandard1005_atlas-DesikanKilliany_desc-projection_sensors/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_scale-1000_desc-SC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_scale-1000_desc-SC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-1000_desc-SC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-1000_desc-SC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-100_desc-SC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-100_desc-SC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-200_desc-SC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-200_desc-SC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-300_desc-SC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-300_desc-SC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-400_desc-SC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-400_desc-SC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-500_desc-SC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-500_desc-SC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-600_desc-SC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-600_desc-SC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-700_desc-SC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-700_desc-SC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-800_desc-SC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-800_desc-SC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-900_desc-SC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-900_desc-SC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-1000_desc-SC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-1000_desc-SC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-100_desc-SC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-100_desc-SC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-200_desc-SC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-200_desc-SC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-300_desc-SC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-300_desc-SC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-400_desc-SC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-400_desc-SC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-500_desc-SC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-500_desc-SC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-600_desc-SC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-600_desc-SC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-700_desc-SC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-700_desc-SC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-800_desc-SC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-800_desc-SC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-900_desc-SC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-900_desc-SC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-Hansen2022_atlas-Schaefer2018_seg-7Networks_scale-100_desc-SCFC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-HCPYA_rec-Hansen2022_atlas-Schaefer2018_seg-7Networks_scale-100_desc-SCFC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-FSLMNI152_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-Schaefer2018_scale-1000_desc-SC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-Schaefer2018_scale-1000_desc-SC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-FSLMNI152_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-Schaefer2018_seg-17Networks_scale-1000_desc-SC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-Schaefer2018_seg-17Networks_scale-1000_desc-SC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-FSLMNI152_cohort-PPMI85_rec-PPMI85_atlas-Schaefer2018_scale-1000_desc-SC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-PPMI85_rec-PPMI85_atlas-Schaefer2018_scale-1000_desc-SC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-FSLMNI152_cohort-PPMI85_rec-PPMI85_atlas-Schaefer2018_seg-17Networks_scale-1000_desc-SC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-PPMI85_rec-PPMI85_atlas-Schaefer2018_seg-17Networks_scale-1000_desc-SC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-MNI152NLin2009bAsym_cohort-HCPYA_rec-dTOR_atlas-HCPMMP1_desc-SC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009bAsym_cohort-HCPYA_rec-dTOR_atlas-HCPMMP1_desc-SC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-MNI152NLin2009bAsym_cohort-HCPYA_rec-dTOR_atlas-HCPMMP1_seg-ordered_desc-SC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009bAsym_cohort-HCPYA_rec-dTOR_atlas-HCPMMP1_seg-ordered_desc-SC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-MNI152NLin2009bAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-HCPMMP1_desc-SC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009bAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-HCPMMP1_desc-SC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-MNI152NLin2009bAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-HCPMMP1_seg-ordered_desc-SC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009bAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-HCPMMP1_seg-ordered_desc-SC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-MNI152NLin2009bAsym_cohort-PPMI85_rec-PPMI85_atlas-HCPMMP1_desc-SC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009bAsym_cohort-PPMI85_rec-PPMI85_atlas-HCPMMP1_desc-SC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-MNI152NLin2009bAsym_cohort-PPMI85_rec-PPMI85_atlas-HCPMMP1_seg-ordered_desc-SC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009bAsym_cohort-PPMI85_rec-PPMI85_atlas-HCPMMP1_seg-ordered_desc-SC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_atlas-Lobar8_desc-surf_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-HCPYA_atlas-Lobar8_desc-surf_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_atlas-Lobar8_hemi-L_desc-surf_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-HCPYA_atlas-Lobar8_hemi-L_desc-surf_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_atlas-Lobar8_hemi-R_desc-surf_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-HCPYA_atlas-Lobar8_hemi-R_desc-surf_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-DesikanKilliany_desc-SC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-DesikanKilliany_desc-SC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Destrieux_desc-SC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Destrieux_desc-SC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-HCPex_desc-SC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-HCPex_desc-SC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Lobar8_desc-SCFC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Lobar8_desc-SCFC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Lobar_desc-SC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Lobar_desc-SC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Lobar_desc-surf_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Lobar_desc-surf_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-virtualdbs_desc-SC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-virtualdbs_desc-SC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Yeo17_desc-SC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Yeo17_desc-SC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-DesikanKilliany_desc-SC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-DesikanKilliany_desc-SC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-Destrieux_desc-SC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-Destrieux_desc-SC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-HOCPA_desc-SC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-HOCPA_desc-SC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-virtualdbs_desc-SC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-virtualdbs_desc-SC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-Yeo17_desc-SC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-Yeo17_desc-SC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-MNI152NLin2009cAsym_cohort-PPMI85_rec-PPMI85_atlas-DesikanKilliany_desc-SC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-PPMI85_rec-PPMI85_atlas-DesikanKilliany_desc-SC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-MNI152NLin2009cAsym_cohort-PPMI85_rec-PPMI85_atlas-Destrieux_desc-SC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-PPMI85_rec-PPMI85_atlas-Destrieux_desc-SC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-MNI152NLin2009cAsym_cohort-PPMI85_rec-PPMI85_atlas-virtualdbs_desc-SC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-PPMI85_rec-PPMI85_atlas-virtualdbs_desc-SC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-MNI152NLin2009cAsym_cohort-PPMI85_rec-PPMI85_atlas-Yeo17_desc-SC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-PPMI85_rec-PPMI85_atlas-Yeo17_desc-SC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-MNI152NLin2009cAsym_rec-avgMatrix_atlas-DesikanKilliany_desc-SCFC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_rec-avgMatrix_atlas-DesikanKilliany_desc-SCFC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conduction_speed (tpl-MNI152NLin2009cAsym_rec-avgMatrix_atlas-Lobar8_desc-SCFC_relmat parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_rec-avgMatrix_atlas-Lobar8_desc-SCFC_relmat/parameters/conduction_speed

belongs to
Parameter c
has facts
default Value ap "3.0"^^double
notation ap "conduction_speed"
unit (slot) dp "mm_per_ms"

conductivity (eeg parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/observation_models/eeg/parameters/conductivity

belongs to
Parameter c
has facts
description ap "Volume conductor conductivity for the single-sphere analytic approximation. Only used when no precomputed gain is available."
default Value ap "1.0"^^double
notation ap "conductivity"
unit (slot) dp "S_per_m"

conductivity (ieeg parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/observation_models/ieeg/parameters/conductivity

belongs to
Parameter c
has facts
description ap "Tissue conductivity for the analytic point-dipole approximation. Only used when no precomputed gain is available."
default Value ap "1.0"^^double
notation ap "conductivity"
unit (slot) dp "S_per_m"

Continuation solverni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ContinuationSolver

belongs to
Backend capability c

CoombesByrneni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/CoombesByrne

belongs to
Dynamics c
has facts
exhibits bifurcation op ""
exhibits regime op Oscillatory ni
exhibits regime op Quiescent ni
has attractor op Fixed point ni
has attractor op Limit cycle ni
has stochasticity character op Deterministic ni
models anatomical region op U B E R O N 0000956 ni
phase-space dimension dp "4"^^integer
description ap "4D model describing the Ott-Antonsen reduction of infinite all-to-all coupled QIF neurons (Theta-neurons). Note: the original equations describe the dynamics of the Kuramoto parameter $Z$. Using the conformal transformation $Z=(1-W^\star)/(1+W^\star)$ and $W= \pi r + i V$, we express the system dynamics in terms of two state variables $r$ and $V$ representing the average firing rate and the average membrane potential of our QIF neurons. The conductance variable and its derivative are $g$ and $q$. "
references ap Byrne2020 ni
pref Label ap "Coombes-Byrne"@en
has Parameter ap Delta (CoombesByrne parameter) ni
has Parameter ap alpha (CoombesByrne parameter) ni
has Parameter ap eta (CoombesByrne parameter) ni
has Parameter ap k (CoombesByrne parameter) ni
has Parameter ap v_syn (CoombesByrne parameter) ni
has State Variable ap V (CoombesByrne state variable) ni
has State Variable ap g (CoombesByrne state variable) ni
has State Variable ap q (CoombesByrne state variable) ni
has State Variable ap r (CoombesByrne state variable) ni
model_type (slot) ap "mean_field"

CoreNEURONni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/CoreNEURON

belongs to
Software package c
has facts
description ap "Optimized compute engine for the NEURON simulator. Provides efficient execution of NEURON models on CPUs and GPUs using NMODL code generation."
license ap "BSD-3-Clause"
code Repository ap "https://github.com/BlueBrain/CoreNeuron"
url ap "https://github.com/BlueBrain/CoreNeuron"

coupled_input (ZetterbergJansen derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZetterbergJansen/derived_variables/coupled_input

belongs to
DerivedVariable c
has facts
notation ap "coupled_input"
lhs ap "coupled_input"
rhs ap "2*e0/(exp(rho_1*(-c_pop0 - local_coupling*v6 + rho_2)) + 1)"

coupling (ReducedWongWangExcInh derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWangExcInh/derived_variables/coupling

belongs to
DerivedVariable c
has facts
notation ap "coupling"
lhs ap "coupling"
rhs ap "G*J_N*(S_e*local_coupling + c_glob)"

CouplingInputni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/CouplingInput

belongs to
SKOS Concept c
is also defined as
class

Courtiol2020ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Courtiol2020

belongs to
Scholarly article c
has facts
issued ap "2020"
title ap "The brain resting state: dynamics and models"
author ap "Courtiol, Julie"
author ap "others"
is Part Of ap "Journal of Neuroscience Methods"

cr (GastSchmidtKnosche_SD parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/GastSchmidtKnosche_SD/parameters/cr

It is the weight on Coupling through variable r.
belongs to
Parameter c
has facts
description ap "It is the weight on Coupling through variable r"
default Value ap "1.0"^^double
definition ap "It is the weight on Coupling through variable r."
notation ap "cr"

cr (GastSchmidtKnosche_SF parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/GastSchmidtKnosche_SF/parameters/cr

It is the weight on Coupling through variable r.
belongs to
Parameter c
has facts
description ap "It is the weight on Coupling through variable r"
default Value ap "1.0"^^double
definition ap "It is the weight on Coupling through variable r."
notation ap "cr"

cr (MontbrioPazoRoxin parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/MontbrioPazoRoxin/parameters/cr

It is the weight on Coupling through variable r.
belongs to
Parameter c
has facts
description ap "It is the weight on Coupling through variable r"
default Value ap "1.0"^^double
definition ap "It is the weight on Coupling through variable r."
notation ap "cr"

cv (GastSchmidtKnosche_SD parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/GastSchmidtKnosche_SD/parameters/cv

It is the weight on Coupling through variable V.
belongs to
Parameter c
has facts
description ap "It is the weight on Coupling through variable V"
default Value ap "0.0"^^double
definition ap "It is the weight on Coupling through variable V."
notation ap "cv"

cv (GastSchmidtKnosche_SF parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/GastSchmidtKnosche_SF/parameters/cv

It is the weight on Coupling through variable V.
belongs to
Parameter c
has facts
description ap "It is the weight on Coupling through variable V"
default Value ap "0.0"^^double
definition ap "It is the weight on Coupling through variable V."
notation ap "cv"

cv (MontbrioPazoRoxin parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/MontbrioPazoRoxin/parameters/cv

It is the weight on Coupling through variable V.
belongs to
Parameter c
has facts
description ap "It is the weight on Coupling through variable V"
default Value ap "0.0"^^double
definition ap "It is the weight on Coupling through variable V."
notation ap "cv"

CxSystem2ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/CxSystem2

belongs to
Software package c
has facts
description ap "A simulation framework for cortical microcircuit models with support for data-driven customization and modular circuit specification. Uses Brian2 as its simulation backend."
license ap "MIT"
code Repository ap "https://github.com/VisualNeuroscience-UH/CxSystem2"
identifier ap "10.1016/j.neucom.2019.11.004"
url ap "https://cxsystem2.readthedocs.io"

d (Epileptor2D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor2D/parameters/d

Coefficient of the squared term in the first state-variable x_E2D via the function f in Epileptor2D (Proix et al.,2014).
belongs to
Parameter c
has facts
description ap "Coefficient of the squared term in the first state-variable x_E2D via the function f in Epileptor2D (Proix et al"
default Value ap "5.0"^^double
definition ap "Coefficient of the squared term in the first state-variable x_E2D via the function f in Epileptor2D (Proix et al.,2014)."
notation ap "d"

d (Epileptor5D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor5D/parameters/d

Coefficient of the squared term in the derivative of the second state-variable y1_E5D in Epileptor5D (Jirsa et al.,2014).
belongs to
Parameter c
has facts
description ap "Coefficient of the squared term in the derivative of the second state-variable y1_E5D in Epileptor5D (Jirsa et al"
default Value ap "5.0"^^double
definition ap "Coefficient of the squared term in the derivative of the second state-variable y1_E5D in Epileptor5D (Jirsa et al.,2014)."
notation ap "d"

d (EpileptorRestingState parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/EpileptorRestingState/parameters/d

Coefficient of the squared term in the second state-variable y1.
belongs to
Parameter c
has facts
description ap "Coefficient of the squared term in the second state-variable y1"
default Value ap "5.0"^^double
definition ap "Coefficient of the squared term in the second state-variable y1."
notation ap "d"

d (Generic2dOscillator parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Generic2dOscillator/parameters/d

Temporal scale factor. Warning: do not use it unless you know what you are doing and know about time tides.
belongs to
Parameter c
has facts
description ap "Temporal scale factor"
default Value ap "0.02"^^double
definition ap "Temporal scale factor. Warning: do not use it unless you know what you are doing and know about time tides."
notation ap "d"

d (ReducedWongWang parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWang/parameters/d

Scaling parameter of the sigmoid input-output function H_RWW (Deco et al., 2013). Note: ------ In the original publication, the parameter 'd' is set in second. In TVB, the parameter has been converted in millisecond for setting the system in millisecond.
belongs to
Parameter c
has facts
description ap "Scaling parameter of the sigmoid input-output function H_RWW (Deco et al"
default Value ap "154.0"^^double
definition ap "Scaling parameter of the sigmoid input-output function H_RWW (Deco et al., 2013). Note: ------ In the original publication, the parameter 'd' is set in second. In TVB, the parameter has been converted in millisecond for setting the system in millisecond."
notation ap "d"
unit (slot) dp "ms"

d (ReducedWongWangTvboptim parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWangTvboptim/parameters/d

Scaling parameter of the sigmoid transfer function H(x).
belongs to
Parameter c
has facts
description ap "Scaling parameter"
default Value ap "154.0"^^double
definition ap "Scaling parameter of the sigmoid transfer function H(x)."
notation ap "d"
unit (slot) dp "ms"

d (StefanescuJirsa3D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa3D/parameters/d

Hindmarsh-Rose dimensionless coefficient d.
belongs to
Parameter c
has facts
default Value ap "5.0"^^double
definition ap "Hindmarsh-Rose dimensionless coefficient d."
notation ap "d"

d_e (ReducedWongWangExcInh parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWangExcInh/parameters/d_e

Scaling parameter of the sigmoid function HE_RWW_EI of the excitatory population (Deco et al., 2014).
belongs to
Parameter c
has facts
description ap "Scaling parameter of the sigmoid function HE_RWW_EI of the excitatory population (Deco et al"
default Value ap "0.16"^^double
definition ap "Scaling parameter of the sigmoid function HE_RWW_EI of the excitatory population (Deco et al., 2014)."
notation ap "d_e"
unit (slot) dp "s"

d_i (ReducedWongWangExcInh parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWangExcInh/parameters/d_i

Scaling parameter of the sigmoid function HI_RWW_EI of the inhibitory population (Deco et al., 2014).
belongs to
Parameter c
has facts
description ap "Scaling parameter of the sigmoid function HI_RWW_EI of the inhibitory population (Deco et al"
default Value ap "0.087"^^double
definition ap "Scaling parameter of the sigmoid function HI_RWW_EI of the inhibitory population (Deco et al., 2014)."
notation ap "d_i"
unit (slot) dp "s"

d_i (StefanescuJirsa3D derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa3D/derived_variables/d_i

belongs to
DerivedVariable c
has facts
description ap "Per-mode quadratic coefficient for the excitatory eta dynamics."
has Db Xref ap G O 0060079 ep
notation ap "d_i"
lhs ap "d_i"
rhs ap "d"

d_rs (EpileptorRestingState parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/EpileptorRestingState/parameters/d_rs

Temporal scaling of the whole third system (x_rs, y_rs).
belongs to
Parameter c
has facts
description ap "Temporal scaling of the whole third system (x_rs, y_rs)"
default Value ap "0.02"^^double
definition ap "Temporal scaling of the whole third system (x_rs, y_rs)."
notation ap "d_rs"

Datseris2019ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Datseris2019

belongs to
Scholarly article c
has facts
issued ap "2019"
title ap "Abrupt Phase-Space Contraction in a Magnetotransport System"
author ap "Datseris, George"
author ap "et al."
identifier ap "10.1088/1367-2630/ab19cc"
is Part Of ap "New Journal of Physics"
issue Number ap "5"
pagination ap "053036"
volume Number ap "21"

DChn (KIonEx parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/parameters/DChn

belongs to
Parameter c
has facts
default Value ap "-8.0"^^double
notation ap "DChn"

DCkp (KIonEx parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/parameters/DCkp

belongs to
Parameter c
has facts
default Value ap "1.0"^^double
notation ap "DCkp"
unit (slot) dp "mol_per_m3"

DCmna (KIonEx parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/parameters/DCmna

belongs to
Parameter c
has facts
default Value ap "12.0"^^double
notation ap "DCmna"
unit (slot) dp "mV"

DCnap (KIonEx parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/parameters/DCnap

belongs to
Parameter c
has facts
default Value ap "2.0"^^double
notation ap "DCnap"
unit (slot) dp "mol_per_m3"

DCnk (KIonEx parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/parameters/DCnk

belongs to
Parameter c
has facts
default Value ap "18.0"^^double
notation ap "DCnk"
unit (slot) dp "mV"

DDE integrationni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/DDEIntegration

Forward integration of a delay differential equation (e.g. long-range axonal delays).
belongs to
Simulation task c

Deco2013ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Deco2013

belongs to
Scholarly article c
has facts
issued ap "2013"
title ap "Resting-State Functional Connectivity Emerges from Structurally and Dynamically Shaped Slow Linear Fluctuations"
author ap "Corbetta, M."
author ap "Deco, G."
author ap "Hagmann, P."
author ap "Mantini, D."
author ap "Ponce-Alvarez, A."
author ap "Romani, G. L."
identifier ap "10.1523/jneurosci.1091-13.2013"
is Part Of ap "Journal of Neuroscience"
issue Number ap "27"
pagination ap "11239--11252"
publisher ap "Society for Neuroscience"
volume Number ap "33"

Deco2014ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Deco2014

belongs to
Scholarly article c
has facts
issued ap "2014"
title ap "How local excitation--inhibition ratio impacts the whole brain dynamics"
author ap "Deco, Gustavo"
author ap "others"
is Part Of ap "Journal of Neuroscience"

Deco2017ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Deco2017

belongs to
Scholarly article c
has facts
issued ap "2017"
title ap "The dynamics of resting fluctuations in the brain: metastability and its dynamical cortical core"
author ap "Deco, Gustavo"
author ap "Kringelbach, Morten L."
author ap "others"
is Part Of ap "Scientific Reports"
pagination ap "3095"
volume Number ap "7"

Delay history bufferni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/DelayHistoryBuffer

Storage and interpolation of past states required for DDE/SDDE integration.
belongs to
Backend capability c

Delta (CoombesByrne parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/CoombesByrne/parameters/Delta

Half-width of heterogeneous noise distribution
belongs to
Parameter c
has facts
description ap "Half-width of heterogeneous noise distribution"
default Value ap "0.5"^^double
definition ap "Half-width of heterogeneous noise distribution"
notation ap "Delta"

Delta (CoombesByrne2D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/CoombesByrne2D/parameters/Delta

Half-width of heterogeneous noise distribution
belongs to
Parameter c
has facts
description ap "Half-width of heterogeneous noise distribution"
default Value ap "1.0"^^double
definition ap "Half-width of heterogeneous noise distribution"
notation ap "Delta"

Delta (GastSchmidtKnosche_SD parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/GastSchmidtKnosche_SD/parameters/Delta

Half-width of heterogeneous noise distribution
belongs to
Parameter c
has facts
description ap "Half-width of heterogeneous noise distribution"
default Value ap "2.0"^^double
definition ap "Half-width of heterogeneous noise distribution"
notation ap "Delta"

Delta (GastSchmidtKnosche_SF parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/GastSchmidtKnosche_SF/parameters/Delta

Half-width of heterogeneous noise distribution
belongs to
Parameter c
has facts
description ap "Half-width of heterogeneous noise distribution"
default Value ap "2.0"^^double
definition ap "Half-width of heterogeneous noise distribution"
notation ap "Delta"

Delta (KIonEx parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/parameters/Delta

HWHM heterogeneous noise
belongs to
Parameter c
has facts
description ap "HWHM heterogeneous noise"
default Value ap "1.0"^^double
definition ap "HWHM heterogeneous noise"
notation ap "Delta"

Delta (MontbrioPazoRoxin parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/MontbrioPazoRoxin/parameters/Delta

Mean heterogeneous noise
belongs to
Parameter c
has facts
description ap "Mean heterogeneous noise"
default Value ap "1.0"^^double
has Db Xref ap G O 0061669 ep
definition ap "Mean heterogeneous noise"
notation ap "Delta"

delta_Ca (LarterBreakspear parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/LarterBreakspear/parameters/delta_Ca

Variance of Calcium channel threshold. Defines the steepness of the sigmoid $m_{Ca}$.
belongs to
Parameter c
has facts
description ap "Variance of Calcium channel threshold"
default Value ap "0.15"^^double
has Db Xref ap G O 0005262 ep
definition ap "Variance of Calcium channel threshold. Defines the steepness of the sigmoid $m_{Ca}$."
notation ap "delta_Ca"

Delta_e (DumontGutkin parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/DumontGutkin/parameters/Delta_e

Half-width of heterogeneous noise distribution over excitatory population
belongs to
Parameter c
has facts
description ap "Half-width of heterogeneous noise distribution over excitatory population"
default Value ap "1.0"^^double
has Db Xref ap G O 0060079 ep
has Db Xref ap G O 0098815 ep
definition ap "Half-width of heterogeneous noise distribution over excitatory population"
notation ap "Delta_e"

Delta_i (DumontGutkin parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/DumontGutkin/parameters/Delta_i

Half-width of heterogeneous noise distribution over inhibitory population
belongs to
Parameter c
has facts
description ap "Half-width of heterogeneous noise distribution over inhibitory population"
default Value ap "1.0"^^double
has Db Xref ap G O 0032228 ep
has Db Xref ap G O 0060080 ep
has Db Xref ap G O 0098828 ep
definition ap "Half-width of heterogeneous noise distribution over inhibitory population"
notation ap "Delta_i"

delta_K (LarterBreakspear parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/LarterBreakspear/parameters/delta_K

Variance of Potassium channel threshold. Defines the steepness of the sigmoid $m_K$.
belongs to
Parameter c
has facts
description ap "Variance of Potassium channel threshold"
default Value ap "0.3"^^double
has Db Xref ap G O 0005267 ep
definition ap "Variance of Potassium channel threshold. Defines the steepness of the sigmoid $m_K$."
notation ap "delta_K"

delta_Na (LarterBreakspear parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/LarterBreakspear/parameters/delta_Na

Variance of sodium channel threshold. Defines the steepness of the sigmoid $m_{Na}$.
belongs to
Parameter c
has facts
description ap "Variance of sodium channel threshold"
default Value ap "0.15"^^double
has Db Xref ap G O 0005272 ep
definition ap "Variance of sodium channel threshold. Defines the steepness of the sigmoid $m_{Na}$."
notation ap "delta_Na"

delta_V (LarterBreakspear parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/LarterBreakspear/parameters/delta_V

Variance of excitatory threshold. Defines the steepness of sigmoid $Q_V$.
belongs to
Parameter c
has facts
description ap "Variance of excitatory threshold"
default Value ap "0.65"^^double
has Db Xref ap G O 0060079 ep
has Db Xref ap Excitability Threshold Variance ep
definition ap "Variance of excitatory threshold. Defines the steepness of sigmoid $Q_V$."
notation ap "delta_V"

delta_Z (LarterBreakspear parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/LarterBreakspear/parameters/delta_Z

Variance of inhibitory threshold. Defines the steepness of sigmoid $Q_Z$.
belongs to
Parameter c
has facts
description ap "Variance of inhibitory threshold"
default Value ap "0.7"^^double
has Db Xref ap G O 0060080 ep
definition ap "Variance of inhibitory threshold. Defines the steepness of sigmoid $Q_Z$."
notation ap "delta_Z"

Depannemaecker2023ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Depannemaecker2023

belongs to
Scholarly article c
has facts
issued ap "2023"
title ap "K Ion Exchange model extensions"
author ap "Depannemaecker, Damien"
author ap "others"
is Part Of ap "Preprint"

Differenceni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/coupling_functions/Difference

belongs to
Coupling c
has facts
has Parameter ap a (Difference parameter) ni

DifferentialEquations.jlni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/DifferentialEquations.jl

belongs to
Software package c
has facts
description ap "A suite for numerically solving differential equations in Julia. Supports ODEs, SDEs, DAEs, DDEs, and PDEs with a unified interface, high performance, and extensive algorithm selection."
license ap "MIT"
code Repository ap "https://github.com/SciML/DifferentialEquations.jl"
identifier ap "10.5334/jors.151"
url ap "https://docs.sciml.ai/DiffEqDocs/stable/"

DifferentialEquations.jl integratorsni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/DiffEqIntegrators

belongs to
Backend capability c

DK_o (KIonEx derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/derived_variables/DK_o

belongs to
DerivedVariable c
has facts
notation ap "DK_o"
lhs ap "DK_o"
rhs ap "-DKi*beta"

DKi (KIonEx state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/state_variables/DKi

belongs to
StateVariable c
has facts
notation ap "DKi"
lhs ap "Derivative(DKi, t)"
rhs ap "-gamma*(I_K - 2.0*I_pump)/w_i"

DmuV0 (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/DmuV0

Normalization factors page 48 after the equation 4 from [ZD_2018]
belongs to
Parameter c
has facts
description ap "Normalization factors page 48 after the equation 4 from [ZD_2018]"
default Value ap "10.0"^^double
definition ap "Normalization factors page 48 after the equation 4 from [ZD_2018]"
notation ap "DmuV0"

DNa_i (KIonEx derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/derived_variables/DNa_i

belongs to
DerivedVariable c
has facts
notation ap "DNa_i"
lhs ap "DNa_i"
rhs ap "-DKi"

DNa_o (KIonEx derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/derived_variables/DNa_o

belongs to
DerivedVariable c
has facts
notation ap "DNa_o"
lhs ap "DNa_o"
rhs ap "-DNa_i*beta"

Dopri5ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/integrators/Dopri5

belongs to
Integrator c

Dopri853ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/integrators/Dopri853

belongs to
Integrator c

DsV0 (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/DsV0

Normalization factors page 48 after the equation 4 from [ZD_2018]
belongs to
Parameter c
has facts
description ap "Normalization factors page 48 after the equation 4 from [ZD_2018]"
default Value ap "6.0"^^double
definition ap "Normalization factors page 48 after the equation 4 from [ZD_2018]"
notation ap "DsV0"

DTvN0 (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/DTvN0

Normalization factors page 48 after the equation 4 from [ZD_2018]
belongs to
Parameter c
has facts
description ap "Normalization factors page 48 after the equation 4 from [ZD_2018]"
default Value ap "1.0"^^double
definition ap "Normalization factors page 48 after the equation 4 from [ZD_2018]"
notation ap "DTvN0"

Duffing1918ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Duffing1918

belongs to
Book c
has facts
issued ap "1918"
title ap "Erzwungene Schwingungen bei ver"anderlicher Eigenfrequenz und ihre technische Bedeutung"
author ap "Duffing, Georg"
publisher ap "Vieweg+Teubner"

Dumont2019ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Dumont2019

belongs to
Scholarly article c
has facts
issued ap "2019"
title ap "A reduced model of coupled neural masses with complex dynamics"
author ap "Dumont, Gr\'egoire"
author ap "Gutkin, Boris"
is Part Of ap "eNeuro"

DumontGutkinni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/DumontGutkin

belongs to
Dynamics c
has facts
exhibits bifurcation op ""
exhibits regime op Bistable ni
exhibits regime op Oscillatory ni
has attractor op Fixed point ni
has attractor op Limit cycle ni
has model feature op Excitatory/inhibitory subpopulations ni
has stochasticity character op Deterministic ni
models anatomical region op U B E R O N 0000956 ni
phase-space dimension dp "8"^^integer
references ap Dumont2019 ni
pref Label ap "Dumont-Gutkin"@en
has Parameter ap Delta_e (DumontGutkin parameter) ni
has Parameter ap Delta_i (DumontGutkin parameter) ni
has Parameter ap Gamma (DumontGutkin parameter) ni
has Parameter ap I_e (DumontGutkin parameter) ni
has Parameter ap I_i (DumontGutkin parameter) ni
has Parameter ap J_ee (DumontGutkin parameter) ni
has Parameter ap J_ei (DumontGutkin parameter) ni
has Parameter ap J_ie (DumontGutkin parameter) ni
has Parameter ap J_ii (DumontGutkin parameter) ni
has Parameter ap eta_e (DumontGutkin parameter) ni
has Parameter ap eta_i (DumontGutkin parameter) ni
has Parameter ap tau_e (DumontGutkin parameter) ni
has Parameter ap tau_i (DumontGutkin parameter) ni
has Parameter ap tau_s (DumontGutkin parameter) ni
has State Variable ap V_e (DumontGutkin state variable) ni
has State Variable ap V_i (DumontGutkin state variable) ni
has State Variable ap r_e (DumontGutkin state variable) ni
has State Variable ap r_i (DumontGutkin state variable) ni
has State Variable ap s_ee (DumontGutkin state variable) ni
has State Variable ap s_ei (DumontGutkin state variable) ni
has State Variable ap s_ie (DumontGutkin state variable) ni
has State Variable ap s_ii (DumontGutkin state variable) ni
model_type (slot) ap "mean_field"

e (Generic2dOscillator parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Generic2dOscillator/parameters/e

Coefficient of the quadratic term of the cubic nullcline.
belongs to
Parameter c
has facts
description ap "Coefficient of the quadratic term of the cubic nullcline"
default Value ap "3.0"^^double
definition ap "Coefficient of the quadratic term of the cubic nullcline."
notation ap "e"

E (KIonEx parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/parameters/E

Reversal Potential
belongs to
Parameter c
has facts
description ap "Reversal Potential"
default Value ap "0.0"^^double
has Db Xref ap G O 0019228 ep
definition ap "Reversal Potential"
notation ap "E"

E (TsodyksMarkram state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/TsodyksMarkram/state_variables/E

belongs to
StateVariable c
has facts
description ap "Mean firing rate of the excitatory population"
notation ap "E"
lhs ap "Derivative(E, t)"
rhs ap "(-E + SS1)/tau"

E (WilsonCowan state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/WilsonCowan/state_variables/E

belongs to
StateVariable c
has facts
description ap "State-variable of the Wilson and Cowan model (Wilson and Cowan, 1973), denoting the mean firing rate of all excitatory neurons of the population"
has Db Xref ap G O 0098815 ep
notation ap "E"
lhs ap "Derivative(E, t)"
rhs ap "(-E + s_e*(-E*r_e + k_e))/tau_e"

E (ZerlautAdaptationFirstOrder state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/state_variables/E

belongs to
StateVariable c
has facts
description ap "Firing rate of excitatory population in KHz"
notation ap "E"
lhs ap "Derivative(E, t)"
rhs ap "(-E + f_out_e)/T"

E/I balanceni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/EIBalance

Dynamic equilibrium between excitatory and inhibitory drive.
belongs to
SKOS Concept c
has facts
broad Match ap G O 0099177 ep
pref Label ap "E/I balance"@en

e0 (JansenRit1995 parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/JansenRit1995/parameters/e0

belongs to
Parameter c
has facts
description ap "Half of maximum firing rate (2*e0 = max rate)"
default Value ap "2.5"^^double
notation ap "e0"
unit (slot) dp "per_s"

e0 (ModelJansen1995 parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ModelJansen1995/parameters/e0

belongs to
Parameter c
has facts
default Value ap "0.0025"^^double
notation ap "e0"
unit (slot) dp "per_ms"

E0 (TsodyksMarkram parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/TsodyksMarkram/parameters/E0

belongs to
Parameter c
has facts
description ap "External input (baseline excitability)"
default Value ap "-2.0"^^double
notation ap "E0"

e0 (ZetterbergJansen parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZetterbergJansen/parameters/e0

Half of the maximum population mean firing rate [ms^-1].
belongs to
Parameter c
has facts
description ap "Half of the maximum population mean firing rate [ms^-1]"
default Value ap "0.0025"^^double
has Db Xref ap G O 0099605 ep
definition ap "Half of the maximum population mean firing rate [ms^-1]."
notation ap "e0"

E_A (CakanObermayer parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/CakanObermayer/parameters/E_A

Reversal potential of the adaptation current.
belongs to
Parameter c
has facts
default Value ap "-80.0"^^double
has Db Xref ap G O 0042391 ep
definition ap "Reversal potential of the adaptation current."
notation ap "E_A"
unit (slot) dp "mV"

E_e (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/E_e

excitatory reversal potential [mV]
belongs to
Parameter c
has facts
description ap "excitatory reversal potential [mV]"
default Value ap "0.0"^^double
has Db Xref ap G O 0060079 ep
definition ap "excitatory reversal potential [mV]"
notation ap "E_e"

e_i (StefanescuJirsa2D derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa2D/derived_variables/e_i

belongs to
DerivedVariable c
has facts
description ap "Per-mode cubic-coefficient projection for the excitatory subnetwork."
notation ap "e_i"
lhs ap "e_i"
rhs ap "1.0"

e_i (StefanescuJirsa3D derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa3D/derived_variables/e_i

belongs to
DerivedVariable c
has facts
description ap "Per-mode cubic coefficient for the inhibitory alpha dynamics."
notation ap "e_i"
lhs ap "e_i"
rhs ap "a"

E_i (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/E_i

inhibitory reversal potential [mV]
belongs to
Parameter c
has facts
description ap "inhibitory reversal potential [mV]"
default Value ap "-80.0"^^double
has Db Xref ap G O 0060080 ep
definition ap "inhibitory reversal potential [mV]"
notation ap "E_i"

E_L (CakanObermayer parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/CakanObermayer/parameters/E_L

Leak reversal potential of a single AdEx neuron.
belongs to
Parameter c
has facts
default Value ap "-65.0"^^double
has Db Xref ap G O 0022840 ep
definition ap "Leak reversal potential of a single AdEx neuron."
notation ap "E_L"
unit (slot) dp "mV"

E_L_e (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/E_L_e

leak reversal potential for excitatory [mV]
belongs to
Parameter c
has facts
description ap "leak reversal potential for excitatory [mV]"
default Value ap "-65.0"^^double
has Db Xref ap G O 0022840 ep
definition ap "leak reversal potential for excitatory [mV]"
notation ap "E_L_e"

E_L_i (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/E_L_i

leak reversal potential for inhibitory [mV]
belongs to
Parameter c
has facts
description ap "leak reversal potential for inhibitory [mV]"
default Value ap "-65.0"^^double
has Db Xref ap G O 0022840 ep
definition ap "leak reversal potential for inhibitory [mV]"
notation ap "E_L_i"

e_rs (EpileptorRestingState parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/EpileptorRestingState/parameters/e_rs

Coefficient of the squared term in the sixth state-variable x_rs.
belongs to
Parameter c
has facts
description ap "Coefficient of the squared term in the sixth state-variable x_rs"
default Value ap "3.0"^^double
definition ap "Coefficient of the squared term in the sixth state-variable x_rs."
notation ap "e_rs"

EEGni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/observation_models/eeg

belongs to
Observation c
has facts
description ap "Forward solution for scalp electroencephalography. Projects source neural activity through a lead field (gain) matrix to electrode locations on the scalp. If no precomputed gain is available, uses a single-sphere analytic approximation (Sarvas 1987, Eq. 12). Supports re-referencing: common average, single-electrode, or ideal reference-free recording."
has Parameter ap conductivity (eeg parameter) ni
has Parameter ap reference_electrode (eeg parameter) ni

EEGLABni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/EEGLAB

belongs to
Software package c
has facts
description ap "An interactive MATLAB toolbox for processing continuous and event-related EEG, MEG, and other electrophysiological data using independent component analysis, time/frequency analysis, and other methods."
license ap "BSD-2-Clause"
code Repository ap "https://github.com/sccn/eeglab"
identifier ap "10.1016/j.jneumeth.2003.10.009"
url ap "https://eeglab.org"

EI Tuning: Functional Connectivity Fittingni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/experiments/EI_Tuning_FIC_EIB_Optimization

belongs to
SimulationExperiment c
has facts
description ap "Fitting functional connectivity using the two-population Reduced Wong-Wang model with explicit excitatory and inhibitory populations. Combines Feedback Inhibition Control (FIC) to maintain local E-I balance with EIB tuning to globally optimize network connectivity. Supports both iterative (FIC+EIB) and gradient-based optimization approaches. "

Eisenberg1975ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Eisenberg1975

belongs to
Book c
has facts
issued ap "1975"
title ap "Nuclear Theory: Nuclear Models Collective and Single-Particle Phenomena"
author ap "Eisenberg, Judah M."
author ap "Greiner, Walter"
publisher ap "North-Holland"

Elephantni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/Elephant

belongs to
Software package c
has facts
description ap "Electrophysiology Analysis Toolkit — a Python library for the analysis of electrophysiological data, including spike-train statistics, spectral analysis, and unitary event analysis."
license ap "BSD-3-Clause"
code Repository ap "https://github.com/NeuralEnsemble/elephant"
identifier ap "10.5281/zenodo.1186602"
url ap "https://elephant.readthedocs.io"

Epileptor2Dni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor2D

belongs to
Dynamics c
has facts
exhibits bifurcation op ""
exhibits regime op Bistable ni
exhibits regime op Oscillatory ni
has attractor op Fixed point ni
has attractor op Limit cycle ni
has stochasticity character op Deterministic ni
models anatomical region op U B E R O N 0002728 ni
phase-space dimension dp "2"^^integer
description ap "Epileptor2D (E2D) is a phenomenological neural mass model consisting in the two-dimensional reduction ('x', 'z') of the original Epileptor model (see Epileptor5D; Proix et al., 2014, 2017). Note: ------ - Equations and default parameters are taken from (Proix et al.,2014), - The slow permittivity state-variable (z_E2D) can be modified to account for the time difference between the interictal (between seizures) and ictal (during seizure) states (see Proix et al., 2014)."
references ap Proix2014 ni
references ap Proix2017 ni
subject ap D004827 ep
pref Label ap "Epileptor 2D"@en
has Derived Variable ap h (Epileptor2D derived variable) ni
has Derived Variable ap x1cond (Epileptor2D derived variable) ni
has Derived Variable ap zcond (Epileptor2D derived variable) ni
has Parameter ap Iext (Epileptor2D parameter) ni
has Parameter ap Ks (Epileptor2D parameter) ni
has Parameter ap Kvf (Epileptor2D parameter) ni
has Parameter ap a (Epileptor2D parameter) ni
has Parameter ap b (Epileptor2D parameter) ni
has Parameter ap c (Epileptor2D parameter) ni
has Parameter ap d (Epileptor2D parameter) ni
has Parameter ap modification (Epileptor2D parameter) ni
has Parameter ap r (Epileptor2D parameter) ni
has Parameter ap slope (Epileptor2D parameter) ni
has Parameter ap tt (Epileptor2D parameter) ni
has Parameter ap x0 (Epileptor2D parameter) ni
has State Variable ap x1 (Epileptor2D state variable) ni
has State Variable ap z (Epileptor2D state variable) ni
model_type (slot) ap "phenomenological"

Epileptor3DStefanescuMcDonaldni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor3DStefanescuMcDonald

belongs to
Dynamics c
has facts
exhibits regime op Bistable ni
exhibits regime op Bursting ni
has attractor op Fixed point ni
has attractor op Limit cycle ni
has model feature op Fast-slow decomposition ni
has stochasticity character op Deterministic ni
models anatomical region op U B E R O N 0002728 ni
has timescale separation dp "true"^^boolean
phase-space dimension dp "3"^^integer
description ap "Stefanescu-McDonald reduced 3D Epileptor variant migrated as a placeholder scaffold from the legacy tvb-o.owl ontology. The original publication for this exact variant could not be located; the only OWL-side parameter is `N` (population size, grounded to "regulation of resting membrane potential"). Equations are minimal placeholders: a fast (x1) - slow (z) excitable system inspired by the canonical Epileptor (Jirsa et al. 2014), gated by N. This scaffold preserves the ontology lineage and parameter grounding; it should be replaced with the published equations once located, or removed if the variant is confirmed obsolete."
subject ap D004827 ep
pref Label ap "Epileptor 3D (Stefanescu-McDonald)"@en
has Parameter ap N (Epileptor3DStefanescuMcDonald parameter) ni
has Parameter ap tau_z (Epileptor3DStefanescuMcDonald parameter) ni
has Parameter ap x_0 (Epileptor3DStefanescuMcDonald parameter) ni
has State Variable ap x1 (Epileptor3DStefanescuMcDonald state variable) ni
has State Variable ap z (Epileptor3DStefanescuMcDonald state variable) ni
model_type (slot) ap "neural_mass"

Epileptor5Dni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor5D

belongs to
Dynamics c
has facts
exhibits bifurcation op ""
exhibits regime op Bistable ni
exhibits regime op Bursting ni
exhibits regime op Oscillatory ni
has attractor op Fixed point ni
has attractor op Limit cycle ni
has model feature op Fast-slow decomposition ni
has stochasticity character op Deterministic ni
models anatomical region op U B E R O N 0002728 ni
has timescale separation dp "true"^^boolean
phase-space dimension dp "5"^^integer
description ap "Epilepor5D (E5D) is a phenomenological, coupled, nonlinear five-dimensional (i.e., five state-variables ('x1', 'y1', 'z', 'x2', 'y2')) neural mass model able to realistically reproduce the temporal dynamics of epileptic seizures and the alternating sequence of seizures (ictal and interictal state; Jirsa et al.,2014; El Houssaini et al., 2015, 2020). Epileptor5D comprises three different time scales interacting together and accounting for various electrographic patterns: - the fastest and intermediate time scales are two coupled oscillators ((x1, y1) and (x2, y2)), accounting respectively for the low-voltage fast discharges (i.e., very fast oscillations) and spike-and-wave discharges. - the slowest time scale is responsible for leading the autonomous switch between interictal and ictal states and is driven by a slow-permittivity variable z. This switching is accompanied by a direct current (DC) shift that has been recorded in vitro and in vivo. The main output of the model: -x1+ x2, bears analogy with the field potential, while the precise biophysical equivalent of the z variable is unknown and will be likely complex. Note: ------ - Equations and default parameters are taken from (Jirsa et al.,2014 & El Houssaini et al., 2015), - The integral coupling function g(x1) can be rewritten as an ordinary differential equation, which is technically introduced, here, as a sixth state-variable (see Jirsa et al.,2014), - The slow permittivity state-variable (z_E5D) can be modified to account for the time difference between the interictal (between seizures) and ictal (during seizure) states (see Proix et al., 2014)."
references ap Jirsa2014 ni
references ap Proix2014 ni
subject ap D004827 ep
pref Label ap "Epileptor 5D"@en
has Derived Variable ap h (Epileptor5D derived variable) ni
has Derived Variable ap x1cond (Epileptor5D derived variable) ni
has Derived Variable ap y2cond (Epileptor5D derived variable) ni
has Derived Variable ap zcond (Epileptor5D derived variable) ni
has Parameter ap Iext (Epileptor5D parameter) ni
has Parameter ap Iext2 (Epileptor5D parameter) ni
has Parameter ap Kf (Epileptor5D parameter) ni
has Parameter ap Ks (Epileptor5D parameter) ni
has Parameter ap Kvf (Epileptor5D parameter) ni
has Parameter ap a (Epileptor5D parameter) ni
has Parameter ap aa (Epileptor5D parameter) ni
has Parameter ap b (Epileptor5D parameter) ni
has Parameter ap bb (Epileptor5D parameter) ni
has Parameter ap c (Epileptor5D parameter) ni
has Parameter ap d (Epileptor5D parameter) ni
has Parameter ap modification (Epileptor5D parameter) ni
has Parameter ap r (Epileptor5D parameter) ni
has Parameter ap s (Epileptor5D parameter) ni
has Parameter ap slope (Epileptor5D parameter) ni
has Parameter ap tau (Epileptor5D parameter) ni
has Parameter ap tt (Epileptor5D parameter) ni
has Parameter ap x0 (Epileptor5D parameter) ni
has State Variable ap g (Epileptor5D state variable) ni
has State Variable ap x1 (Epileptor5D state variable) ni
has State Variable ap x2 (Epileptor5D state variable) ni
has State Variable ap y1 (Epileptor5D state variable) ni
has State Variable ap y2 (Epileptor5D state variable) ni
has State Variable ap z (Epileptor5D state variable) ni
model_type (slot) ap "phenomenological"

EpileptorRestingStateni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/EpileptorRestingState

belongs to
Dynamics c
has facts
exhibits bifurcation op ""
exhibits regime op Bistable ni
exhibits regime op Bursting ni
exhibits regime op Oscillatory ni
has attractor op Fixed point ni
has attractor op Limit cycle ni
has model feature op Fast-slow decomposition ni
has stochasticity character op Deterministic ni
models anatomical region op U B E R O N 0000956 ni
models anatomical region op U B E R O N 0002728 ni
has timescale separation dp "true"^^boolean
phase-space dimension dp "8"^^integer
description ap "Epileptor Resting-State (ERS) is an extension of the phenomenological neural mass model of Epileptor5D, tuned to express regionally specific physiological oscillations in addition to the epileptiform discharges (Courtiol et al., 2020). This extension was made using the Generic 2-dimensional Oscillator model (parametrized close to a supercritical Hopf Bifurcation) (Sanz-Leon et al., 2013, 2015) to reproduce the spontaneous local field potential-like signal. This model, its motivation and derivation can be found in the published article (Courtiol et al., 2020)."
references ap Courtiol2020 ni
references ap Jirsa2014 ni
subject ap D004827 ep
pref Label ap "Epileptor (resting-state)"@en
has Derived Variable ap lc_1 (EpileptorRestingState derived variable) ni
has Derived Variable ap output (EpileptorRestingState derived variable) ni
has Derived Variable ap x1cond (EpileptorRestingState derived variable) ni
has Derived Variable ap y2cond (EpileptorRestingState derived variable) ni
has Derived Variable ap zcond (EpileptorRestingState derived variable) ni
has Parameter ap I_rs (EpileptorRestingState parameter) ni
has Parameter ap Iext (EpileptorRestingState parameter) ni
has Parameter ap Iext2 (EpileptorRestingState parameter) ni
has Parameter ap K_rs (EpileptorRestingState parameter) ni
has Parameter ap Kf (EpileptorRestingState parameter) ni
has Parameter ap Ks (EpileptorRestingState parameter) ni
has Parameter ap Kvf (EpileptorRestingState parameter) ni
has Parameter ap a (EpileptorRestingState parameter) ni
has Parameter ap a_rs (EpileptorRestingState parameter) ni
has Parameter ap aa (EpileptorRestingState parameter) ni
has Parameter ap alpha_rs (EpileptorRestingState parameter) ni
has Parameter ap b (EpileptorRestingState parameter) ni
has Parameter ap b_rs (EpileptorRestingState parameter) ni
has Parameter ap bb (EpileptorRestingState parameter) ni
has Parameter ap beta_rs (EpileptorRestingState parameter) ni
has Parameter ap c (EpileptorRestingState parameter) ni
has Parameter ap d (EpileptorRestingState parameter) ni
has Parameter ap d_rs (EpileptorRestingState parameter) ni
has Parameter ap e_rs (EpileptorRestingState parameter) ni
has Parameter ap f_rs (EpileptorRestingState parameter) ni
has Parameter ap gamma_rs (EpileptorRestingState parameter) ni
has Parameter ap p (EpileptorRestingState parameter) ni
has Parameter ap r (EpileptorRestingState parameter) ni
has Parameter ap slope (EpileptorRestingState parameter) ni
has Parameter ap tau (EpileptorRestingState parameter) ni
has Parameter ap tau_rs (EpileptorRestingState parameter) ni
has Parameter ap tt (EpileptorRestingState parameter) ni
has Parameter ap x0 (EpileptorRestingState parameter) ni
has State Variable ap g (EpileptorRestingState state variable) ni
has State Variable ap x1 (EpileptorRestingState state variable) ni
has State Variable ap x2 (EpileptorRestingState state variable) ni
has State Variable ap x_rs (EpileptorRestingState state variable) ni
has State Variable ap y1 (EpileptorRestingState state variable) ni
has State Variable ap y2 (EpileptorRestingState state variable) ni
has State Variable ap y_rs (EpileptorRestingState state variable) ni
has State Variable ap z (EpileptorRestingState state variable) ni
model_type (slot) ap "phenomenological"

epsilon (KIonEx parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/parameters/epsilon

diffusion rate
belongs to
Parameter c
has facts
description ap "diffusion rate"
default Value ap "0.001"^^double
definition ap "diffusion rate"
notation ap "epsilon"

eq_in_ani back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/continuations/Generic2dOscillator-bifurcation

belongs to
Continuation c
has facts
description ap "Continue the equilibrium branch of the Generic2dOscillator as parameter a is varied. Detect Hopf bifurcations and continue periodic orbits from all Hopf points."

eq_in_a_fullni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/continuations/Generic2dOscillator-bifurcation-full

belongs to
Continuation c
has facts
description ap "Comprehensive bifurcation analysis of the Generic2dOscillator. Continues the equilibrium branch as parameter a is varied, detects fold and Hopf bifurcations, then branches to periodic orbits from both Hopf points with fine-tuned solver settings."

Ermentrout2010ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Ermentrout2010

belongs to
Book c
has facts
issued ap "2010"
title ap "Mathematical Foundations of Neuroscience"
author ap "Ermentrout, G. Bard"
author ap "Terman, David H."
publisher ap "Springer"

eta (CoombesByrne parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/CoombesByrne/parameters/eta

Constant parameter to scale the rate of feedback from the firing rate variable to itself
belongs to
Parameter c
has facts
description ap "Constant parameter to scale the rate of feedback from the firing rate variable to itself"
default Value ap "20.0"^^double
has Db Xref ap G O 0099605 ep
definition ap "Constant parameter to scale the rate of feedback from the firing rate variable to itself"
notation ap "eta"

eta (CoombesByrne2D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/CoombesByrne2D/parameters/eta

Constant parameter to scale the rate of feedback from the firing rate variable to itself
belongs to
Parameter c
has facts
description ap "Constant parameter to scale the rate of feedback from the firing rate variable to itself"
default Value ap "2.0"^^double
has Db Xref ap G O 0099605 ep
definition ap "Constant parameter to scale the rate of feedback from the firing rate variable to itself"
notation ap "eta"

eta (GastSchmidtKnosche_SD parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/GastSchmidtKnosche_SD/parameters/eta

Mean of heterogeneous noise distribution
belongs to
Parameter c
has facts
description ap "Mean of heterogeneous noise distribution"
default Value ap "-6.0"^^double
definition ap "Mean of heterogeneous noise distribution"
notation ap "eta"

eta (GastSchmidtKnosche_SF parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/GastSchmidtKnosche_SF/parameters/eta

Mean of heterogeneous noise distribution
belongs to
Parameter c
has facts
description ap "Mean of heterogeneous noise distribution"
default Value ap "1.0"^^double
definition ap "Mean of heterogeneous noise distribution"
notation ap "eta"

eta (KIonEx parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/parameters/eta

Mean heterogeneous noise
belongs to
Parameter c
has facts
description ap "Mean heterogeneous noise"
default Value ap "0.0"^^double
definition ap "Mean heterogeneous noise"
notation ap "eta"

eta (MontbrioPazoRoxin parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/MontbrioPazoRoxin/parameters/eta

Constant parameter to scale the rate of feedback from the firing rate variable to itself
belongs to
Parameter c
has facts
description ap "Constant parameter to scale the rate of feedback from the firing rate variable to itself"
default Value ap "-5.0"^^double
has Db Xref ap G O 0099605 ep
definition ap "Constant parameter to scale the rate of feedback from the firing rate variable to itself"
notation ap "eta"

eta (StefanescuJirsa2D state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa2D/state_variables/eta

belongs to
StateVariable c
has facts
description ap "Excitatory slow recovery variable (per mode)."
has Db Xref ap G O 0060079 ep
notation ap "eta"
lhs ap "Derivative(eta, t)"
rhs ap "(xi - b*eta + m_i)/tau"

eta (StefanescuJirsa3D state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa3D/state_variables/eta

belongs to
StateVariable c
has facts
description ap "Excitatory recovery variable (per mode)."
has Db Xref ap G O 0060079 ep
notation ap "eta"
lhs ap "Derivative(eta, t)"
rhs ap "c_i - d_i*xi**2 - eta"

eta_e (DumontGutkin parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/DumontGutkin/parameters/eta_e

Mean heterogeneous current on excitatory population
belongs to
Parameter c
has facts
description ap "Mean heterogeneous current on excitatory population"
default Value ap "-5.0"^^double
has Db Xref ap G O 0098815 ep
definition ap "Mean heterogeneous current on excitatory population"
notation ap "eta_e"

eta_i (DumontGutkin parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/DumontGutkin/parameters/eta_i

Mean heterogeneous current on inhibitory population
belongs to
Parameter c
has facts
description ap "Mean heterogeneous current on inhibitory population"
default Value ap "-5.0"^^double
has Db Xref ap G O 0060080 ep
definition ap "Mean heterogeneous current on inhibitory population"
notation ap "eta_i"

Eulerni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/integrators/Euler

belongs to
Integrator c

Event-driven integrationni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/EventDrivenIntegration

Spike-based or hybrid event-driven simulation of a neural network.
belongs to
Simulation task c

example_3node_networkni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/example_3node_network

belongs to
Network c
has facts
description ap "Example network with 3 nodes and two different coupling types (excitatory and inhibitory)"
alt Label ap "Simple 3-Node Network Example"
has Parameter ap G (example_3node_network parameter) ni
has Parameter ap conduction_speed (example_3node_network parameter) ni

Excitationni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Excitation

Generic depolarising synaptic effect; abstract parent of model-specific excitatory currents and conductances.
belongs to
SKOS Concept c
has facts
broad Match ap G O 0060079 ep
pref Label ap "Excitation"@en

Excitatory/inhibitory subpopulationsni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ExcitatoryInhibitorySubpopulations

belongs to
Model feature c

external_input_ex_ex (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/external_input_ex_ex

external drive
belongs to
Parameter c
has facts
description ap "external drive"
default Value ap "0.0"^^double
definition ap "external drive"
notation ap "external_input_ex_ex"

external_input_ex_in (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/external_input_ex_in

external drive
belongs to
Parameter c
has facts
description ap "external drive"
default Value ap "0.0"^^double
definition ap "external drive"
notation ap "external_input_ex_in"

external_input_in_ex (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/external_input_in_ex

external drive
belongs to
Parameter c
has facts
description ap "external drive"
default Value ap "0.0"^^double
definition ap "external drive"
notation ap "external_input_in_ex"

external_input_in_in (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/external_input_in_in

external drive
belongs to
Parameter c
has facts
description ap "external drive"
default Value ap "0.0"^^double
definition ap "external drive"
notation ap "external_input_in_in"

f (Generic2dOscillator parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Generic2dOscillator/parameters/f

Coefficient of the cubic term of the cubic nullcline.
belongs to
Parameter c
has facts
description ap "Coefficient of the cubic term of the cubic nullcline"
default Value ap "1.0"^^double
definition ap "Coefficient of the cubic term of the cubic nullcline."
notation ap "f"

f_i (StefanescuJirsa2D derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa2D/derived_variables/f_i

belongs to
DerivedVariable c
has facts
description ap "Per-mode cubic-coefficient projection for the inhibitory subnetwork."
notation ap "f_i"
lhs ap "f_i"
rhs ap "1.0"

f_i (StefanescuJirsa3D derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa3D/derived_variables/f_i

belongs to
DerivedVariable c
has facts
description ap "Per-mode quadratic coefficient for the inhibitory alpha dynamics."
notation ap "f_i"
lhs ap "f_i"
rhs ap "b"

f_out_e (ZerlautAdaptationFirstOrder derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/derived_variables/f_out_e

belongs to
DerivedVariable c
has facts
notation ap "f_out_e"
lhs ap "f_out_e"
rhs ap "erfc(sqrt(2)*(V_thre_e - mu_V_e)/(2*sigma_V_e))/(2*T_V_e)"

f_out_i (ZerlautAdaptationFirstOrder derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/derived_variables/f_out_i

belongs to
DerivedVariable c
has facts
notation ap "f_out_i"
lhs ap "f_out_i"
rhs ap "erfc(sqrt(2)*(V_thre_i - mu_V_i)/(2*sigma_V_i))/(2*T_V_i)"

f_rs (EpileptorRestingState parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/EpileptorRestingState/parameters/f_rs

Coefficient of the cubic term in the sixth state-variable x_rs.
belongs to
Parameter c
has facts
description ap "Coefficient of the cubic term in the sixth state-variable x_rs"
default Value ap "1.0"^^double
definition ap "Coefficient of the cubic term in the sixth state-variable x_rs."
notation ap "f_rs"

Fast-slow decompositionni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/FastSlowDecomposition

belongs to
Model feature c

FastDMFni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/FastDMF

belongs to
Software package c
has facts
description ap "A fast C++ implementation of the Dynamic Mean Field (DMF) model for whole-brain simulation, with Python bindings. Optimized for rapid parameter exploration on connectome data."
license ap "MIT"
code Repository ap "https://github.com/Picardian14/FastDMF"
identifier ap "10.3389/fncom.2022.866517"

FastLinearCouplingni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/coupling_functions/FastLinearCoupling

belongs to
Coupling c
has facts
description ap "Instantaneous linear coupling using vectorized matrix multiplication. Applies global coupling strength G to the weighted sum of source states. Faster than element-wise LinearCoupling for dense all-to-all connectivity."
has Parameter ap G (FastLinearCoupling parameter) ni
has Parameter ap b (FastLinearCoupling parameter) ni

fe_e (ZerlautAdaptationFirstOrder derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/derived_variables/fe_e

belongs to
DerivedVariable c
has facts
notation ap "fe_e"
lhs ap "fe_e"
rhs ap "K_ext_e*(Fe_ext + external_input_ex_ex) + N_tot*p_connect_e*(1.0 - g)*(E + 1/1000000)"

Fe_ext (ZerlautAdaptationFirstOrder derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/derived_variables/Fe_ext

belongs to
DerivedVariable c
has facts
notation ap "Fe_ext"
lhs ap "Fe_ext"
rhs ap "Piecewise((0, K_ext_e*(c_pop0 + lc_E + ou_drift*weight_noise) < 0), (c_pop0 + lc_E + ou_drift*weight_noise, True))"

fe_i (ZerlautAdaptationFirstOrder derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/derived_variables/fe_i

belongs to
DerivedVariable c
has facts
notation ap "fe_i"
lhs ap "fe_i"
rhs ap "K_ext_e*(Fe_ext + external_input_in_ex) + N_tot*p_connect_e*(1.0 - g)*(E + 1/1000000)"

FeedbackScalingni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/FeedbackScaling

Multiplicative gain applied to recurrent feedback. Control-theoretic concept with no faithful upstream GO mapping.
belongs to
SKOS Concept c
has facts
pref Label ap "FeedbackScaling"@en

Feigenbaum1978ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Feigenbaum1978

belongs to
Scholarly article c
has facts
issued ap "1978"
title ap "Quantitative Universality for a Class of Nonlinear Transformations"
author ap "Feigenbaum, Mitchell J."
identifier ap "10.1007/bf01020332"
is Part Of ap "Journal of Statistical Physics"
pagination ap "25--52"
volume Number ap "19"

fi_e (ZerlautAdaptationFirstOrder derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/derived_variables/fi_e

belongs to
DerivedVariable c
has facts
notation ap "fi_e"
lhs ap "fi_e"
rhs ap "K_ext_i*(Fi_ext + external_input_ex_in) + N_tot*g*p_connect_i*(I + 1/1000000)"

Fi_ext (ZerlautAdaptationFirstOrder derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/derived_variables/Fi_ext

belongs to
DerivedVariable c
has facts
notation ap "Fi_ext"
lhs ap "Fi_ext"
rhs ap "lc_I"

fi_i (ZerlautAdaptationFirstOrder derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/derived_variables/fi_i

belongs to
DerivedVariable c
has facts
notation ap "fi_i"
lhs ap "fi_i"
rhs ap "K_ext_i*(Fi_ext + external_input_in_in) + N_tot*g*p_connect_i*(I + 1/1000000)"

FieldTripni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/FieldTrip

belongs to
Software package c
has facts
description ap "A MATLAB toolbox for MEG, EEG, iEEG and NIRS analysis, including preprocessing, source reconstruction, statistical testing, and connectivity analysis."
license ap "GPL-3.0-only"
code Repository ap "https://github.com/fieldtrip/fieldtrip"
identifier ap "10.1155/2011/156869"
url ap "https://www.fieldtriptoolbox.org"

fisher_z (FC parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/observation_models/FC/parameters/fisher_z

belongs to
Parameter c
has facts
description ap "Apply Fisher z-transformation to correlations"
default Value ap "true"^^boolean
notation ap "fisher_z"

FitzHugh1961ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/FitzHugh1961

belongs to
Scholarly article c
has facts
issued ap "1961"
title ap "Impulses and physiological states in theoretical models of nerve membrane"
author ap "FitzHugh, Richard"
is Part Of ap "Biophysical Journal"

FitzHughNagumoni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/FitzHughNagumo

belongs to
Creative work c
has facts
title ap "FitzHugh--Nagumo model"
identifier ap "10.4249/scholarpedia.1349"

Freire2008ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Freire2008

belongs to
Scholarly article c
has facts
issued ap "2008"
title ap "Multistability, phase diagrams, and intransitivity in the Lorenz-84 low-order atmospheric circulation model"
author ap "Freire, Jos\'e G."
author ap "others"
is Part Of ap "Chaos"
pagination ap "033121"
volume Number ap "18"

FunctionalConnectivityni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/observation_models/FC

belongs to
Observation c
has facts
description ap "Functional Connectivity (FC) observation model that computes pairwise Pearson correlation coefficients between regional time series. Commonly used to characterize the statistical dependencies between brain regions from fMRI or simulated neural activity."
has Parameter ap TR (FC parameter) ni
has Parameter ap fisher_z (FC parameter) ni

g (CoombesByrne state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/CoombesByrne/state_variables/g

belongs to
StateVariable c
has facts
notation ap "g"
lhs ap "Derivative(g, t)"
rhs ap "alpha*q"

g (Epileptor5D state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor5D/state_variables/g

belongs to
StateVariable c
has facts
description ap "g_E5D is a low-pass filtered excitatory coupling function from sub-population (x1_E5D, y1_E5D) to (x2_E5D, y2_E5D) in Epileptor5D (Jirsa et al"
notation ap "g"
lhs ap "Derivative(g, t)"
rhs ap "tt*(-0.01*g + 0.001*x1)"

g (EpileptorRestingState state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/EpileptorRestingState/state_variables/g

belongs to
StateVariable c
has facts
notation ap "g"
lhs ap "Derivative(g, t)"
rhs ap "tt*(-0.01*g + 0.001*x1)"

G (example_3node_network parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/example_3node_network/parameters/G

belongs to
Parameter c
has facts
default Value ap "1.0"^^double
notation ap "G"

G (FastLinearCoupling parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/coupling_functions/FastLinearCoupling/parameters/G

belongs to
Parameter c
has facts
description ap "Global coupling strength scaling long-range connections"
default Value ap "0.1"^^double
notation ap "G"

g (Generic2dOscillator parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Generic2dOscillator/parameters/g

Coefficient of the linear term of the cubic nullcline.
belongs to
Parameter c
has facts
description ap "Coefficient of the linear term of the cubic nullcline"
default Value ap "0.0"^^double
definition ap "Coefficient of the linear term of the cubic nullcline."
notation ap "g"

G (PreSigmoidal parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/coupling_functions/PreSigmoidal/parameters/G

belongs to
Parameter c
has facts
description ap "Gain"
default Value ap "60.0"^^double
notation ap "G"

G (ReducedWongWangExcInh parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWangExcInh/parameters/G

Global coupling scaling
belongs to
Parameter c
has facts
description ap "Global coupling scaling"
default Value ap "2.0"^^double
definition ap "Global coupling scaling"
notation ap "G"

g (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/g

fraction of inhibitory cells
belongs to
Parameter c
has facts
description ap "fraction of inhibitory cells"
default Value ap "0.2"^^double
has Db Xref ap G O 0060077 ep
definition ap "fraction of inhibitory cells"
notation ap "g"

g_Ca (LarterBreakspear parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/LarterBreakspear/parameters/g_Ca

Conductance of population of calcium (Ca++) channels. Describes the maximal conductance if all channels are open.
belongs to
Parameter c
has facts
description ap "Conductance of population of calcium (Ca++) channels"
default Value ap "1.1"^^double
has Db Xref ap G O 0005262 ep
definition ap "Conductance of population of calcium (Ca++) channels. Describes the maximal conductance if all channels are open."
notation ap "g_Ca"

g_Cl (KIonEx parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/parameters/g_Cl

chloride conductance
belongs to
Parameter c
has facts
description ap "chloride conductance"
default Value ap "7.5"^^double
definition ap "chloride conductance"
notation ap "g_Cl"
unit (slot) dp "nS"

g_K (KIonEx parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/parameters/g_K

maximal potassium conductance
belongs to
Parameter c
has facts
description ap "maximal potassium conductance"
default Value ap "22.0"^^double
definition ap "maximal potassium conductance"
notation ap "g_K"
unit (slot) dp "nS"

g_K (LarterBreakspear parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/LarterBreakspear/parameters/g_K

Conductance of population of potassium (K) channels. Describes the maximal conductance if all channels are open.
belongs to
Parameter c
has facts
description ap "Conductance of population of potassium (K) channels"
default Value ap "2.0"^^double
has Db Xref ap G O 0005267 ep
definition ap "Conductance of population of potassium (K) channels. Describes the maximal conductance if all channels are open."
notation ap "g_K"

g_Kl (KIonEx parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/parameters/g_Kl

potassium leak conductance
belongs to
Parameter c
has facts
description ap "potassium leak conductance"
default Value ap "0.12"^^double
definition ap "potassium leak conductance"
notation ap "g_Kl"
unit (slot) dp "nS"

g_L (LarterBreakspear parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/LarterBreakspear/parameters/g_L

Conductance of population of leak channels.
belongs to
Parameter c
has facts
description ap "Conductance of population of leak channels"
default Value ap "0.5"^^double
has Db Xref ap G O 0022840 ep
definition ap "Conductance of population of leak channels."
notation ap "g_L"

g_L (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/g_L

leak conductance [nS]
belongs to
Parameter c
has facts
description ap "leak conductance [nS]"
default Value ap "10.0"^^double
has Db Xref ap G O 0022840 ep
definition ap "leak conductance [nS]"
notation ap "g_L"

g_Na (KIonEx parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/parameters/g_Na

maximal sodiumconductance
belongs to
Parameter c
has facts
description ap "maximal sodiumconductance"
default Value ap "40.0"^^double
definition ap "maximal sodiumconductance"
notation ap "g_Na"
unit (slot) dp "nS"

g_Na (LarterBreakspear parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/LarterBreakspear/parameters/g_Na

Conductance of population of Na channels.
belongs to
Parameter c
has facts
description ap "Conductance of population of Na channels"
default Value ap "6.7"^^double
has Db Xref ap G O 0005272 ep
definition ap "Conductance of population of Na channels."
notation ap "g_Na"

g_Nal (KIonEx parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/parameters/g_Nal

sodium leak conductance
belongs to
Parameter c
has facts
description ap "sodium leak conductance"
default Value ap "0.02"^^double
definition ap "sodium leak conductance"
notation ap "g_Nal"
unit (slot) dp "nS"

Galan2008ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Galan2008

belongs to
Scholarly article c
has facts
issued ap "2008"
title ap "Optimal time scale for spike-time reliability: theory, simulations, and experiments"
author ap "Ermentrout, G. Bard"
author ap "Gal\'an, R. F."
author ap "Urban, N. N."
is Part Of ap "Journal of Neurophysiology"

Gamma (DumontGutkin parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/DumontGutkin/parameters/Gamma

Ratio of excitatory VS inhibitory global couplings G_ie/G_ee .
belongs to
Parameter c
has facts
description ap "Ratio of excitatory VS inhibitory global couplings G_ie/G_ee "
default Value ap "5.0"^^double
has Db Xref ap G O 0060079 ep
has Db Xref ap G O 0060080 ep
definition ap "Ratio of excitatory VS inhibitory global couplings G_ie/G_ee ."
notation ap "Gamma"

gamma (Generic2dOscillator parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Generic2dOscillator/parameters/gamma

Constant parameter to reproduce FHN dynamics where excitatory input currents are negative. It scales both I and the long range coupling term.
belongs to
Parameter c
has facts
description ap "Constant parameter to reproduce FHN dynamics where excitatory input currents are negative"
default Value ap "1.0"^^double
definition ap "Constant parameter to reproduce FHN dynamics where excitatory input currents are negative. It scales both I and the long range coupling term."
notation ap "gamma"

gamma (GenericLinear parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/GenericLinear/parameters/gamma

Slope parameter of the state-variable 'x_GL', representing the inverse of the relaxation time. Note: The ‘minus’ sign for the self-connections, scaled by 'gamma_GL', guarantees that the nodes have a stable equilibrium point (ref).
belongs to
Parameter c
has facts
description ap "Slope parameter of the state-variable 'x_GL', representing the inverse of the relaxation time"
default Value ap "-10.0"^^double
definition ap "Slope parameter of the state-variable 'x_GL', representing the inverse of the relaxation time. Note: The ‘minus’ sign for the self-connections, scaled by 'gamma_GL', guarantees that the nodes have a stable equilibrium point (ref)."
notation ap "gamma"

gamma (KIonEx parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/parameters/gamma

conversion factor
belongs to
Parameter c
has facts
description ap "conversion factor"
default Value ap "0.04"^^double
definition ap "conversion factor"
notation ap "gamma"

gamma (ReducedWongWang parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWang/parameters/gamma

Kinetic parameter
belongs to
Parameter c
has facts
description ap "Kinetic parameter"
default Value ap "0.641"^^double
definition ap "Kinetic parameter"
notation ap "gamma"

gamma (ReducedWongWangTvboptim parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWangTvboptim/parameters/gamma

Kinetic parameter governing the rate of NMDA channel dynamics.
belongs to
Parameter c
has facts
description ap "Kinetic parameter"
default Value ap "0.641"^^double
definition ap "Kinetic parameter governing the rate of NMDA channel dynamics."
notation ap "gamma"

gamma (StefanescuJirsa3D state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa3D/state_variables/gamma

belongs to
StateVariable c
has facts
description ap "Inhibitory slow adaptation variable (per mode)."
has Db Xref ap G O 0060080 ep
notation ap "gamma"
lhs ap "Derivative(gamma, t)"
rhs ap "r*s*alpha - r*gamma - n_i"

gamma_1 (ZetterbergJansen parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZetterbergJansen/parameters/gamma_1

Average number of synapses between populations (pyramidal to stellate).
belongs to
Parameter c
has facts
description ap "Average number of synapses between populations (pyramidal to stellate)"
default Value ap "135.0"^^double
has Db Xref ap C L 0000598 ni
has Db Xref ap G O 0099536 ep
definition ap "Average number of synapses between populations (pyramidal to stellate)."
notation ap "gamma_1"

gamma_1T (ZetterbergJansen parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZetterbergJansen/parameters/gamma_1T

Coupling factor from the extrinisic input to the spiny stellate population.
belongs to
Parameter c
has facts
description ap "Coupling factor from the extrinisic input to the spiny stellate population"
default Value ap "1.0"^^double
has Db Xref ap G O 0099536 ep
definition ap "Coupling factor from the extrinisic input to the spiny stellate population."
notation ap "gamma_1T"

gamma_2 (ZetterbergJansen parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZetterbergJansen/parameters/gamma_2

Average number of synapses between populations (stellate to pyramidal).
belongs to
Parameter c
has facts
description ap "Average number of synapses between populations (stellate to pyramidal)"
default Value ap "108.0"^^double
has Db Xref ap G O 0099536 ep
definition ap "Average number of synapses between populations (stellate to pyramidal)."
notation ap "gamma_2"

gamma_2T (ZetterbergJansen parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZetterbergJansen/parameters/gamma_2T

Coupling factor from the extrinisic input to the pyramidal population.
belongs to
Parameter c
has facts
description ap "Coupling factor from the extrinisic input to the pyramidal population"
default Value ap "1.0"^^double
has Db Xref ap C L 0000598 ni
has Db Xref ap G O 0099536 ep
definition ap "Coupling factor from the extrinisic input to the pyramidal population."
notation ap "gamma_2T"

gamma_3 (ZetterbergJansen parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZetterbergJansen/parameters/gamma_3

Connectivity constant (pyramidal to interneurons)
belongs to
Parameter c
has facts
description ap "Connectivity constant (pyramidal to interneurons)"
default Value ap "33.75"^^double
has Db Xref ap C L 0000099 ni
has Db Xref ap C L 0000598 ni
has Db Xref ap G O 0099536 ep
definition ap "Connectivity constant (pyramidal to interneurons)"
notation ap "gamma_3"

gamma_3T (ZetterbergJansen parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZetterbergJansen/parameters/gamma_3T

Coupling factor from the extrinisic input to the inhibitory population.
belongs to
Parameter c
has facts
description ap "Coupling factor from the extrinisic input to the inhibitory population"
default Value ap "1.0"^^double
has Db Xref ap G O 0099536 ep
definition ap "Coupling factor from the extrinisic input to the inhibitory population."
notation ap "gamma_3T"

gamma_4 (ZetterbergJansen parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZetterbergJansen/parameters/gamma_4

Connectivity constant (interneurons to pyramidal)
belongs to
Parameter c
has facts
description ap "Connectivity constant (interneurons to pyramidal)"
default Value ap "33.75"^^double
has Db Xref ap C L 0000099 ni
has Db Xref ap C L 0000598 ni
definition ap "Connectivity constant (interneurons to pyramidal)"
notation ap "gamma_4"

gamma_5 (ZetterbergJansen parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZetterbergJansen/parameters/gamma_5

Connectivity constant (interneurons to interneurons)
belongs to
Parameter c
has facts
description ap "Connectivity constant (interneurons to interneurons)"
default Value ap "15.0"^^double
has Db Xref ap C L 0000099 ni
definition ap "Connectivity constant (interneurons to interneurons)"
notation ap "gamma_5"

gamma_e (ReducedWongWangExcInh parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWangExcInh/parameters/gamma_e

Excitatory population kinetic parameter
belongs to
Parameter c
has facts
description ap "Excitatory population kinetic parameter"
default Value ap "6.41E-4"^^double
has Db Xref ap G O 0060079 ep
definition ap "Excitatory population kinetic parameter"
notation ap "gamma_e"

gamma_i (ReducedWongWangExcInh parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWangExcInh/parameters/gamma_i

Inhibitory population kinetic parameter
belongs to
Parameter c
has facts
description ap "Inhibitory population kinetic parameter"
default Value ap "0.001"^^double
has Db Xref ap G O 0060080 ep
definition ap "Inhibitory population kinetic parameter"
notation ap "gamma_i"

gamma_rs (EpileptorRestingState parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/EpileptorRestingState/parameters/gamma_rs

Constant parameter to reproduce FHN dynamics where excitatory input currents are negative. Note: It scales both I_rs and the long-range coupling term.
belongs to
Parameter c
has facts
description ap "Constant parameter to reproduce FHN dynamics where excitatory input currents are negative"
default Value ap "1.0"^^double
definition ap "Constant parameter to reproduce FHN dynamics where excitatory input currents are negative. Note: It scales both I_rs and the long-range coupling term."
notation ap "gamma_rs"

Gast2020ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Gast2020

belongs to
Scholarly article c
has facts
issued ap "2020"
title ap "A mean-field description of bursting dynamics in neural populations"
author ap "Gast, Richard"
author ap "Kn\"osche, T. R."
author ap "Schmidt, Helmut"
is Part Of ap "PLOS Computational Biology"

GastSchmidtKnosche_SDni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/GastSchmidtKnosche_SD

belongs to
Dynamics c
has facts
exhibits bifurcation op ""
exhibits regime op Oscillatory ni
exhibits regime op Quiescent ni
has attractor op Fixed point ni
has attractor op Limit cycle ni
has stochasticity character op Deterministic ni
models anatomical region op U B E R O N 0000956 ni
models neurotransmitter system op G O 0035249 ni
phase-space dimension dp "4"^^integer
description ap "4D model describing the Ott-Antonsen reduction of infinite all-to-all coupled QIF neurons (Theta-neurons) with Synaptic Depression adaptation mechanisms [Gastetal_2020]_. The two state variables :math:`r` and :math:`V` represent the average firing rate and the average membrane potential of our QIF neurons. :math:`A` and :math:`B` are respectively the adaptation variable and its derivative. The equations of the infinite QIF 2D population model read .. math:: \dot{r} &= 1/\tau (\Delta/(\pi \tau) + 2 V r)\\ \dot{V} &= 1/\tau (V^2 - \tau^2 \pi^2 r^2 + \eta + J \tau r (1 - A) + I)\\ \dot{A} &= 1/\tau_A (B)\\ \dot{B} &= 1/\tau_A (-2 B - A + \alpha r) \\ .. [Gastetal_2020] Gast, R., Schmidt, H., & Knösche, T. R. (2020). A mean-field description of bursting dynamics in spiking neural networks with short-term adaptation. *Neural Computation*, 32(9), 1615-1634."
references ap Gast2020 ni
pref Label ap "Gast-Schmidt-Knosche (synaptic depression)"@en
has Parameter ap Delta (GastSchmidtKnosche_SD parameter) ni
has Parameter ap I (GastSchmidtKnosche_SD parameter) ni
has Parameter ap J (GastSchmidtKnosche_SD parameter) ni
has Parameter ap alpha (GastSchmidtKnosche_SD parameter) ni
has Parameter ap cr (GastSchmidtKnosche_SD parameter) ni
has Parameter ap cv (GastSchmidtKnosche_SD parameter) ni
has Parameter ap eta (GastSchmidtKnosche_SD parameter) ni
has Parameter ap tau (GastSchmidtKnosche_SD parameter) ni
has Parameter ap tau_A (GastSchmidtKnosche_SD parameter) ni
has State Variable ap A (GastSchmidtKnosche_SD state variable) ni
has State Variable ap B (GastSchmidtKnosche_SD state variable) ni
has State Variable ap V (GastSchmidtKnosche_SD state variable) ni
has State Variable ap r (GastSchmidtKnosche_SD state variable) ni
model_type (slot) ap "neural_mass"

Generic2dOscillatorni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Generic2dOscillator

belongs to
Dynamics c
has facts
exhibits bifurcation op ""
exhibits bifurcation op ""
exhibits regime op Bistable ni
exhibits regime op Excitable ni
exhibits regime op Oscillatory ni
has attractor op Fixed point ni
has attractor op Limit cycle ni
has stochasticity character op Deterministic ni
has timescale separation dp "true"^^boolean
phase-space dimension dp "2"^^integer
description ap "The Generic 2-Dimensional Oscillator (G2D) is a phenomenological, coupled, nonlinear two-dimensional (i.e., two state-variables ('V', 'W')) oscillatory, neural mass model. The G2D is a generalization of the well-known FitzHugh-Nagumo model (FitzHugh, 1961; Nagumo et. al, 1962), adapted here for reproducing a wilder class of dynamical configurations of physiological phenomena as observed in neuronal population using phase-portrait method."
references ap FitzHugh1961 ni
references ap Nagumo1962 ni
pref Label ap "Generic 2-D oscillator"@en
has Parameter ap I (Generic2dOscillator parameter) ni
has Parameter ap a (Generic2dOscillator parameter) ni
has Parameter ap alpha (Generic2dOscillator parameter) ni
has Parameter ap b (Generic2dOscillator parameter) ni
has Parameter ap beta (Generic2dOscillator parameter) ni
has Parameter ap c (Generic2dOscillator parameter) ni
has Parameter ap d (Generic2dOscillator parameter) ni
has Parameter ap e (Generic2dOscillator parameter) ni
has Parameter ap f (Generic2dOscillator parameter) ni
has Parameter ap g (Generic2dOscillator parameter) ni
has Parameter ap gamma (Generic2dOscillator parameter) ni
has Parameter ap tau (Generic2dOscillator parameter) ni
has State Variable ap V (Generic2dOscillator state variable) ni
has State Variable ap W (Generic2dOscillator state variable) ni
model_type (slot) ap "generic"

GenericLinearni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/GenericLinear

belongs to
Dynamics c
has facts
exhibits regime op Quiescent ni
has attractor op Fixed point ni
has stochasticity character op Deterministic ni
has timescale separation dp "false"^^boolean
phase-space dimension dp "1"^^integer
description ap "The Generic Linear (GL) is a phenomenological, linear one-dimensional (i.e., one state-variable ('x')) neural mass model (Galán, 2008)."
references ap Galan2008 ni
pref Label ap "Generic linear"@en
has Parameter ap gamma (GenericLinear parameter) ni
has State Variable ap x (GenericLinear state variable) ni
model_type (slot) ap "generic"

GENESISni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/GENESIS

belongs to
Software package c
has facts
description ap "GEneral NEural SImulation System — one of the earliest simulators for biologically realistic modeling of neural systems, from sub-cellular components to large networks."
license ap "GPL-2.0-only"
code Repository ap "https://github.com/genesis-sim/genesis-2.4"
url ap "http://www.genesis-sim.org"

GeNNni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/GeNN

belongs to
Software package c
has facts
description ap "GPU Enhanced Neuronal Networks — a framework for GPU-accelerated spiking neural network simulations using NVIDIA CUDA. Generates optimized GPU kernels from model descriptions."
license ap "GPL-2.0-only"
code Repository ap "https://github.com/genn-team/genn"
identifier ap "10.1038/s43588-022-00222-7"
url ap "https://genn-team.github.io/genn/"

Gissinger2012ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Gissinger2012

belongs to
Scholarly article c
has facts
issued ap "2012"
title ap "A New Deterministic Model of Chaotic Reversals"
author ap "Gissinger, Christophe"
identifier ap "10.1140/epjb/e2012-30024-x"
is Part Of ap "The European Physical Journal B"
issue Number ap "4"
pagination ap "137"
volume Number ap "85"

GlobalAverageni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/observation_models/global_average

belongs to
Observation c
has facts
description ap "Spatial mean across all network nodes at each sampling period. Reduces spatial dimension to a single global signal per state variable."

GPU executionni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/GPUSupport

belongs to
Backend capability c

Gradient-based optimisationni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/GradientBasedOptimization

belongs to
Simulation task c

Grebogi1983ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Grebogi1983

belongs to
Scholarly article c
has facts
issued ap "1983"
title ap "Final state sensitivity: An obstruction to predictability"
author ap "Grebogi, Celso"
author ap "McDonald, S. W."
author ap "Ott, Edward"
author ap "Yorke, James A."
is Part Of ap "Physics Letters A"
issue Number ap "9"
pagination ap "373--375"
volume Number ap "99"

Greene1979ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Greene1979

belongs to
Scholarly article c
has facts
issued ap "1979"
title ap "A Method for Determining a Stochastic Transition"
author ap "Greene, J. M."
identifier ap "10.1201/9781003069515-23"
is Part Of ap "Journal of Mathematical Physics"
pagination ap "1183--1201"
volume Number ap "20"

Guckenheimer1983ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Guckenheimer1983

belongs to
Book c
has facts
issued ap "1983"
title ap "Nonlinear Oscillations, Dynamical Systems, and Bifurcations of Vector Fields"
author ap "Guckenheimer, John"
author ap "Holmes, Philip"
identifier ap "10.1007/978-1-4612-1140-2"
publisher ap "Springer"
volume Number ap "42"

GuckenheimerHolmes1983ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/GuckenheimerHolmes1983

belongs to
Book c
has facts
issued ap "1983"
title ap "Nonlinear Oscillations, Dynamical Systems, and Bifurcations of Vector Fields"
author ap "Guckenheimer, John"
author ap "Holmes, Philip"
publisher ap "Springer"
volume Number ap "42"

GuckenheimerHolmes1983Aliasni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/GuckenheimerHolmes1983Alias

belongs to
Scholarly article c
has facts
title ap "Alias for GuckenheimerHolmes1983"

h (Epileptor2D derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor2D/derived_variables/h

belongs to
DerivedVariable c
has facts
notation ap "h"
lhs ap "h"
rhs ap "Piecewise((x0 + 3.0/(exp((-x1 - 1*0.5)/0.1) + 1.0), modification > 0), (zcond + 4*(-x0 + x1), True))"

h (Epileptor5D derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor5D/derived_variables/h

belongs to
DerivedVariable c
has facts
notation ap "h"
lhs ap "h"
rhs ap "Piecewise((x0 + 3/(exp((-x1 - 1*0.5)/0.1) + 1), modification > 0), (zcond + 4*(-x0 + x1), True))"

h (KIonEx derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/derived_variables/h

belongs to
DerivedVariable c
has facts
notation ap "h"
lhs ap "h"
rhs ap "1.1 - 1.0/(1.0 + 24.5325301971094*exp(-8.0*n))"

H (PreSigmoidal parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/coupling_functions/PreSigmoidal/parameters/H

belongs to
Parameter c
has facts
description ap "Global Factor"
default Value ap "0.5"^^double
notation ap "H"

H (ReducedWongWang derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWang/derived_variables/H

belongs to
DerivedVariable c
has facts
description ap "Sigmoid input-output function of the synaptic input current, x_RWW, that computes the averaged firing rate of the neurons population (Deco et al., 2013)."
has Db Xref ap G O 0099605 ep
notation ap "H"
lhs ap "H"
rhs ap "(a*x - b)/(1 - exp(-d*(a*x - b)))"

H_e (ReducedWongWangExcInh derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWangExcInh/derived_variables/H_e

belongs to
DerivedVariable c
has facts
description ap "Sigmoid function that computes the averaged firing rate of the excitatory neuron population IE_RWW_EI (Deco et al., 2014; Abbott & Chance, 2005)."
has Db Xref ap G O 0060079 ep
has Db Xref ap G O 0099605 ep
notation ap "H_e"
lhs ap "H_e"
rhs ap "x_e/(1 - exp(-d_e*x_e))"

H_i (ReducedWongWangExcInh derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWangExcInh/derived_variables/H_i

belongs to
DerivedVariable c
has facts
description ap "Sigmoid function that computes the averaged firing rate of the inhibitory neuron population II_RWW (Deco et al., 2014; Abbott & Chance, 2005)."
has Db Xref ap G O 0060080 ep
has Db Xref ap G O 0099605 ep
notation ap "H_i"
lhs ap "H_i"
rhs ap "x_i/(1 - exp(-d_i*x_i))"

h_i (StefanescuJirsa3D derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa3D/derived_variables/h_i

belongs to
DerivedVariable c
has facts
description ap "Per-mode constant for the inhibitory beta dynamics."
notation ap "h_i"
lhs ap "h_i"
rhs ap "c"

H_x (ReducedWongWangTvboptim derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWangTvboptim/derived_variables/H_x

belongs to
DerivedVariable c
has facts
description ap "Average population firing rate H evaluated at the total synaptic input x."
notation ap "H_x"
lhs ap "H_x"
rhs ap "H(x)"

Halvorsen2000ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Halvorsen2000

belongs to
Creative work c
has facts
issued ap "2000"
title ap "An algebraically simple chaotic system"
author ap "Halvorsen, E."

He (ZetterbergJansen parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZetterbergJansen/parameters/He

Maximum amplitude of EPSP [mV]. Also called average synaptic gain.
belongs to
Parameter c
has facts
description ap "Maximum amplitude of EPSP [mV]"
default Value ap "3.25"^^double
has Db Xref ap G O 0060079 ep
has Db Xref ap G O 0098815 ep
definition ap "Maximum amplitude of EPSP [mV]. Also called average synaptic gain."
notation ap "He"

Henon1964ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Henon1964

belongs to
Scholarly article c
has facts
issued ap "1964"
title ap "The Applicability of the Third Integral of Motion: Some Numerical Experiments"
author ap "Heiles, Carl"
author ap "Henon, Michel"
identifier ap "10.1086/109234"
is Part Of ap "The Astronomical Journal"
pagination ap "73--79"
volume Number ap "69"

Henon1976ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Henon1976

belongs to
Scholarly article c
has facts
issued ap "1976"
title ap "A Two-Dimensional Mapping with a Strange Attractor"
author ap "H\'enon, Michel"
identifier ap "10.1007/978-0-387-21830-4_8"
is Part Of ap "Communications in Mathematical Physics"
pagination ap "69--77"
volume Number ap "50"

HenonHeiles1964ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/HenonHeiles1964

belongs to
Scholarly article c
has facts
issued ap "1964"
title ap "The Applicability of the Third Integral of Motion: Some Numerical Experiments"
author ap "H\'enon, Michel"
author ap "Heiles, Carl"
identifier ap "10.1086/109234"
is Part Of ap "The Astronomical Journal"
pagination ap "73--79"
volume Number ap "69"

Heunni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/integrators/Heun

belongs to
Integrator c

Hi (ZetterbergJansen parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZetterbergJansen/parameters/Hi

Maximum amplitude of IPSP [mV]. Also called average synaptic gain.
belongs to
Parameter c
has facts
description ap "Maximum amplitude of IPSP [mV]"
default Value ap "22.0"^^double
has Db Xref ap G O 0060080 ep
has Db Xref ap G O 0098828 ep
definition ap "Maximum amplitude of IPSP [mV]. Also called average synaptic gain."
notation ap "Hi"

Hindmarsh1984ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Hindmarsh1984

belongs to
Scholarly article c
has facts
issued ap "1984"
title ap "A model of neuronal bursting using three coupled first order differential equations"
author ap "Hindmarsh, J. L."
author ap "Rose, R. M."
is Part Of ap "Proceedings of the Royal Society of London. Series B, Biological Sciences"
pagination ap "87--102"
volume Number ap "221"

HindmarshRose1984ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/HindmarshRose1984

belongs to
Scholarly article c
has facts
issued ap "1984"
title ap "A model of neuronal bursting using three coupled first order differential equations"
author ap "Hindmarsh, J. L."
author ap "Rose, R. M."
is Part Of ap "Proceedings of the Royal Society of London. Series B, Biological Sciences"
pagination ap "87--102"
volume Number ap "221"

HNN-coreni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/HNN-core

belongs to
Software package c
has facts
description ap "Human Neocortical Neurosolver — a tool for simulating the cellular and network-level origin of MEG/EEG signals using biophysically detailed neocortical column models on NEURON."
license ap "BSD-3-Clause"
code Repository ap "https://github.com/jonescompneurolab/hnn-core"
identifier ap "10.1523/ENEURO.0460-21.2022"
url ap "https://jonescompneurolab.github.io/hnn-core/"

Hodgkin1952ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Hodgkin1952

belongs to
Scholarly article c
has facts
issued ap "1952"
title ap "A Quantitative Description of Membrane Current and Its Application to Conduction and Excitation in Nerve"
author ap "Hodgkin, A. L."
author ap "Huxley, A. F."
identifier ap "10.1113/jphysiol.1952.sp004764"
is Part Of ap "The Journal of Physiology"
issue Number ap "4"
pagination ap "500--544"
volume Number ap "117"

HodgkinHuxley1952ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/HodgkinHuxley1952

belongs to
Scholarly article c
has facts
issued ap "1952"
title ap "A Quantitative Description of Membrane Current and Its Application to Conduction and Excitation in Nerve"
author ap "Hodgkin, A. L."
author ap "Huxley, A. F."
identifier ap "10.1113/jphysiol.1952.sp004764"
is Part Of ap "The Journal of Physiology"
issue Number ap "4"
pagination ap "500--544"
volume Number ap "117"

Hoover1995ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Hoover1995

belongs to
Scholarly article c
has facts
issued ap "1995"
title ap "Remark on ``Some Simple Chaotic Flows''"
author ap "Hoover, William G."
identifier ap "10.1103/PhysRevE.51.759"
is Part Of ap "Physical Review E"
pagination ap "759--760"
volume Number ap "51"

Hopfieldni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Hopfield

belongs to
Dynamics c
has facts
exhibits regime op Multistable ni
has attractor op Fixed point ni
has model feature op Sigmoid activation ni
has stochasticity character op Deterministic ni
phase-space dimension dp "2"^^integer
description ap "The Hopfield neural network is a discrete time dynamical system composed of multiple binary nodes, with a connectivity matrix built from a predetermined set of patterns. The update, inspired from the spin-glass model (used to describe magnetic properties of dilute alloys), is based on a random scanning of every node. The existence of a fixed point dynamics is guaranteed by a Lyapunov function. The Hopfield network is expected to have those multiple patterns as attractors (multistable dynamical system). When the initial conditions are close to one of the 'learned' patterns, the dynamical system is expected to relax on the corresponding attractor. A possible output of the system is the final attractive state (interpreted as an associative memory). Various extensions of the initial model have been proposed, among which a noiseless and continuous version [Hopfield 1984] having a slightly different Lyapunov function, but essentially the same dynamical properties, with more straightforward physiological Interpretation. A continuous Hopfield neural network (with a sigmoid transfer function) can indeed be interpreted as a network of neural masses with every node corresponding to the mean field activity of a local brain region, with many bridges with the Wilson Cowan model [WC_1972]. Note: - This model uses the modifications implemented by Golos et al. (2015)."
references ap Hopfield1982 ni
references ap Hopfield1984 ni
pref Label ap "Hopfield"@en
has Parameter ap tauT (Hopfield parameter) ni
has Parameter ap taux (Hopfield parameter) ni
has State Variable ap theta (Hopfield state variable) ni
has State Variable ap x (Hopfield state variable) ni
model_type (slot) ap "neural_mass"

Hopfield1982ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Hopfield1982

belongs to
Scholarly article c
has facts
issued ap "1982"
title ap "Neural networks and physical systems with emergent collective computational abilities"
author ap "Hopfield, John J."
is Part Of ap "Proceedings of the National Academy of Sciences"

Hopfield1984ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Hopfield1984

belongs to
Scholarly article c
has facts
issued ap "1984"
title ap "Neurons with graded response have collective computational properties like those of two-state neurons"
author ap "Hopfield, John J."
is Part Of ap "Proceedings of the National Academy of Sciences"

Hoppensteadt2006ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Hoppensteadt2006

belongs to
Scholarly article c
has facts
issued ap "2006"
title ap "Predator-prey model"
author ap "Hoppensteadt, Frank"
is Part Of ap "Scholarpedia"
issue Number ap "10"
pagination ap "1563"
volume Number ap "1"

hrf_length (bold_region_roi parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/observation_models/bold_region_roi/parameters/hrf_length

belongs to
Parameter c
has facts
default Value ap "20000.0"^^double
notation ap "hrf_length"
unit (slot) dp "ms"

Huisman2001ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Huisman2001

belongs to
Scholarly article c
has facts
issued ap "2001"
title ap "Fundamental Unpredictability in Multispecies Competition"
author ap "Huisman, Johan"
author ap "Weissing, Franz J."
is Part Of ap "The American Naturalist"
issue Number ap "5"
volume Number ap "157"

Hussain2015ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Hussain2015

belongs to
Scholarly article c
has facts
issued ap "2015"
title ap "Construction of dynamical non-linear components based on Lorenz system and symmetric group of permutations"
author ap "Gondal, M. A."
author ap "Hussain, A."
author ap "Hussain, I."
is Part Of ap "3D Research"
pagination ap "1--6"
volume Number ap "6"

HyperbolicTangentni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/coupling_functions/HyperbolicTangent

belongs to
Coupling c
has facts
has Parameter ap a (HyperbolicTangent parameter) ni
has Parameter ap b (HyperbolicTangent parameter) ni
has Parameter ap midpoint (HyperbolicTangent parameter) ni
has Parameter ap sigma (HyperbolicTangent parameter) ni

I (GastSchmidtKnosche_SD parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/GastSchmidtKnosche_SD/parameters/I

External homogeneous current
belongs to
Parameter c
has facts
description ap "External homogeneous current"
default Value ap "0.0"^^double
definition ap "External homogeneous current"
notation ap "I"

I (GastSchmidtKnosche_SF parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/GastSchmidtKnosche_SF/parameters/I

External homogeneous current
belongs to
Parameter c
has facts
description ap "External homogeneous current"
default Value ap "0.0"^^double
definition ap "External homogeneous current"
notation ap "I"

I (Generic2dOscillator parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Generic2dOscillator/parameters/I

Baseline shift of the cubic nullcline
belongs to
Parameter c
has facts
description ap "Baseline shift of the cubic nullcline"
default Value ap "0.0"^^double
has Db Xref ap G O 0060079 ep
definition ap "Baseline shift of the cubic nullcline"
notation ap "I"

I (Kuramoto derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Kuramoto/derived_variables/I

belongs to
DerivedVariable c
has facts
description ap "Input via local and long range connectivity, passing first through the Kuramoto coupling function"
notation ap "I"
lhs ap "I"
rhs ap "c_pop0 + lc_0"

I (KuramotoModel2 derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KuramotoModel2/derived_variables/I

belongs to
DerivedVariable c
has facts
description ap "`I` is the input via local and long range connectivity, passing first through the Kuramoto coupling function"
notation ap "I"
lhs ap "I"
rhs ap "c_glob+lc_0"

I (MontbrioPazoRoxin parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/MontbrioPazoRoxin/parameters/I

External Current
belongs to
Parameter c
has facts
description ap "External Current"
default Value ap "0.0"^^double
definition ap "External Current"
notation ap "I"

I (WilsonCowan state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/WilsonCowan/state_variables/I

belongs to
StateVariable c
has facts
description ap "State-variable of the Wilson and Cowan model (Wilson and Cowan, 1973), denoting the mean firing rate of all inhibitory neurons of the population"
has Db Xref ap G O 0060080 ep
notation ap "I"
lhs ap "Derivative(I, t)"
rhs ap "(-I + s_i*(-I*r_i + k_i))/tau_i"

I (ZerlautAdaptationFirstOrder state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/state_variables/I

belongs to
StateVariable c
has facts
description ap "Firing rate of inhibitory population in KHz"
notation ap "I"
lhs ap "Derivative(I, t)"
rhs ap "(-I + f_out_i)/T"

I_A (CakanObermayer parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/CakanObermayer/parameters/I_A

Subthreshold adaptation conductance amplitude (a in AdEx).
belongs to
Parameter c
has facts
default Value ap "0.0"^^double
has Db Xref ap G O 0060079 ep
definition ap "Subthreshold adaptation conductance amplitude (a in AdEx)."
notation ap "I_A"
unit (slot) dp "nS"

I_A_var (CakanObermayer state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/CakanObermayer/state_variables/I_A_var

belongs to
StateVariable c
has facts
description ap "Adaptation current."
notation ap "I_A_var"
lhs ap "Derivative(I_A_var, t)"
rhs ap "(I_A*(mu_se - E_A) - I_A_var)/tau_A"

I_Cl (KIonEx derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/derived_variables/I_Cl

belongs to
DerivedVariable c
has facts
notation ap "I_Cl"
lhs ap "I_Cl"
rhs ap "g_Cl*(V + 26.64*log(Cl_o0/Cl_i0))"

I_e (DumontGutkin parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/DumontGutkin/parameters/I_e

External homogeneous current on excitatory population
belongs to
Parameter c
has facts
description ap "External homogeneous current on excitatory population"
default Value ap "0.0"^^double
has Db Xref ap G O 0060079 ep
definition ap "External homogeneous current on excitatory population"
notation ap "I_e"

I_ext (LarterBreakspear parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/LarterBreakspear/parameters/I_ext

Subcortical input current. Represents a non-specific excitation or thalamic inputs.
belongs to
Parameter c
has facts
description ap "Subcortical input current"
default Value ap "0.3"^^double
has Db Xref ap G O 0060079 ep
definition ap "Subcortical input current. Represents a non-specific excitation or thalamic inputs."
notation ap "I_ext"

I_ext (ReducedWongWangExcInh parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWangExcInh/parameters/I_ext

External stimulation parameter for evoked potential simulated activity applied to the excitatory population firing rate IE (Deco et al., 2014).
belongs to
Parameter c
has facts
description ap "External stimulation parameter for evoked potential simulated activity applied to the excitatory population firing rate IE (Deco et al"
default Value ap "0.0"^^double
has Db Xref ap G O 0060079 ep
has Db Xref ap G O 0099605 ep
definition ap "External stimulation parameter for evoked potential simulated activity applied to the excitatory population firing rate IE (Deco et al., 2014)."
notation ap "I_ext"

I_i (DumontGutkin parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/DumontGutkin/parameters/I_i

External current on inhibitory population
belongs to
Parameter c
has facts
description ap "External current on inhibitory population"
default Value ap "0.0"^^double
has Db Xref ap G O 0060080 ep
has Db Xref ap G O 0098828 ep
definition ap "External current on inhibitory population"
notation ap "I_i"

I_K (KIonEx derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/derived_variables/I_K

belongs to
DerivedVariable c
has facts
notation ap "I_K"
lhs ap "I_K"
rhs ap "(V - 26.64*log(K_o/K_i))*(g_K*n + g_Kl)"

I_Na (KIonEx derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/derived_variables/I_Na

belongs to
DerivedVariable c
has facts
notation ap "I_Na"
lhs ap "I_Na"
rhs ap "(V - 26.64*log(Na_o/Na_i))*(g_Na*h*minf + g_Nal)"

I_o (ReducedWongWang parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWang/parameters/I_o

External input current to the neurons population (Deco et al., 2013). Note: ------ In TVB, the default value is set to 0.33 (instead of 0.30 as in Deco et al. (2013)) for setting the system is bistability (see Hansen et al., 2015).
belongs to
Parameter c
has facts
description ap "External input current to the neurons population (Deco et al"
default Value ap "0.33"^^double
definition ap "External input current to the neurons population (Deco et al., 2013). Note: ------ In TVB, the default value is set to 0.33 (instead of 0.30 as in Deco et al. (2013)) for setting the system is bistability (see Hansen et al., 2015)."
notation ap "I_o"
unit (slot) dp "nA"

I_o (ReducedWongWangExcInh parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWangExcInh/parameters/I_o

Effective external input parameter to the excitatory E and inhibitory I population (Deco et al., 2014).
belongs to
Parameter c
has facts
description ap "Effective external input parameter to the excitatory E and inhibitory I population (Deco et al"
default Value ap "0.382"^^double
has Db Xref ap G O 0060079 ep
has Db Xref ap G O 0060080 ep
definition ap "Effective external input parameter to the excitatory E and inhibitory I population (Deco et al., 2014)."
notation ap "I_o"
unit (slot) dp "nA"

I_o (ReducedWongWangTvboptim parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWangTvboptim/parameters/I_o

Effective external input current to each cortical population. Default 0.34 nA sets the system in bistability (Hansen et al., 2015). Together with w, this is a key parameter for fitting functional connectivity.
belongs to
Parameter c
has facts
description ap "External input current"
default Value ap "0.34"^^double
definition ap "Effective external input current to each cortical population. Default 0.34 nA sets the system in bistability (Hansen et al., 2015). Together with w, this is a key parameter for fitting functional connectivity."
notation ap "I_o"
unit (slot) dp "nA"

I_pump (KIonEx derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/derived_variables/I_pump

belongs to
DerivedVariable c
has facts
notation ap "I_pump"
lhs ap "I_pump"
rhs ap "1.0*rho/((exp((Ckp - K_o)/DCkp) + 1.0)*(exp((Cnap - Na_i)/DCnap) + 1.0))"

I_rs (EpileptorRestingState parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/EpileptorRestingState/parameters/I_rs

External input current to the third population (x_rs, y_rs).
belongs to
Parameter c
has facts
description ap "External input current to the third population (x_rs, y_rs)"
default Value ap "0.0"^^double
definition ap "External input current to the third population (x_rs, y_rs)."
notation ap "I_rs"

Identityni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/integrators/Identity

belongs to
Integrator c

IE_i (StefanescuJirsa2D derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa2D/derived_variables/IE_i

belongs to
DerivedVariable c
has facts
description ap "Per-mode constant excitatory input from the heterogeneity distribution."
has Db Xref ap G O 0042391 ep
notation ap "IE_i"
lhs ap "IE_i"
rhs ap "0.0"

IE_i (StefanescuJirsa3D derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa3D/derived_variables/IE_i

belongs to
DerivedVariable c
has facts
description ap "Per-mode constant excitatory input."
has Db Xref ap G O 0060079 ep
notation ap "IE_i"
lhs ap "IE_i"
rhs ap "0.0"

iEEGni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/observation_models/ieeg

belongs to
Observation c
has facts
description ap "Forward solution for intracranial/stereoelectroencephalography (SEEG). Projects source activity through a lead field matrix to implanted depth electrode contacts. Uses the same single-sphere analytic formula as scalp EEG (Sarvas 1987, Eq. 12), but with electrode positions inside the brain volume."
has Parameter ap conductivity (ieeg parameter) ni

Iext (Epileptor2D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor2D/parameters/Iext

External input current to the first state-variable x_E2D, in Epileptor2D (Proix et al.,2014).
belongs to
Parameter c
has facts
description ap "External input current to the first state-variable x_E2D, in Epileptor2D (Proix et al"
default Value ap "3.1"^^double
definition ap "External input current to the first state-variable x_E2D, in Epileptor2D (Proix et al.,2014)."
notation ap "Iext"

Iext (Epileptor5D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor5D/parameters/Iext

External input current to the first sub-population (x1_E5D, y1_E5D) via the state-variable x1_E5D, in Epileptor5D (Jirsa et al.,2014).
belongs to
Parameter c
has facts
description ap "External input current to the first sub-population (x1_E5D, y1_E5D) via the state-variable x1_E5D, in Epileptor5D (Jirsa et al"
default Value ap "3.1"^^double
definition ap "External input current to the first sub-population (x1_E5D, y1_E5D) via the state-variable x1_E5D, in Epileptor5D (Jirsa et al.,2014)."
notation ap "Iext"

Iext (EpileptorRestingState parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/EpileptorRestingState/parameters/Iext

External input current to the first population (x1, y1).
belongs to
Parameter c
has facts
description ap "External input current to the first population (x1, y1)"
default Value ap "3.1"^^double
definition ap "External input current to the first population (x1, y1)."
notation ap "Iext"

Iext2 (Epileptor5D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor5D/parameters/Iext2

External input current to the second population
belongs to
Parameter c
has facts
description ap "External input current to the second population"
default Value ap "0.45"^^double
definition ap "External input current to the second population"
notation ap "Iext2"

Iext2 (EpileptorRestingState parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/EpileptorRestingState/parameters/Iext2

External input current to the second population (x2, y2).
belongs to
Parameter c
has facts
description ap "External input current to the second population (x2, y2)"
default Value ap "0.45"^^double
definition ap "External input current to the second population (x2, y2)."
notation ap "Iext2"

II_i (StefanescuJirsa2D derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa2D/derived_variables/II_i

belongs to
DerivedVariable c
has facts
description ap "Per-mode constant inhibitory input from the heterogeneity distribution."
has Db Xref ap G O 0042391 ep
notation ap "II_i"
lhs ap "II_i"
rhs ap "0.0"

II_i (StefanescuJirsa3D derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa3D/derived_variables/II_i

belongs to
DerivedVariable c
has facts
description ap "Per-mode constant inhibitory input."
has Db Xref ap G O 0060080 ep
notation ap "II_i"
lhs ap "II_i"
rhs ap "0.0"

Inhibitionni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Inhibition

Generic hyperpolarising synaptic effect; abstract parent of model-specific inhibitory currents and conductances.
belongs to
SKOS Concept c
has facts
broad Match ap G O 0060080 ep
pref Label ap "Inhibition"@en

InternalCouplingni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/InternalCoupling

Within-population synaptic coupling, distinct from long-range inter-node coupling.
belongs to
SKOS Concept c
has facts
broad Match ap G O 0007268 ep
pref Label ap "InternalCoupling"@en

IzhikevichBookni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/IzhikevichBook

belongs to
Book c
has facts
issued ap "2007"
title ap "Dynamical Systems in Neuroscience: The Geometry of Excitability and Bursting"
author ap "Izhikevich, Eugene M."
publisher ap "MIT Press"

J (GastSchmidtKnosche_SD parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/GastSchmidtKnosche_SD/parameters/J

Synaptic weight
belongs to
Parameter c
has facts
description ap "Synaptic weight"
default Value ap "21.2132"^^double
has Db Xref ap G O 0099536 ep
definition ap "Synaptic weight"
notation ap "J"

J (GastSchmidtKnosche_SF parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/GastSchmidtKnosche_SF/parameters/J

Synaptic weight
belongs to
Parameter c
has facts
description ap "Synaptic weight"
default Value ap "21.2132"^^double
has Db Xref ap G O 0099536 ep
definition ap "Synaptic weight"
notation ap "J"

J (JansenRit parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/JansenRit/parameters/J

Average number of synapses between three neuronal populations of the model. It accounts for synaptic phenomena such as neurotransmitter depletion.
belongs to
Parameter c
has facts
description ap "Average number of synapses between three neuronal populations of the model"
default Value ap "135.0"^^double
has Db Xref ap G O 0051124 ep
has Db Xref ap G O 0150092 ep
definition ap "Average number of synapses between three neuronal populations of the model. It accounts for synaptic phenomena such as neurotransmitter depletion."
notation ap "J"

J (KIonEx parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/parameters/J

Mean Synaptic weight
belongs to
Parameter c
has facts
description ap "Mean Synaptic weight"
default Value ap "0.1"^^double
has Db Xref ap G O 0099536 ep
definition ap "Mean Synaptic weight"
notation ap "J"

J (MontbrioPazoRoxin parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/MontbrioPazoRoxin/parameters/J

Mean Synaptic weight.
belongs to
Parameter c
has facts
description ap "Mean Synaptic weight"
default Value ap "15.0"^^double
has Db Xref ap G O 0042391 ep
has Db Xref ap G O 0099536 ep
definition ap "Mean Synaptic weight."
notation ap "J"

J (TsodyksMarkram parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/TsodyksMarkram/parameters/J

belongs to
Parameter c
has facts
description ap "Synaptic coupling strength"
default Value ap "3.07"^^double
notation ap "J"

J_EE (CakanObermayer parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/CakanObermayer/parameters/J_EE

Maximum excitatory-to-excitatory PSC amplitude (Jee_max in neurolib).
belongs to
Parameter c
has facts
default Value ap "2.43"^^double
has Db Xref ap G O 0060076 ep
has Db Xref ap G O 0060079 ep
has Db Xref ap G O 0098817 ep
definition ap "Maximum excitatory-to-excitatory PSC amplitude (Jee_max in neurolib)."
notation ap "J_EE"
unit (slot) dp "mV_per_ms"

J_ee (DumontGutkin parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/DumontGutkin/parameters/J_ee

Synaptic weight e-->e
belongs to
Parameter c
has facts
description ap "Synaptic weight e-->e"
default Value ap "0.0"^^double
has Db Xref ap G O 0060076 ep
has Db Xref ap G O 0097060 ep
has Db Xref ap G O 0099536 ep
definition ap "Synaptic weight e-->e"
notation ap "J_ee"

J_EI (CakanObermayer parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/CakanObermayer/parameters/J_EI

Maximum inhibitory-to-excitatory PSC amplitude (Jei_max in neurolib, signed negative).
belongs to
Parameter c
has facts
default Value ap "-3.3"^^double
has Db Xref ap G O 0060080 ep
has Db Xref ap G O 0099536 ep
definition ap "Maximum inhibitory-to-excitatory PSC amplitude (Jei_max in neurolib, signed negative)."
notation ap "J_EI"
unit (slot) dp "mV_per_ms"

J_ei (DumontGutkin parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/DumontGutkin/parameters/J_ei

Synaptic weight i-->e
belongs to
Parameter c
has facts
description ap "Synaptic weight i-->e"
default Value ap "10.0"^^double
has Db Xref ap G O 0042391 ep
has Db Xref ap G O 0097060 ep
definition ap "Synaptic weight i-->e"
notation ap "J_ei"

J_i (ReducedWongWangExcInh parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWangExcInh/parameters/J_i

Local feedback inhibitory synaptic coupling to the excitatory population firing rate IE (Deco et al., 2014).
belongs to
Parameter c
has facts
description ap "Local feedback inhibitory synaptic coupling to the excitatory population firing rate IE (Deco et al"
default Value ap "1.0"^^double
has Db Xref ap G O 0060080 ep
has Db Xref ap G O 0099605 ep
definition ap "Local feedback inhibitory synaptic coupling to the excitatory population firing rate IE (Deco et al., 2014)."
notation ap "J_i"

J_IE (CakanObermayer parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/CakanObermayer/parameters/J_IE

Maximum excitatory-to-inhibitory PSC amplitude (Jie_max in neurolib).
belongs to
Parameter c
has facts
default Value ap "2.6"^^double
has Db Xref ap G O 0060079 ep
definition ap "Maximum excitatory-to-inhibitory PSC amplitude (Jie_max in neurolib)."
notation ap "J_IE"
unit (slot) dp "mV_per_ms"

J_ie (DumontGutkin parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/DumontGutkin/parameters/J_ie

Synaptic weight e-->i
belongs to
Parameter c
has facts
description ap "Synaptic weight e-->i"
default Value ap "0.0"^^double
has Db Xref ap G O 0097060 ep
has Db Xref ap G O 0099536 ep
definition ap "Synaptic weight e-->i"
notation ap "J_ie"

J_II (CakanObermayer parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/CakanObermayer/parameters/J_II

Maximum inhibitory-to-inhibitory PSC amplitude (Jii_max in neurolib, signed negative).
belongs to
Parameter c
has facts
default Value ap "-1.64"^^double
has Db Xref ap G O 0060080 ep
definition ap "Maximum inhibitory-to-inhibitory PSC amplitude (Jii_max in neurolib, signed negative)."
notation ap "J_II"
unit (slot) dp "mV_per_ms"

J_ii (DumontGutkin parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/DumontGutkin/parameters/J_ii

Synaptic weight i-->i
belongs to
Parameter c
has facts
description ap "Synaptic weight i-->i"
default Value ap "15.0"^^double
has Db Xref ap G O 0060077 ep
has Db Xref ap G O 0097060 ep
definition ap "Synaptic weight i-->i"
notation ap "J_ii"

J_N (ReducedWongWang parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWang/parameters/J_N

Excitatory recurrence
belongs to
Parameter c
has facts
description ap "Excitatory recurrence"
default Value ap "0.2609"^^double
has Db Xref ap G O 0098815 ep
definition ap "Excitatory recurrence"
notation ap "J_N"
unit (slot) dp "nA"

J_N (ReducedWongWangExcInh parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWangExcInh/parameters/J_N

Excitatory synaptic coupling parameter (Deco et al., 2014).
belongs to
Parameter c
has facts
description ap "Excitatory synaptic coupling parameter (Deco et al"
default Value ap "0.15"^^double
has Db Xref ap G O 0060079 ep
definition ap "Excitatory synaptic coupling parameter (Deco et al., 2014)."
notation ap "J_N"

J_N (ReducedWongWangTvboptim parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWangTvboptim/parameters/J_N

NMDA synaptic coupling strength. Scales both local recurrence and long-range network coupling inputs.
belongs to
Parameter c
has facts
description ap "NMDA synaptic coupling strength"
default Value ap "0.2609"^^double
definition ap "NMDA synaptic coupling strength. Scales both local recurrence and long-range network coupling inputs."
notation ap "J_N"
unit (slot) dp "nA"

J_N_S_e (ReducedWongWangExcInh derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWangExcInh/derived_variables/J_N_S_e

belongs to
DerivedVariable c
has facts
notation ap "J_N_S_e"
lhs ap "J_N_S_e"
rhs ap "J_N*S_e"

Jansen1993ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Jansen1993

belongs to
Scholarly article c
has facts
issued ap "1993"
title ap "Electroencephalogram and visual evoked potential generation in a mathematical model of coupled cortical columns"
author ap "Jansen, Ben H."
author ap "Rit, Vincent G."
is Part Of ap "Biological Cybernetics"

Jansen1995ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Jansen1995

belongs to
Scholarly article c
has facts
issued ap "1995"
title ap "Parameter exploration of a realistic neural mass model of visual cortex"
author ap "Jansen, Ben H."
author ap "Rit, Vincent G."
is Part Of ap "Biological Cybernetics"

JansenRitni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/JansenRit

belongs to
Dynamics c
has facts
exhibits bifurcation op ""
exhibits regime op Oscillatory ni
exhibits regime op Quiescent ni
has attractor op Fixed point ni
has attractor op Limit cycle ni
has model feature op Sigmoid activation ni
has stochasticity character op Deterministic ni
models anatomical region op U B E R O N 0000956 ni
models cell type op C L 0000099 ni
models cell type op C L 0000598 ni
models neurotransmitter system op G O 0007214 ni
models neurotransmitter system op G O 0035249 ni
has timescale separation dp "false"^^boolean
phase-space dimension dp "6"^^integer
description ap "The Jansen-Rit is a neurophysiologically-inspired neural mass model of a cortical column (or area), developed to simulate the electrical brain activity, i.e., the electroencephalogram (EEG), and evoked-potentials (EPs; Jansen et al., 1993; Jansen & Rit, 1995). It is a 6-dimensional, non-linear, model describing the local average states of three interconnected neural populations: pyramidal cells (PCs), excitatory and inhibitory interneurons (EINs and IINs), interacting through positive and negative feedback loops. The main output of the model is the average membrane potential of the pyramidal cell population, as the sum of the potential of these cells is thought to be the source of the potential recorded in the EEG."
references ap Jansen1993 ni
references ap Jansen1995 ni
pref Label ap "Jansen-Rit"@en
has Derived Variable ap sigma_y0_1 (JansenRit derived variable) ni
has Derived Variable ap sigma_y0_3 (JansenRit derived variable) ni
has Derived Variable ap sigma_y1_y2 (JansenRit derived variable) ni
has Parameter ap A (JansenRit parameter) ni
has Parameter ap B (JansenRit parameter) ni
has Parameter ap J (JansenRit parameter) ni
has Parameter ap a (JansenRit parameter) ni
has Parameter ap a_1 (JansenRit parameter) ni
has Parameter ap a_2 (JansenRit parameter) ni
has Parameter ap a_3 (JansenRit parameter) ni
has Parameter ap a_4 (JansenRit parameter) ni
has Parameter ap b (JansenRit parameter) ni
has Parameter ap mu (JansenRit parameter) ni
has Parameter ap nu_max (JansenRit parameter) ni
has Parameter ap r (JansenRit parameter) ni
has Parameter ap v0 (JansenRit parameter) ni
has State Variable ap y0 (JansenRit state variable) ni
has State Variable ap y1 (JansenRit state variable) ni
has State Variable ap y2 (JansenRit state variable) ni
has State Variable ap y3 (JansenRit state variable) ni
has State Variable ap y4 (JansenRit state variable) ni
has State Variable ap y5 (JansenRit state variable) ni
model_type (slot) ap "neural_mass"

JansenRit1995ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/JansenRit1995

belongs to
Dynamics c
has facts
exhibits bifurcation op ""
exhibits regime op Oscillatory ni
exhibits regime op Quiescent ni
has attractor op Fixed point ni
has attractor op Limit cycle ni
has model feature op Sigmoid activation ni
has stochasticity character op Deterministic ni
models anatomical region op U B E R O N 0000956 ni
phase-space dimension dp "6"^^integer
description ap "Lumped-parameter cortical column model with three neural populations: pyramidal cells, excitatory interneurons, and inhibitory interneurons. Each population is modeled by a PSP block (2nd-order linear filter) and a sigmoidal potential-to-firing-rate transformation. The model produces EEG-like output as the pyramidal PSP difference v_pyr = y1 - y2. Based on Lopes da Silva et al. (1974, 1976) and Jansen et al. (1993)."
pref Label ap "Jansen-Rit 1995"@en
has Derived Variable ap v_pyr (JansenRit1995 derived variable) ni
has Parameter ap A (JansenRit1995 parameter) ni
has Parameter ap B (JansenRit1995 parameter) ni
has Parameter ap C (JansenRit1995 parameter) ni
has Parameter ap a (JansenRit1995 parameter) ni
has Parameter ap b (JansenRit1995 parameter) ni
has Parameter ap e0 (JansenRit1995 parameter) ni
has Parameter ap p (JansenRit1995 parameter) ni
has Parameter ap r (JansenRit1995 parameter) ni
has Parameter ap v0 (JansenRit1995 parameter) ni
has State Variable ap y0 (JansenRit1995 state variable) ni
has State Variable ap y1 (JansenRit1995 state variable) ni
has State Variable ap y2 (JansenRit1995 state variable) ni
has State Variable ap y3 (JansenRit1995 state variable) ni
has State Variable ap y4 (JansenRit1995 state variable) ni
has State Variable ap y5 (JansenRit1995 state variable) ni
model_type (slot) ap "neural_mass"

jaxleyni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/jaxley

belongs to
Software package c
has facts
description ap "A differentiable simulator for biophysical neuron models built on JAX. Supports multi-compartment Hodgkin-Huxley models with automatic differentiation for gradient-based parameter inference."
license ap "Apache-2.0"
code Repository ap "https://github.com/jaxleyverse/jaxley"
identifier ap "10.7554/eLife.99205"
url ap "https://jaxley.readthedocs.io"

Jirsa2014ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Jirsa2014

belongs to
Scholarly article c
has facts
issued ap "2014"
title ap "On the nature of seizure dynamics"
author ap "Jirsa, Viktor"
author ap "others"
is Part Of ap "Brain"

jNeuroMLni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/jNeuroML

belongs to
Software package c
has facts
description ap "Java-based toolchain for NeuroML/LEMS model validation, simulation, and export to multiple simulator backends including NEURON, NEST, and Brian2."
license ap "LGPL-3.0-only"
code Repository ap "https://github.com/NeuroML/jNeuroML"
url ap "https://docs.neuroml.org/Userdocs/Software/jNeuroML.html"

JR Peak Frequency Optimizationni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/experiments/JR_MEG_FrequencyGradient_Optimization

belongs to
SimulationExperiment c
has facts
description ap "Reproducing MEG Resting-State Frequency Gradients with Network Dynamics. This experiment fits region-specific Jansen-Rit parameters to reproduce the empirical frequency gradient from visual cortex (11 Hz) to association areas (7 Hz). "

Julia JITni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/JuliaJIT

belongs to
Backend capability c

Just-in-time compilationni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/JITCompilation

belongs to
Backend capability c

k (CoombesByrne parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/CoombesByrne/parameters/k

Local coupling strength
belongs to
Parameter c
has facts
description ap "Local coupling strength"
default Value ap "1.0"^^double
definition ap "Local coupling strength"
notation ap "k"

k (CoombesByrne2D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/CoombesByrne2D/parameters/k

Local coupling strength
belongs to
Parameter c
has facts
description ap "Local coupling strength"
default Value ap "1.0"^^double
definition ap "Local coupling strength"
notation ap "k"

K11 (StefanescuJirsa2D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa2D/parameters/K11

Internal coupling, excitatory to excitatory.
belongs to
Parameter c
has facts
default Value ap "0.5"^^double
has Db Xref ap G O 0060079 ep
definition ap "Internal coupling, excitatory to excitatory."
notation ap "K11"

K12 (StefanescuJirsa2D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa2D/parameters/K12

Internal coupling, inhibitory to excitatory.
belongs to
Parameter c
has facts
default Value ap "0.15"^^double
has Db Xref ap G O 0060079 ep
definition ap "Internal coupling, inhibitory to excitatory."
notation ap "K12"

K21 (StefanescuJirsa2D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa2D/parameters/K21

Internal coupling, excitatory to inhibitory.
belongs to
Parameter c
has facts
default Value ap "0.15"^^double
has Db Xref ap G O 0060080 ep
definition ap "Internal coupling, excitatory to inhibitory."
notation ap "K21"

K_11 (StefanescuJirsa3D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa3D/parameters/K_11

Internal coupling, excitatory to excitatory.
belongs to
Parameter c
has facts
default Value ap "0.5"^^double
has Db Xref ap G O 0060079 ep
definition ap "Internal coupling, excitatory to excitatory."
notation ap "K_11"

K_12 (StefanescuJirsa3D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa3D/parameters/K_12

Internal coupling, inhibitory to excitatory.
belongs to
Parameter c
has facts
default Value ap "0.1"^^double
has Db Xref ap G O 0060080 ep
definition ap "Internal coupling, inhibitory to excitatory."
notation ap "K_12"

K_21 (StefanescuJirsa3D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa3D/parameters/K_21

Internal coupling, excitatory to inhibitory.
belongs to
Parameter c
has facts
default Value ap "0.15"^^double
has Db Xref ap G O 0060079 ep
definition ap "Internal coupling, excitatory to inhibitory."
notation ap "K_21"

K_bath (KIonEx parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/parameters/K_bath

Potassium concentration in bath
belongs to
Parameter c
has facts
description ap "Potassium concentration in bath"
default Value ap "5.5"^^double
has Db Xref ap G O 0055075 ep
definition ap "Potassium concentration in bath"
notation ap "K_bath"

k_e (WilsonCowan parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/WilsonCowan/parameters/k_e

Maximum value of the excitatory response function
belongs to
Parameter c
has facts
description ap "Maximum value of the excitatory response function"
default Value ap "1.0"^^double
has Db Xref ap G O 0060079 ep
definition ap "Maximum value of the excitatory response function"
notation ap "k_e"

K_ext_e (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/K_ext_e

Number of excitatory connexions from external population
belongs to
Parameter c
has facts
description ap "Number of excitatory connexions from external population"
default Value ap "400.0"^^double
definition ap "Number of excitatory connexions from external population"
notation ap "K_ext_e"

K_ext_i (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/K_ext_i

Number of inhibitory connexions from external population
belongs to
Parameter c
has facts
description ap "Number of inhibitory connexions from external population"
default Value ap "0.0"^^double
definition ap "Number of inhibitory connexions from external population"
notation ap "K_ext_i"

K_i (KIonEx derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/derived_variables/K_i

belongs to
DerivedVariable c
has facts
notation ap "K_i"
lhs ap "K_i"
rhs ap "DKi + K_i0"

k_i (WilsonCowan parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/WilsonCowan/parameters/k_i

Maximum value of the inhibitory response function
belongs to
Parameter c
has facts
description ap "Maximum value of the inhibitory response function"
default Value ap "1.0"^^double
has Db Xref ap G O 0060080 ep
definition ap "Maximum value of the inhibitory response function"
notation ap "k_i"

K_i0 (KIonEx parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/parameters/K_i0

initial concentration of intracellular K
belongs to
Parameter c
has facts
description ap "initial concentration of intracellular K"
default Value ap "130.0"^^double
definition ap "initial concentration of intracellular K"
notation ap "K_i0"
unit (slot) dp "mmol_per_m3"

K_o (KIonEx derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/derived_variables/K_o

belongs to
DerivedVariable c
has facts
notation ap "K_o"
lhs ap "K_o"
rhs ap "DK_o + K_o0 + Kg"

K_o0 (KIonEx parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/parameters/K_o0

initial concentration of extracellular K
belongs to
Parameter c
has facts
description ap "initial concentration of extracellular K"
default Value ap "4.8"^^double
definition ap "initial concentration of extracellular K"
notation ap "K_o0"
unit (slot) dp "mmol_per_m3"

k_phi (CakanObermayer parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/CakanObermayer/parameters/k_phi

Steepness of the sigmoid transfer-function surrogate.
belongs to
Parameter c
has facts
default Value ap "1.0"^^double
definition ap "Steepness of the sigmoid transfer-function surrogate."
notation ap "k_phi"

K_rs (EpileptorRestingState parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/EpileptorRestingState/parameters/K_rs

Coupling scaling on a fast time scale.
belongs to
Parameter c
has facts
description ap "Coupling scaling on a fast time scale"
default Value ap "1.0"^^double
definition ap "Coupling scaling on a fast time scale."
notation ap "K_rs"

Kanamaru2007ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Kanamaru2007

belongs to
Scholarly article c
has facts
issued ap "2007"
title ap "Van der Pol Oscillator"
author ap "Kanamaru, Takashi"
is Part Of ap "Scholarpedia"
issue Number ap "1"
pagination ap "2202"
volume Number ap "2"

KantzGrassberger1988ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/KantzGrassberger1988

belongs to
Scholarly article c
has facts
issued ap "1988"
title ap "On a Robust Method to Detect Intermittency"
author ap "Grassberger, Peter"
author ap "Kantz, Holger"
is Part Of ap "Journal of Physics A: Mathematical and General"
pagination ap "127--133"
volume Number ap "21"

ke (ZetterbergJansen parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZetterbergJansen/parameters/ke

Reciprocal of the time constant of passive membrane and all other spatially distributed delays in the dendritic network [ms^-1]. Also called average synaptic time constant.
belongs to
Parameter c
has facts
description ap "Reciprocal of the time constant of passive membrane and all other spatially distributed delays in the dendritic network [ms^-1]"
default Value ap "0.1"^^double
definition ap "Reciprocal of the time constant of passive membrane and all other spatially distributed delays in the dendritic network [ms^-1]. Also called average synaptic time constant."
notation ap "ke"

Kf (Epileptor5D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor5D/parameters/Kf

Correspond to the coupling scaling on a fast time scale.
belongs to
Parameter c
has facts
description ap "Correspond to the coupling scaling on a fast time scale"
default Value ap "0.0"^^double
definition ap "Correspond to the coupling scaling on a fast time scale."
notation ap "Kf"

Kf (EpileptorRestingState parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/EpileptorRestingState/parameters/Kf

Coupling scaling on a fast time scale.
belongs to
Parameter c
has facts
description ap "Coupling scaling on a fast time scale"
default Value ap "0.0"^^double
definition ap "Coupling scaling on a fast time scale."
notation ap "Kf"

Kg (KIonEx state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/state_variables/Kg

belongs to
StateVariable c
has facts
notation ap "Kg"
lhs ap "Derivative(Kg, t)"
rhs ap "epsilon*(K_bath - K_o)"

ki (ZetterbergJansen parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZetterbergJansen/parameters/ki

Reciprocal of the time constant of passive membrane and all other spatially distributed delays in the dendritic network [ms^-1]. Also called average synaptic time constant.
belongs to
Parameter c
has facts
description ap "Reciprocal of the time constant of passive membrane and all other spatially distributed delays in the dendritic network [ms^-1]"
default Value ap "0.05"^^double
definition ap "Reciprocal of the time constant of passive membrane and all other spatially distributed delays in the dendritic network [ms^-1]. Also called average synaptic time constant."
notation ap "ki"

KIonExni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx

belongs to
Dynamics c
has facts
exhibits bifurcation op ""
exhibits regime op Bistable ni
exhibits regime op Bursting ni
exhibits regime op Oscillatory ni
has attractor op Fixed point ni
has attractor op Limit cycle ni
has model feature op Fast-slow decomposition ni
has stochasticity character op Deterministic ni
models anatomical region op U B E R O N 0000956 ni
models anatomical region op U B E R O N 0002728 ni
has timescale separation dp "true"^^boolean
phase-space dimension dp "5"^^integer
description ap "It describes the mean-field activity of a population of Hodgkin-Huxley-type neurons (Depannemaker et al 2022) linking the slow fluctuations of intra- and extra-cellular potassium ion concentrations to the mean membrane potential, and the synaptic input to the population firing rate. The model is derived as the mathematical limit of an infinite number of all-to-all coupled neurons, resulting in 5 state variables: :math:`x` represents a phenomenological variable connected to the firing rate, :math:`V` represent the average membrane potential, :math:`n` represents the gating variable for potassium K, :math:`\Delta K_{int}` represent the intracellular potassium concentration, :math:`K_g` represents the extracellular potassium buffering by the external bath """"
references ap Depannemaecker2023 ni
subject ap D004827 ep
pref Label ap "K-ion exchange"@en
has Derived Variable ap DK_o (KIonEx derived variable) ni
has Derived Variable ap DNa_i (KIonEx derived variable) ni
has Derived Variable ap DNa_o (KIonEx derived variable) ni
has Derived Variable ap I_Cl (KIonEx derived variable) ni
has Derived Variable ap I_K (KIonEx derived variable) ni
has Derived Variable ap I_Na (KIonEx derived variable) ni
has Derived Variable ap I_pump (KIonEx derived variable) ni
has Derived Variable ap K_i (KIonEx derived variable) ni
has Derived Variable ap K_o (KIonEx derived variable) ni
has Derived Variable ap Na_i (KIonEx derived variable) ni
has Derived Variable ap Na_o (KIonEx derived variable) ni
has Derived Variable ap V_temp (KIonEx derived variable) ni
has Derived Variable ap Vcond (KIonEx derived variable) ni
has Derived Variable ap beta (KIonEx derived variable) ni
has Derived Variable ap h (KIonEx derived variable) ni
has Derived Variable ap minf (KIonEx derived variable) ni
has Derived Variable ap ninf (KIonEx derived variable) ni
has Derived Variable ap r (KIonEx derived variable) ni
has Derived Variable ap xcond (KIonEx derived variable) ni
has Parameter ap Chn (KIonEx parameter) ni
has Parameter ap Ckp (KIonEx parameter) ni
has Parameter ap Cl_i0 (KIonEx parameter) ni
has Parameter ap Cl_o0 (KIonEx parameter) ni
has Parameter ap Cm (KIonEx parameter) ni
has Parameter ap Cmna (KIonEx parameter) ni
has Parameter ap Cnap (KIonEx parameter) ni
has Parameter ap Cnk (KIonEx parameter) ni
has Parameter ap DChn (KIonEx parameter) ni
has Parameter ap DCkp (KIonEx parameter) ni
has Parameter ap DCmna (KIonEx parameter) ni
has Parameter ap DCnap (KIonEx parameter) ni
has Parameter ap DCnk (KIonEx parameter) ni
has Parameter ap Delta (KIonEx parameter) ni
has Parameter ap E (KIonEx parameter) ni
has Parameter ap J (KIonEx parameter) ni
has Parameter ap K_bath (KIonEx parameter) ni
has Parameter ap K_i0 (KIonEx parameter) ni
has Parameter ap K_o0 (KIonEx parameter) ni
has Parameter ap Na_i0 (KIonEx parameter) ni
has Parameter ap Na_o0 (KIonEx parameter) ni
has Parameter ap R_minus (KIonEx parameter) ni
has Parameter ap R_plus (KIonEx parameter) ni
has Parameter ap Vstar (KIonEx parameter) ni
has Parameter ap c_minus (KIonEx parameter) ni
has Parameter ap c_plus (KIonEx parameter) ni
has Parameter ap epsilon (KIonEx parameter) ni
has Parameter ap eta (KIonEx parameter) ni
has Parameter ap g_Cl (KIonEx parameter) ni
has Parameter ap g_K (KIonEx parameter) ni
has Parameter ap g_Kl (KIonEx parameter) ni
has Parameter ap g_Na (KIonEx parameter) ni
has Parameter ap g_Nal (KIonEx parameter) ni
has Parameter ap gamma (KIonEx parameter) ni
has Parameter ap rho (KIonEx parameter) ni
has Parameter ap tau_n (KIonEx parameter) ni
has Parameter ap w_i (KIonEx parameter) ni
has Parameter ap w_o (KIonEx parameter) ni
has State Variable ap DKi (KIonEx state variable) ni
has State Variable ap Kg (KIonEx state variable) ni
has State Variable ap V (KIonEx state variable) ni
has State Variable ap n (KIonEx state variable) ni
has State Variable ap x (KIonEx state variable) ni
model_type (slot) ap "mean_field"

Ks (Epileptor2D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor2D/parameters/Ks

Permittivity coupling on the slow permittivity state-variable z_E2D in Epileptor2D (Proix et al., 2014). The coupling quantifies the influence of neuronal fast discharges x_E2D on the local slow permittivity variable z_E2D.
belongs to
Parameter c
has facts
description ap "Permittivity coupling on the slow permittivity state-variable z_E2D in Epileptor2D (Proix et al"
default Value ap "0.0"^^double
definition ap "Permittivity coupling on the slow permittivity state-variable z_E2D in Epileptor2D (Proix et al., 2014). The coupling quantifies the influence of neuronal fast discharges x_E2D on the local slow permittivity variable z_E2D."
notation ap "Ks"

Ks (Epileptor5D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor5D/parameters/Ks

Permittivity coupling on the slow permittivity state-variable z_E5D in Epileptor5D (Proix et al., 2014). The coupling quantifies the influence of neuronal fast discharges x1_E5D on the local slow permittivity variable z_E5D.
belongs to
Parameter c
has facts
description ap "Permittivity coupling on the slow permittivity state-variable z_E5D in Epileptor5D (Proix et al"
default Value ap "0.0"^^double
definition ap "Permittivity coupling on the slow permittivity state-variable z_E5D in Epileptor5D (Proix et al., 2014). The coupling quantifies the influence of neuronal fast discharges x1_E5D on the local slow permittivity variable z_E5D."
notation ap "Ks"

Ks (EpileptorRestingState parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/EpileptorRestingState/parameters/Ks

Permittivity coupling, that is from the very fast time scale toward the slow time scale.
belongs to
Parameter c
has facts
description ap "Permittivity coupling, that is from the very fast time scale toward the slow time scale"
default Value ap "0.0"^^double
definition ap "Permittivity coupling, that is from the very fast time scale toward the slow time scale."
notation ap "Ks"

Kuramotoni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Kuramoto

belongs to
Dynamics c
has facts
exhibits regime op Oscillatory ni
has attractor op Limit cycle ni
has attractor op Torus ni
has stochasticity character op Deterministic ni
has timescale separation dp "false"^^boolean
phase-space dimension dp "1"^^integer
description ap "The Kuramoto model is a model of synchronization phenomena derived by Yoshiki Kuramoto in 1975 which has since been applied to diverse domains including the study of neuronal oscillations and synchronization."
references ap Cabral2011 ni
references ap Kuramoto1975 ni
references ap Strogatz2000 ni
pref Label ap "Kuramoto"@en
has Derived Variable ap I (Kuramoto derived variable) ni
has Derived Variable ap lc_0 (Kuramoto derived variable) ni
has Parameter ap omega (Kuramoto parameter) ni
has State Variable ap theta (Kuramoto state variable) ni
model_type (slot) ap "phase_oscillator"

Kuramoto (extended)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Kuramoto2

has facts
exhibits regime op Oscillatory ni
has attractor op Limit cycle ni
has attractor op Torus ni
has stochasticity character op Deterministic ni
phase-space dimension dp "2"^^integer
pref Label ap "Kuramoto (extended)"@en

Kuramoto1975ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Kuramoto1975

belongs to
Scholarly article c
has facts
issued ap "1975"
title ap "Self-entrainment of a Population of Coupled Nonlinear Oscillators"
author ap "Kuramoto, Yoshiki"
is Part Of ap "International Symposium on Mathematical Problems in Theoretical Physics"
volume Number ap "39"

KuramotoCouplingni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/coupling_functions/KuramotoCoupling

belongs to
Coupling c
has facts
has Parameter ap N (KuramotoCoupling parameter) ni
has Parameter ap a (KuramotoCoupling parameter) ni

Kvf (Epileptor2D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor2D/parameters/Kvf

Coupling scaling on a very fast time scale.
belongs to
Parameter c
has facts
description ap "Coupling scaling on a very fast time scale"
default Value ap "0.0"^^double
definition ap "Coupling scaling on a very fast time scale."
notation ap "Kvf"

Kvf (Epileptor5D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor5D/parameters/Kvf

Coupling scaling on a very fast time scale.
belongs to
Parameter c
has facts
description ap "Coupling scaling on a very fast time scale"
default Value ap "0.0"^^double
definition ap "Coupling scaling on a very fast time scale."
notation ap "Kvf"

Kvf (EpileptorRestingState parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/EpileptorRestingState/parameters/Kvf

Coupling scaling on a very fast time scale.
belongs to
Parameter c
has facts
description ap "Coupling scaling on a very fast time scale"
default Value ap "0.0"^^double
definition ap "Coupling scaling on a very fast time scale."
notation ap "Kvf"

lamda (ReducedWongWangExcInh parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWangExcInh/parameters/lamda

Inhibitory global coupling scaling
belongs to
Parameter c
has facts
description ap "Inhibitory global coupling scaling"
default Value ap "0.0"^^double
has Db Xref ap G O 0060080 ep
definition ap "Inhibitory global coupling scaling"
notation ap "lamda"

Landau1944ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Landau1944

belongs to
Scholarly article c
has facts
issued ap "1944"
title ap "On the problem of turbulence"
author ap "Landau, L. D."
is Part Of ap "Doklady Akademii Nauk SSSR"
issue Number ap "8"
pagination ap "339--349"
volume Number ap "44"

LarterBreakspearni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/LarterBreakspear

belongs to
Dynamics c
has facts
exhibits bifurcation op ""
exhibits regime op Bistable ni
exhibits regime op Chaotic ni
exhibits regime op Oscillatory ni
has attractor op Fixed point ni
has attractor op Limit cycle ni
has attractor op Strange attractor ni
has model feature op Excitatory/inhibitory subpopulations ni
has stochasticity character op Deterministic ni
models anatomical region op U B E R O N 0000956 ni
models cell type op C L 0000099 ni
models cell type op C L 0000598 ni
models neurotransmitter system op G O 0007214 ni
models neurotransmitter system op G O 0035249 ni
has timescale separation dp "true"^^boolean
phase-space dimension dp "3"^^integer
description ap "The Larter-Breakspear is an extension (Breakspear et al., 2003a, 2003b) of the biophysical-inspired neural mass model of a cortical column (or area) from Larter et al. (1999), initially developed to simulate firing rate activity from focal region involved in partial seizure. It is determined by voltage- and ligand-gated ions channels and feedback between intensively interconnected excitatory and inhibitory neurons. The Larter-Breakspear is a 3D model describing the local average states of two interconnected neural populations: pyramidal cells (PCs) and inhibitory interneurons (IINs), with an additional variable representing the potassium channels in the population of PCs. The membrane potential of the pyramidal cells is the focus of the model and is governed by sodium, potassium, calcium and “leaky” ion channels, of which the voltage-gated potassium channels are modelled in more detail. The excitatory to excitatory connections are modelled in more detail as glutamatergic connections with AMPA and NMDA receptors. Note: - Equations and default parameters are taken from (Breakspear et al., 2003b), - All equations and parameters are non-dimensional and normalized to neural capacitance C = 1."
pref Label ap "Larter-Breakspear"@en
has Derived Variable ap Q_V (LarterBreakspear derived variable) ni
has Derived Variable ap Q_Z (LarterBreakspear derived variable) ni
has Derived Variable ap lc_0 (LarterBreakspear derived variable) ni
has Derived Variable ap m_Ca (LarterBreakspear derived variable) ni
has Derived Variable ap m_K (LarterBreakspear derived variable) ni
has Derived Variable ap m_Na (LarterBreakspear derived variable) ni
has Parameter ap C (LarterBreakspear parameter) ni
has Parameter ap I_ext (LarterBreakspear parameter) ni
has Parameter ap Q_Vmax (LarterBreakspear parameter) ni
has Parameter ap Q_Zmax (LarterBreakspear parameter) ni
has Parameter ap T_Ca (LarterBreakspear parameter) ni
has Parameter ap T_K (LarterBreakspear parameter) ni
has Parameter ap T_Na (LarterBreakspear parameter) ni
has Parameter ap V_Ca (LarterBreakspear parameter) ni
has Parameter ap V_K (LarterBreakspear parameter) ni
has Parameter ap V_L (LarterBreakspear parameter) ni
has Parameter ap V_Na (LarterBreakspear parameter) ni
has Parameter ap V_T (LarterBreakspear parameter) ni
has Parameter ap Z_T (LarterBreakspear parameter) ni
has Parameter ap a_ee (LarterBreakspear parameter) ni
has Parameter ap a_ei (LarterBreakspear parameter) ni
has Parameter ap a_ie (LarterBreakspear parameter) ni
has Parameter ap a_ne (LarterBreakspear parameter) ni
has Parameter ap a_ni (LarterBreakspear parameter) ni
has Parameter ap b (LarterBreakspear parameter) ni
has Parameter ap delta_Ca (LarterBreakspear parameter) ni
has Parameter ap delta_K (LarterBreakspear parameter) ni
has Parameter ap delta_Na (LarterBreakspear parameter) ni
has Parameter ap delta_V (LarterBreakspear parameter) ni
has Parameter ap delta_Z (LarterBreakspear parameter) ni
has Parameter ap g_Ca (LarterBreakspear parameter) ni
has Parameter ap g_K (LarterBreakspear parameter) ni
has Parameter ap g_L (LarterBreakspear parameter) ni
has Parameter ap g_Na (LarterBreakspear parameter) ni
has Parameter ap phi (LarterBreakspear parameter) ni
has Parameter ap r_NMDA (LarterBreakspear parameter) ni
has Parameter ap t_scale (LarterBreakspear parameter) ni
has Parameter ap tau_K (LarterBreakspear parameter) ni
has State Variable ap V (LarterBreakspear state variable) ni
has State Variable ap W (LarterBreakspear state variable) ni
has State Variable ap Z (LarterBreakspear state variable) ni
model_type (slot) ap "neural_mass"

lc_0 (Kuramoto derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Kuramoto/derived_variables/lc_0

belongs to
DerivedVariable c
has facts
notation ap "lc_0"
lhs ap "lc_0"
rhs ap "sin(local_coupling*theta)"

lc_0 (KuramotoModel2 derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KuramotoModel2/derived_variables/lc_0

belongs to
DerivedVariable c
has facts
notation ap "lc_0"
lhs ap "lc_0"
rhs ap "sin(local_coupling*theta)"

lc_0 (LarterBreakspear derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/LarterBreakspear/derived_variables/lc_0

belongs to
DerivedVariable c
has facts
notation ap "lc_0"
lhs ap "lc_0"
rhs ap "Q_V*local_coupling"

lc_0 (SupHopf derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/SupHopf/derived_variables/lc_0

belongs to
DerivedVariable c
has facts
notation ap "lc_0"
lhs ap "lc_0"
rhs ap "local_coupling*x"

lc_0 (WilsonCowan derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/WilsonCowan/derived_variables/lc_0

belongs to
DerivedVariable c
has facts
notation ap "lc_0"
lhs ap "lc_0"
rhs ap "local_coupling*E"

lc_1 (EpileptorRestingState derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/EpileptorRestingState/derived_variables/lc_1

belongs to
DerivedVariable c
has facts
notation ap "lc_1"
lhs ap "lc_1"
rhs ap "local_coupling*x_rs"

lc_1 (WilsonCowan derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/WilsonCowan/derived_variables/lc_1

belongs to
DerivedVariable c
has facts
notation ap "lc_1"
lhs ap "lc_1"
rhs ap "I*local_coupling"

lc_E (ZerlautAdaptationFirstOrder derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/derived_variables/lc_E

belongs to
DerivedVariable c
has facts
notation ap "lc_E"
lhs ap "lc_E"
rhs ap "local_coupling*E"

lc_I (ZerlautAdaptationFirstOrder derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/derived_variables/lc_I

belongs to
DerivedVariable c
has facts
notation ap "lc_I"
lhs ap "lc_I"
rhs ap "I*local_coupling"

LEMSni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/LEMS

belongs to
Software package c
has facts
description ap "Low Entropy Model Specification — an XML-based language for defining the structure and dynamics of hierarchically structured models of biological systems. Foundation for NeuroML2."
license ap "MIT"
code Repository ap "https://github.com/LEMS/jLEMS"
url ap "https://lems.github.io/LEMS/"

Letellier2007ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Letellier2007

belongs to
Scholarly article c
has facts
issued ap "2007"
title ap "Hyperchaos"
author ap "Letellier, Christophe"
author ap "R"ossler, Otto E."
is Part Of ap "Scholarpedia"
issue Number ap "8"
pagination ap "1936"
volume Number ap "2"

LFPyni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/LFPy

belongs to
Software package c
has facts
description ap "A Python module for calculating local field potentials (LFPs) and extracellular potentials from multicompartment neuron models using the line-source method on NEURON simulations."
license ap "GPL-3.0-only"
code Repository ap "https://github.com/LFPy/LFPy"
identifier ap "10.3389/fninf.2013.00041"
url ap "https://lfpy.readthedocs.io"

Li2015ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Li2015

belongs to
Scholarly article c
has facts
issued ap "2015"
title ap "A novel four-wing strange attractor born in bistability"
author ap "Li, Chunbiao"
author ap "et al."
is Part Of ap "IEICE Electronics Express"
issue Number ap "4"
volume Number ap "12"

Linearni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/coupling_functions/Linear

belongs to
Coupling c
has facts
has Parameter ap a (Linear parameter) ni
has Parameter ap b (Linear parameter) ni

Lorenz1963ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Lorenz1963

belongs to
Scholarly article c
has facts
issued ap "1963"
title ap "Deterministic Nonperiodic Flow"
author ap "Lorenz, Edward N."
identifier ap "10.1175/1520-0469(1963)020<0130:DNF>2.0.CO;2"
is Part Of ap "Journal of the Atmospheric Sciences"
pagination ap "130--141"
volume Number ap "20"

Lorenz1996ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Lorenz1996

belongs to
Scholarly article c
has facts
issued ap "1996"
title ap "Predictability: A Problem Partly Solved"
author ap "Lorenz, Edward N."
identifier ap "10.1017/cbo9780511617652.004"
is Part Of ap "Proc. Seminar on Predictability"

m_Ca (LarterBreakspear derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/LarterBreakspear/derived_variables/m_Ca

belongs to
DerivedVariable c
has facts
description ap "Fraction of open calcium channels (Breakspear et al., 2003b). Describes relationship between membrane voltage and channel conductance."
has Db Xref ap G O 0005262 ep
notation ap "m_Ca"
lhs ap "m_Ca"
rhs ap "0.5*tanh((-T_Ca + V)/delta_Ca) + 0.5"

m_i (StefanescuJirsa2D derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa2D/derived_variables/m_i

belongs to
DerivedVariable c
has facts
description ap "Per-mode offset entering the eta dynamics."
notation ap "m_i"
lhs ap "m_i"
rhs ap "a"

m_i (StefanescuJirsa3D derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa3D/derived_variables/m_i

belongs to
DerivedVariable c
has facts
description ap "Per-mode adaptation offset entering the tau dynamics."
notation ap "m_i"
lhs ap "m_i"
rhs ap "r*s*x_0"

m_K (LarterBreakspear derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/LarterBreakspear/derived_variables/m_K

belongs to
DerivedVariable c
has facts
description ap "Fraction of open potassium channels (Breakspear et al., 2003b). Describes relationship between membrane voltage and channel conductance."
has Db Xref ap G O 0005267 ep
notation ap "m_K"
lhs ap "m_K"
rhs ap "0.5*tanh((-T_K + V)/delta_K) + 0.5"

m_Na (LarterBreakspear derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/LarterBreakspear/derived_variables/m_Na

belongs to
DerivedVariable c
has facts
description ap "Fraction of open sodium channels (Breakspear et al., 2003b). Describes relationship between membrane voltage and channel conductance."
has Db Xref ap G O 0005272 ep
notation ap "m_Na"
lhs ap "m_Na"
rhs ap "0.5*tanh((-T_Na + V)/delta_Na) + 0.5"

Manneville1980ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Manneville1980

belongs to
Scholarly article c
has facts
issued ap "1980"
title ap "Intermittency, self-similarity and 1/f spectrum in dissipative dynamical systems"
author ap "Manneville, Paul"
is Part Of ap "Journal de Physique"
issue Number ap "11"
pagination ap "1235--1243"
volume Number ap "41"

MannevillePomeau1980ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/MannevillePomeau1980

belongs to
Scholarly article c
has facts
issued ap "1980"
title ap "Intermittency and the Lorenz Model"
author ap "Manneville, P."
author ap "Pomeau, Y."
is Part Of ap "Communications in Mathematical Physics"
volume Number ap "74"

MatContni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/MatCont

belongs to
Software package c
has facts
description ap "A MATLAB continuation toolbox for interactive bifurcation analysis of dynamical systems. Computes equilibria, limit cycles, and bifurcation curves with graphical user interface."
license ap "GPL-3.0-only"
code Repository ap "https://sourceforge.net/projects/matcont/"
url ap "https://sourceforge.net/projects/matcont/"

May1976ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/May1976

belongs to
Scholarly article c
has facts
issued ap "1976"
title ap "Simple mathematical models with very complicated dynamics"
author ap "May, Robert M."
identifier ap "10.1201/9780203734636-5"
is Part Of ap "Nature"
pagination ap "459--467"
volume Number ap "261"

MCellni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/MCell

belongs to
Software package c
has facts
description ap "Monte Carlo Cell — a program for realistic simulation of cellular signaling using spatially realistic 3D models of sub-cellular reaction-diffusion dynamics."
license ap "GPL-2.0-only"
code Repository ap "https://github.com/mcellteam/mcell"
identifier ap "10.1016/j.cpc.2016.06.013"
url ap "https://mcell.org"

MEGni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/observation_models/meg

belongs to
Observation c
has facts
description ap "Forward solution for magnetoencephalography. Projects source neural activity through a lead field matrix to MEG sensor locations using oriented gradiometers. If no precomputed gain is available, uses the single-sphere analytic formula (Sarvas 1987, Eq. 25) for the magnetic field produced by current dipoles in a conducting sphere."
has Parameter ap permeability (meg parameter) ni

Meyer2019ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Meyer2019

belongs to
Scholarly article c
has facts
issued ap "2019"
title ap "Long-range correlations in intermittent maps"
author ap "Meyer, R."
author ap "et al."
is Part Of ap "New Journal of Physics"
volume Number ap "20"

Micluta-Campeanu2018ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Micluta-Campeanu2018

belongs to
Scholarly article c
has facts
issued ap "2018"
title ap "Chaoticity Evolution in a Quartic Collective Hamiltonian"
author ap "Baran, V."
author ap "Micluta-Campeanu, S."
author ap "Nicolin, A. I."
author ap "Raportaru, M. C."
is Part Of ap "Romanian Reports in Physics"
pagination ap "105"
volume Number ap "70"

MiclutaCampeanu2018ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/MiclutaCampeanu2018

belongs to
Scholarly article c
has facts
issued ap "2018"
title ap "Chaoticity Evolution in a Quartic Collective Hamiltonian"
author ap "Micluta-Campeanu, S."
author ap "Raduta, A."
author ap "others"
is Part Of ap "Romanian Journal of Physics"
pagination ap "105"
volume Number ap "70"

midpoint (HyperbolicTangent parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/coupling_functions/HyperbolicTangent/parameters/midpoint

belongs to
Parameter c
has facts
description ap "Midpoint of the linear portion of the sigmoid"
default Value ap "0.0"^^double
notation ap "midpoint"

midpoint (Sigmoidal parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/coupling_functions/Sigmoidal/parameters/midpoint

belongs to
Parameter c
has facts
default Value ap "0.0"^^double
notation ap "midpoint"

midpoint (SigmoidalJansenRit parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/coupling_functions/SigmoidalJansenRit/parameters/midpoint

belongs to
Parameter c
has facts
description ap "Midpoint of the linear portion of the sigmoid"
default Value ap "6.0"^^double
notation ap "midpoint"

minf (KIonEx derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/derived_variables/minf

belongs to
DerivedVariable c
has facts
notation ap "minf"
lhs ap "minf"
rhs ap "1.0/(exp((Cmna - V)/DCmna) + 1.0)"

Mirshra2018ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Mirshra2018

belongs to
Scholarly article c
has facts
issued ap "2018"
title ap "Dragon-king-like extreme events in coupled bursting neurons"
author ap "Dana, S. K."
author ap "Kapitaniak, T."
author ap "Mishra, A."
author ap "Pal, P."
author ap "Saha, S."
author ap "Vigneshwaran, M."
identifier ap "10.1103/PhysRevE.97.062311"
is Part Of ap "Physical Review E"
issue Number ap "6"
pagination ap "062311"
volume Number ap "97"

Mishra2018ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Mishra2018

belongs to
Scholarly article c
has facts
issued ap "2018"
title ap "Dragon-king-like extreme events in coupled bursting neurons"
author ap "Dana, S. K."
author ap "Kapitaniak, T."
author ap "Mishra, A."
author ap "Pal, P."
author ap "Saha, S."
author ap "Vigneshwaran, M."
identifier ap "10.1103/PhysRevE.97.062311"
is Part Of ap "Physical Review E"
issue Number ap "6"
pagination ap "062311"
volume Number ap "97"

Mishra2018ani back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Mishra2018a

belongs to
Scholarly article c
has facts
issued ap "2018"
title ap "Dragon-king-like extreme events in coupled bursting neurons"
author ap "Dana, S. K."
author ap "Kapitaniak, T."
author ap "Mishra, A."
author ap "Pal, P."
author ap "Saha, S."
author ap "Vigneshwaran, M."
identifier ap "10.1103/PhysRevE.97.062311"
is Part Of ap "Physical Review E"
issue Number ap "6"
pagination ap "062311"
volume Number ap "97"

MNE-Pythonni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/MNE-Python

belongs to
Software package c
has facts
description ap "Open-source Python package for exploring, visualizing, and analyzing human neurophysiological data: MEG, EEG, sEEG, ECoG, NIRS, and more."
license ap "BSD-3-Clause"
code Repository ap "https://github.com/mne-tools/mne-python"
identifier ap "10.3389/fnins.2013.00267"
url ap "https://mne.tools"

MNI152NLin2009bni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/coordinate_spaces/MNI152NLin2009b

belongs to
CommonCoordinateSpace c
has facts
description ap "Nonlinear 6th-generation MNI152 average, 2009b release (symmetric variant). Produced by the McConnell Brain Imaging Centre (Fonov et al., 2011)."
alt Label ap "MNI152NLin2009b"
alt Label ap "MNI152NLin2009bSym"
alt Label ap "tpl-MNI152NLin2009bSym"
anatomical Axes Orientation ap "RAS"
axes Origin ap "anterior commissure"
unit (slot) dp "mm"

MNI152NLin2009cni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/coordinate_spaces/MNI152NLin2009c

belongs to
CommonCoordinateSpace c
has facts
description ap "Nonlinear 6th-generation MNI152 average, 2009c release (symmetric variant). Produced by the McConnell Brain Imaging Centre (Fonov et al., 2011)."
alt Label ap "MNI152NLin2009c"
alt Label ap "MNI152NLin2009cSym"
alt Label ap "tpl-MNI152NLin2009cSym"
anatomical Axes Orientation ap "RAS"
axes Origin ap "anterior commissure"
unit (slot) dp "mm"

MNI152NLin2009cAsymni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/coordinate_spaces/MNI152NLin2009cAsym

belongs to
CommonCoordinateSpace c
has facts
description ap "Nonlinear 6th-generation MNI152 average, 2009c release, asymmetric variant (Fonov et al., 2011). Default template space for fMRIPrep and many modern BIDS pipelines. TemplateFlow id: `tpl-MNI152NLin2009cAsym`."
alt Label ap "MNI152NLin2009cAsym"
alt Label ap "MNI152_2009c_asym"
alt Label ap "tpl-MNI152NLin2009cAsym"
anatomical Axes Orientation ap "RAS"
axes Origin ap "anterior commissure"
unit (slot) dp "mm"

MNI152NLin6Asymni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/coordinate_spaces/MNI152NLin6Asym

belongs to
CommonCoordinateSpace c
has facts
description ap "Sixth-generation nonlinear ICBM152 average (Mazziotta et al., 2001), asymmetric variant. This is the template shipped with FSL as `MNI152_T1_*mm.nii.gz` (commonly referred to as "FSLMNI152" or generic "MNI152" in older literature). TemplateFlow id: `tpl-MNI152NLin6Asym`."
alt Label ap "FSLMNI152"
alt Label ap "MNI152"
alt Label ap "MNI152NLin6"
alt Label ap "MNI152NLin6Asym"
anatomical Axes Orientation ap "RAS"
axes Origin ap "anterior commissure"
unit (slot) dp "mm"

ModelDBni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/ModelDB

belongs to
Software package c
has facts
description ap "A curated database of published computational neuroscience models. Provides source code and metadata for thousands of models linked to peer-reviewed publications."
url ap "https://modeldb.science"

modification (Epileptor2D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor2D/parameters/modification

When modification is True, the function h_E2D uses a nonlinear influence on z_E2D. The default value is False, i.e., linear influence on z_E2D.
belongs to
Parameter c
has facts
description ap "When modification is True, the function h_E2D uses a nonlinear influence on z_E2D"
default Value ap "0.0"^^double
definition ap "When modification is True, the function h_E2D uses a nonlinear influence on z_E2D. The default value is False, i.e., linear influence on z_E2D."
notation ap "modification"

modification (Epileptor5D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor5D/parameters/modification

When modification is True, the function h_E5D uses a nonlinear influence on z_E5D. The default value is False, i.e., linear influence on z_E5D.
belongs to
Parameter c
has facts
description ap "When modification is True, the function h_E5D uses a nonlinear influence on z_E5D"
default Value ap "0.0"^^double
definition ap "When modification is True, the function h_E5D uses a nonlinear influence on z_E5D. The default value is False, i.e., linear influence on z_E5D."
notation ap "modification"

Montbrio2015ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Montbrio2015

belongs to
Scholarly article c
has facts
issued ap "2015"
title ap "Macroscopic description for networks of spiking neurons"
author ap "Montbri\'o, Ernest"
author ap "Paz\'o, Diego"
author ap "Roxin, Alex"
is Part Of ap "Physical Review X"

MOOSEni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/MOOSE

belongs to
Software package c
has facts
description ap "Multiscale Object-Oriented Simulation Environment. Supports models from sub-cellular signaling to large networks, including reaction-diffusion, electrical, and chemical compartmental models."
license ap "GPL-3.0-only"
code Repository ap "https://github.com/BhallaLab/moose-core"
identifier ap "10.3389/fninf.2014.00094"
url ap "https://moose.ncbs.res.in"

MorrisLecar1981ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/MorrisLecar1981

belongs to
Scholarly article c
has facts
issued ap "1981"
title ap "Voltage oscillations in the barnacle giant muscle fiber"
author ap "Lecar, H."
author ap "Morris, C."
is Part Of ap "Biophysical Journal"
url ap "https://www.cell.com/biophysj/pdf/S0006-3495(81)84782-0.pdf"

mu (JansenRit parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/JansenRit/parameters/mu

Mean excitatory external input to the derivative of the state-variable y4_JR (PCs) represented by a pulse density, that consists of activity originating from adjacent and more distant cortical columns, as well as from subcortical structures (e.g., thalamus).
belongs to
Parameter c
has facts
description ap "Mean excitatory external input to the derivative of the state-variable y4_JR (PCs) represented by a pulse density, that consists of activity originating from adjacent and more distant cortical columns, as well as from subcortical structures (e"
default Value ap "0.22"^^double
has Db Xref ap G O 0060079 ep
definition ap "Mean excitatory external input to the derivative of the state-variable y4_JR (PCs) represented by a pulse density, that consists of activity originating from adjacent and more distant cortical columns, as well as from subcortical structures (e.g., thalamus)."
notation ap "mu"
unit (slot) dp "per_ms"

mu (StefanescuJirsa2D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa2D/parameters/mu

Mean of the Gaussian heterogeneity distribution.
belongs to
Parameter c
has facts
default Value ap "0.0"^^double
has Db Xref ap G O 0060079 ep
definition ap "Mean of the Gaussian heterogeneity distribution."
notation ap "mu"

mu (StefanescuJirsa3D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa3D/parameters/mu

Mean of the Gaussian heterogeneity distribution.
belongs to
Parameter c
has facts
default Value ap "3.3"^^double
has Db Xref ap G O 0060079 ep
definition ap "Mean of the Gaussian heterogeneity distribution."
notation ap "mu"

mu_E (CakanObermayer parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/CakanObermayer/parameters/mu_E

Mean external input current to the excitatory population (mue_ext_mean).
belongs to
Parameter c
has facts
default Value ap "0.4"^^double
definition ap "Mean external input current to the excitatory population (mue_ext_mean)."
notation ap "mu_E"
unit (slot) dp "mV_per_ms"

mu_G_e (ZerlautAdaptationFirstOrder derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/derived_variables/mu_G_e

belongs to
DerivedVariable c
has facts
notation ap "mu_G_e"
lhs ap "mu_G_e"
rhs ap "g_L + mu_Ge_e + mu_Gi_e"

mu_G_i (ZerlautAdaptationFirstOrder derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/derived_variables/mu_G_i

belongs to
DerivedVariable c
has facts
notation ap "mu_G_i"
lhs ap "mu_G_i"
rhs ap "g_L + mu_Ge_i + mu_Gi_i"

mu_Ge_e (ZerlautAdaptationFirstOrder derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/derived_variables/mu_Ge_e

belongs to
DerivedVariable c
has facts
notation ap "mu_Ge_e"
lhs ap "mu_Ge_e"
rhs ap "Q_e*fe_e*tau_e"

mu_Ge_i (ZerlautAdaptationFirstOrder derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/derived_variables/mu_Ge_i

belongs to
DerivedVariable c
has facts
notation ap "mu_Ge_i"
lhs ap "mu_Ge_i"
rhs ap "Q_e*fe_i*tau_e"

mu_Gi_e (ZerlautAdaptationFirstOrder derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/derived_variables/mu_Gi_e

belongs to
DerivedVariable c
has facts
notation ap "mu_Gi_e"
lhs ap "mu_Gi_e"
rhs ap "Q_i*fi_e*tau_i"

mu_Gi_i (ZerlautAdaptationFirstOrder derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/derived_variables/mu_Gi_i

belongs to
DerivedVariable c
has facts
notation ap "mu_Gi_i"
lhs ap "mu_Gi_i"
rhs ap "Q_i*fi_i*tau_i"

mu_I (CakanObermayer parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/CakanObermayer/parameters/mu_I

Mean external input current to the inhibitory population (mui_ext_mean).
belongs to
Parameter c
has facts
default Value ap "0.3"^^double
has Db Xref ap G O 0042391 ep
has Db Xref ap G O 0060080 ep
has Db Xref ap G O 0098828 ep
definition ap "Mean external input current to the inhibitory population (mui_ext_mean)."
notation ap "mu_I"
unit (slot) dp "mV_per_ms"

mu_se (CakanObermayer state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/CakanObermayer/state_variables/mu_se

belongs to
StateVariable c
has facts
description ap "Filtered mean synaptic input current to the excitatory population."
notation ap "mu_se"
lhs ap "Derivative(mu_se, t)"
rhs ap "(J_EE*r_E + J_EI*r_I + mu_E + c_pop0 - I_A_var/C - mu_se)/tau_se"

mu_si (CakanObermayer state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/CakanObermayer/state_variables/mu_si

belongs to
StateVariable c
has facts
description ap "Filtered mean synaptic input current to the inhibitory population."
notation ap "mu_si"
lhs ap "Derivative(mu_si, t)"
rhs ap "(J_IE*r_E + J_II*r_I + mu_I - mu_si)/tau_si"

mu_th (CakanObermayer parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/CakanObermayer/parameters/mu_th

Half-maximum input of the sigmoid transfer-function surrogate.
belongs to
Parameter c
has facts
default Value ap "1.0"^^double
definition ap "Half-maximum input of the sigmoid transfer-function surrogate."
notation ap "mu_th"
unit (slot) dp "mV_per_ms"

mu_V_e (ZerlautAdaptationFirstOrder derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/derived_variables/mu_V_e

belongs to
DerivedVariable c
has facts
notation ap "mu_V_e"
lhs ap "mu_V_e"
rhs ap "(E_L_e*g_L + E_e*mu_Ge_e + E_i*mu_Gi_e - W_e)/mu_G_e"

mu_V_i (ZerlautAdaptationFirstOrder derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/derived_variables/mu_V_i

belongs to
DerivedVariable c
has facts
notation ap "mu_V_i"
lhs ap "mu_V_i"
rhs ap "(E_L_i*g_L + E_e*mu_Ge_i + E_i*mu_Gi_i - W_i)/mu_G_i"

Multiscale BNM: Decision-Making with E/I Balance Tuningni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/experiments/Schirner2023_MultiscaleBNM_DM

belongs to
SimulationExperiment c
has facts
description ap "Multiscale brain network model coupling large-scale structural connectivity with a small-scale frontoparietal circuit for decision-making (DM) and working memory (WM). The large-scale model uses the Reduced Wong-Wang model (Deco et al., 2014, JNeurosci) with explicit excitatory and inhibitory populations. The functional circuit implements winner-take-all DM and persistent-activity WM based on Murray, Jaramillo & Wang (2017, JNeurosci). Key innovation: The ratio of long-range excitation (LRE) to feedforward inhibition (FFI) controls functional connectivity between brain regions. This E/I balance tuning enables fitting personalized brain network models to empirical functional connectivity and explains individual differences in cognitive performance (speed-accuracy trade-off in intelligence tests). "

muV0 (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/muV0

Normalization factors page 48 after the equation 4 from [ZD_2018]
belongs to
Parameter c
has facts
description ap "Normalization factors page 48 after the equation 4 from [ZD_2018]"
default Value ap "-60.0"^^double
definition ap "Normalization factors page 48 after the equation 4 from [ZD_2018]"
notation ap "muV0"

N (Epileptor3DStefanescuMcDonald parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor3DStefanescuMcDonald/parameters/N

Effective population size / scaling of the resting-state regulation term.
belongs to
Parameter c
has facts
default Value ap "1.0"^^double
has Db Xref ap G O 0042391 ep
definition ap "Effective population size / scaling of the resting-state regulation term."
notation ap "N"

n (KIonEx state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/state_variables/n

belongs to
StateVariable c
has facts
notation ap "n"
lhs ap "Derivative(n, t)"
rhs ap "(-n + ninf)/tau_n"

N (KuramotoCoupling parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/coupling_functions/KuramotoCoupling/parameters/N

belongs to
Parameter c
has facts
description ap "Number of nodes, i.e., size of network."
default Value ap "1.0"^^double
notation ap "N"

n_i (StefanescuJirsa2D derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa2D/derived_variables/n_i

belongs to
DerivedVariable c
has facts
description ap "Per-mode offset entering the beta dynamics."
notation ap "n_i"
lhs ap "n_i"
rhs ap "a"

n_i (StefanescuJirsa3D derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa3D/derived_variables/n_i

belongs to
DerivedVariable c
has facts
description ap "Per-mode adaptation offset entering the gamma dynamics."
notation ap "n_i"
lhs ap "n_i"
rhs ap "r*s*x_0"

N_tot (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/N_tot

cell number
belongs to
Parameter c
has facts
description ap "cell number"
default Value ap "10000.0"^^double
definition ap "cell number"
notation ap "N_tot"

Na_i (KIonEx derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/derived_variables/Na_i

belongs to
DerivedVariable c
has facts
notation ap "Na_i"
lhs ap "Na_i"
rhs ap "DNa_i + Na_i0"

Na_i0 (KIonEx parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/parameters/Na_i0

initial concentration of intracellular Na
belongs to
Parameter c
has facts
description ap "initial concentration of intracellular Na"
default Value ap "16.0"^^double
definition ap "initial concentration of intracellular Na"
notation ap "Na_i0"
unit (slot) dp "mmol_per_m3"

Na_o (KIonEx derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/derived_variables/Na_o

belongs to
DerivedVariable c
has facts
notation ap "Na_o"
lhs ap "Na_o"
rhs ap "DNa_o + Na_o0"

Na_o0 (KIonEx parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/parameters/Na_o0

initial concentration of extracellular Na
belongs to
Parameter c
has facts
description ap "initial concentration of extracellular Na"
default Value ap "138.0"^^double
definition ap "initial concentration of extracellular Na"
notation ap "Na_o0"
unit (slot) dp "mmol_per_m3"

Nagumo1962ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Nagumo1962

belongs to
Scholarly article c
has facts
issued ap "1962"
title ap "An active pulse transmission line simulating nerve axon"
author ap "Arimoto, S."
author ap "Nagumo, J."
author ap "Yoshizawa, S."
is Part Of ap "Proceedings of the IRE"

Nengoni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/Nengo

belongs to
Software package c
has facts
description ap "A Python library for building and simulating large-scale brain models using the Neural Engineering Framework (NEF). Supports spiking and rate-based neurons with backends including NumPy, TensorFlow (NengoDL), and neuromorphic hardware (NengoLoihi)."
license ap "MIT"
code Repository ap "https://github.com/nengo/nengo"
identifier ap "10.3389/fninf.2013.00048"
url ap "https://www.nengo.ai"

Neoni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/Neo

belongs to
Software package c
has facts
description ap "A Python package for representing electrophysiology data in a common object model independently of the data source. Core I/O library for the NeuralEnsemble ecosystem."
license ap "BSD-3-Clause"
code Repository ap "https://github.com/NeuralEnsemble/python-neo"
identifier ap "10.3389/fninf.2014.00010"
url ap "https://neo.readthedocs.io"

NESTni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/NEST

belongs to
Software package c
has facts
description ap "NEST is a simulator for spiking neural network models that focuses on the dynamics, size, and structure of neural systems rather than on the exact morphology of individual neurons."
license ap "GPL-2.0-or-later"
code Repository ap "https://github.com/nest/nest-simulator"
identifier ap "10.5281/zenodo.882971"
url ap "https://www.nest-simulator.org"

NetPyNEni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/NetPyNE

belongs to
Software package c
has facts
description ap "A high-level Python interface for NEURON that facilitates the development, simulation, and analysis of biological neuronal networks. Supports multiscale models from detailed to abstract."
license ap "MIT"
code Repository ap "https://github.com/Neurosim-lab/netpyne"
identifier ap "10.7554/eLife.44494"
url ap "http://netpyne.org"

NetworkDynamics.jlni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/NetworkDynamics.jl

belongs to
Software package c
has facts
description ap "A Julia package for simulating dynamics on networks. Provides an efficient interface for defining node and edge dynamics that compiles to optimized DifferentialEquations.jl ODE/SDE problems."
license ap "MIT"
code Repository ap "https://github.com/PIK-ICoNe/NetworkDynamics.jl"
identifier ap "10.1063/5.0051387"
url ap "https://juliadynamics.github.io/NetworkDynamics.jl/stable/"

NetworkX topology APIni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/NetworkXTopology

belongs to
Backend capability c

Neuroblox.jlni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/Neuroblox.jl

belongs to
Software package c
has facts
description ap "A Julia package for building brain circuit models from composable neural mass and spiking "blox" components. Built on ModelingToolkit.jl for symbolic model construction and automatic differentiation."
license ap "MIT"
code Repository ap "https://github.com/Neuroblox/Neuroblox.jl"
url ap "https://docs.neuroblox.org"

neuroConstructni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/neuroConstruct

belongs to
Software package c
has facts
description ap "A graphical tool for constructing and simulating biologically realistic 3D neuronal networks with morphologically detailed cells. Exports to NEURON, GENESIS, and NeuroML."
license ap "GPL-2.0-only"
code Repository ap "https://github.com/NeuralEnsemble/neuroConstruct"
url ap "http://www.neuroconstruct.org"

Neurofitterni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/Neurofitter

belongs to
Software package c
has facts
description ap "A parameter optimization tool for neuroscience models. Uses evolutionary algorithms to fit model parameters to experimental electrophysiology data."
license ap "GPL-2.0-only"
code Repository ap "https://github.com/ModelDBRepository/64261"

neurolibni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/neurolib

belongs to
Software package c
has facts
description ap "A simulation framework for whole-brain neural mass models with built-in exploration, optimization, and fMRI/EEG forward-model support on empirical connectomes."
license ap "MIT"
code Repository ap "https://github.com/neurolib-dev/neurolib"
identifier ap "10.1007/s12559-021-09931-9"
url ap "https://neurolib-dev.github.io/"

NeuroMLni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/NeuroML

belongs to
Software package c
has facts
description ap "An XML-based model description language for computational neuroscience. Provides a standardized format for defining models of neurons, synapses, networks, and channels that can be simulated across multiple platforms."
license ap "LGPL-3.0-only"
code Repository ap "https://github.com/NeuroML/NeuroML2"
identifier ap "10.1371/journal.pcbi.1008349"
url ap "https://neuroml.org"

NEURONni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/NEURON

belongs to
Software package c
has facts
description ap "NEURON is a simulation environment for modeling individual neurons and networks of neurons. It provides tools for constructing, managing, and using biophysically realistic models with active membranes."
license ap "BSD-3-Clause"
code Repository ap "https://github.com/neuronsimulator/nrn"
identifier ap "10.3389/fninf.2009.00001"
url ap "https://www.neuron.yale.edu"

NineMLni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/NineML

belongs to
Software package c
has facts
description ap "A language for describing the dynamics and connectivity of spiking neuronal network models. Designed by the INCF to enable simulator-independent model exchange."
license ap "BSD-2-Clause"
code Repository ap "https://github.com/INCF/nineml-spec"
url ap "https://nineml.net"

ninf (KIonEx derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/derived_variables/ninf

belongs to
DerivedVariable c
has facts
notation ap "ninf"
lhs ap "ninf"
rhs ap "1.0/(exp((Cnk - V)/DCnk) + 1.0)"

nu_max (JansenRit parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/JansenRit/parameters/nu_max

Asymptotic of the sigmoid function Sigm_JR corresponds to the maximum firing rate of the neural populations.
belongs to
Parameter c
has facts
description ap "Asymptotic of the sigmoid function Sigm_JR corresponds to the maximum firing rate of the neural populations"
default Value ap "0.0025"^^double
has Db Xref ap G O 0099605 ep
definition ap "Asymptotic of the sigmoid function Sigm_JR corresponds to the maximum firing rate of the neural populations."
notation ap "nu_max"
unit (slot) dp "per_ms"

Numerical continuationni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/NumericalContinuation

Tracking of equilibria, periodic orbits, or invariant manifolds as a parameter is varied.
belongs to
Simulation task c

NumPy executionni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/NumPyExecution

belongs to
Backend capability c

NWBni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/NWB

belongs to
Software package c
has facts
description ap "Neurodata Without Borders — a data standard for neurophysiology providing a common format for storing diverse cellular and systems neuroscience data in HDF5 files."
license ap "BSD-3-Clause"
code Repository ap "https://github.com/NeurodataWithoutBorders/pynwb"
identifier ap "10.7554/eLife.78362"
url ap "https://www.nwb.org"

ODE integrationni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ODEIntegration

Forward integration of a deterministic ordinary differential equation.
belongs to
Simulation task c

omega (Kuramoto parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Kuramoto/parameters/omega

Sets the base line frequency for the Kuramoto oscillator.
belongs to
Parameter c
has facts
description ap "Sets the base line frequency for the Kuramoto oscillator"
default Value ap "1.0"^^double
definition ap "Sets the base line frequency for the Kuramoto oscillator."
notation ap "omega"
unit (slot) dp "rad_per_ms"

omega (KuramotoModel2 parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KuramotoModel2/parameters/omega

Sets the base line frequency for the Kuramoto oscillator in [rad/ms].
belongs to
Parameter c
has facts
default Value ap "1.0"^^double
definition ap "Sets the base line frequency for the Kuramoto oscillator in [rad/ms]."
notation ap "omega"

omega (SupHopf parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/SupHopf/parameters/omega

Angular frequency.
belongs to
Parameter c
has facts
description ap "Angular frequency"
default Value ap "1.0"^^double
definition ap "Angular frequency."
notation ap "omega"

Open Source Brainni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/OpenSourceBrain

belongs to
Software package c
has facts
description ap "A platform for sharing and collaboratively developing computational neuroscience models in standardized formats, primarily NeuroML."
license ap "LGPL-3.0-only"
code Repository ap "https://github.com/OpenSourceBrain"
url ap "https://www.opensourcebrain.org"

OpenWormni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/OpenWorm

belongs to
Software package c
has facts
description ap "An open science project to build a comprehensive computational model of the C. elegans nematode, including its 302-neuron nervous system."
license ap "MIT"
code Repository ap "https://github.com/openworm/OpenWorm"
url ap "http://openworm.org"

Ott2002ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Ott2002

belongs to
Book c
has facts
issued ap "2010"
title ap "Chaos in Dynamical Systems"
author ap "Ott, Edward"
publisher ap "Cambridge University Press"

Ott2010ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Ott2010

belongs to
Book c
has facts
issued ap "2010"
title ap "Chaos in Dynamical Systems"
author ap "Ott, Edward"
publisher ap "Cambridge University Press"

OttRiddled2014ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/OttRiddled2014

belongs to
Creative work c
has facts
title ap "The transition to chaotic attractors with riddled basins"
author ap "Alexander, J. C."
author ap "Kan, I."
author ap "Ott, Edward"
author ap "Sommerer, J. C."
author ap "Yorke, James A."
url ap "http://yorke.umd.edu/Yorke_papers_most_cited_and_post2000/1994_04_Ott_Alexander_Kan_Sommerer_PhysicaD_riddled%20basins.pdf"

ou_drift (ZerlautAdaptationFirstOrder state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/state_variables/ou_drift

belongs to
StateVariable c
has facts
notation ap "ou_drift"
lhs ap "Derivative(ou_drift, t)"
rhs ap "-ou_drift/tau_OU"

output (EpileptorRestingState derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/EpileptorRestingState/derived_variables/output

belongs to
DerivedVariable c
has facts
notation ap "output"
lhs ap "output"
rhs ap "p*(-x1 + x2) + x_rs*(1 - p)"

p (EpileptorRestingState parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/EpileptorRestingState/parameters/p

Linear coefficient.
belongs to
Parameter c
has facts
description ap "Linear coefficient"
default Value ap "0.0"^^double
definition ap "Linear coefficient."
notation ap "p"

p (JansenRit1995 parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/JansenRit1995/parameters/p

belongs to
Parameter c
has facts
description ap "Mean external input (afferent pulse density)"
default Value ap "220"^^integer
notation ap "p"
unit (slot) dp "per_s"

p (ModelJansen1995 parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ModelJansen1995/parameters/p

belongs to
Parameter c
has facts
default Value ap "0.24"^^double
notation ap "p"
unit (slot) dp "per_ms"

P (PreSigmoidal parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/coupling_functions/PreSigmoidal/parameters/P

belongs to
Parameter c
has facts
description ap "Excitation-Inhibition ratio"
default Value ap "1.0"^^double
notation ap "P"

P (WilsonCowan parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/WilsonCowan/parameters/P

External stimulus to the excitatory population (Wilson and Cowan, 1972).
belongs to
Parameter c
has facts
description ap "External stimulus to the excitatory population (Wilson and Cowan, 1972)"
default Value ap "0.0"^^double
has Db Xref ap G O 0060079 ep
definition ap "External stimulus to the excitatory population (Wilson and Cowan, 1972)."
notation ap "P"

P (ZetterbergJansen parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZetterbergJansen/parameters/P

Maximum firing rate to the pyramidal population [ms^-1]. (External stimulus. Constant intensity.Entry point for coupling.)
belongs to
Parameter c
has facts
description ap "Maximum firing rate to the pyramidal population [ms^-1]"
default Value ap "0.12"^^double
has Db Xref ap C L 0000598 ni
has Db Xref ap G O 0099605 ep
definition ap "Maximum firing rate to the pyramidal population [ms^-1]. (External stimulus. Constant intensity.Entry point for coupling.)"
notation ap "P"

P0_e (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/P0_e

Polynome of excitatory phenomenological threshold (order 9)
belongs to
Parameter c
has facts
description ap "Polynome of excitatory phenomenological threshold (order 9)"
default Value ap "-0.04983106"^^double
definition ap "Polynome of excitatory phenomenological threshold (order 9)"
notation ap "P0_e"

P0_i (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/P0_i

Polynome of inhibitory phenomenological threshold (order 9)
belongs to
Parameter c
has facts
description ap "Polynome of inhibitory phenomenological threshold (order 9)"
default Value ap "-0.05149122"^^double
definition ap "Polynome of inhibitory phenomenological threshold (order 9)"
notation ap "P0_i"

P1_e (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/P1_e

Polynome of excitatory phenomenological threshold (order 9)
belongs to
Parameter c
has facts
description ap "Polynome of excitatory phenomenological threshold (order 9)"
default Value ap "0.005063551"^^double
definition ap "Polynome of excitatory phenomenological threshold (order 9)"
notation ap "P1_e"

P1_i (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/P1_i

Polynome of inhibitory phenomenological threshold (order 9)
belongs to
Parameter c
has facts
description ap "Polynome of inhibitory phenomenological threshold (order 9)"
default Value ap "0.004003689"^^double
definition ap "Polynome of inhibitory phenomenological threshold (order 9)"
notation ap "P1_i"

P2_e (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/P2_e

Polynome of excitatory phenomenological threshold (order 9)
belongs to
Parameter c
has facts
description ap "Polynome of excitatory phenomenological threshold (order 9)"
default Value ap "-0.02347012"^^double
definition ap "Polynome of excitatory phenomenological threshold (order 9)"
notation ap "P2_e"

P2_i (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/P2_i

Polynome of inhibitory phenomenological threshold (order 9)
belongs to
Parameter c
has facts
description ap "Polynome of inhibitory phenomenological threshold (order 9)"
default Value ap "-0.008352014"^^double
definition ap "Polynome of inhibitory phenomenological threshold (order 9)"
notation ap "P2_i"

P3_e (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/P3_e

Polynome of excitatory phenomenological threshold (order 9)
belongs to
Parameter c
has facts
description ap "Polynome of excitatory phenomenological threshold (order 9)"
default Value ap "0.002295151"^^double
definition ap "Polynome of excitatory phenomenological threshold (order 9)"
notation ap "P3_e"

P3_i (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/P3_i

Polynome of inhibitory phenomenological threshold (order 9)
belongs to
Parameter c
has facts
description ap "Polynome of inhibitory phenomenological threshold (order 9)"
default Value ap "2.414238E-4"^^double
definition ap "Polynome of inhibitory phenomenological threshold (order 9)"
notation ap "P3_i"

P4_e (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/P4_e

Polynome of excitatory phenomenological threshold (order 9)
belongs to
Parameter c
has facts
description ap "Polynome of excitatory phenomenological threshold (order 9)"
default Value ap "-4.105303E-4"^^double
definition ap "Polynome of excitatory phenomenological threshold (order 9)"
notation ap "P4_e"

P4_i (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/P4_i

Polynome of inhibitory phenomenological threshold (order 9)
belongs to
Parameter c
has facts
description ap "Polynome of inhibitory phenomenological threshold (order 9)"
default Value ap "-5.070645E-4"^^double
definition ap "Polynome of inhibitory phenomenological threshold (order 9)"
notation ap "P4_i"

P5_e (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/P5_e

Polynome of excitatory phenomenological threshold (order 9)
belongs to
Parameter c
has facts
description ap "Polynome of excitatory phenomenological threshold (order 9)"
default Value ap "0.01054705"^^double
definition ap "Polynome of excitatory phenomenological threshold (order 9)"
notation ap "P5_e"

P5_i (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/P5_i

Polynome of inhibitory phenomenological threshold (order 9)
belongs to
Parameter c
has facts
description ap "Polynome of inhibitory phenomenological threshold (order 9)"
default Value ap "0.001434539"^^double
definition ap "Polynome of inhibitory phenomenological threshold (order 9)"
notation ap "P5_i"

P6_e (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/P6_e

Polynome of excitatory phenomenological threshold (order 9)
belongs to
Parameter c
has facts
description ap "Polynome of excitatory phenomenological threshold (order 9)"
default Value ap "-0.03659253"^^double
definition ap "Polynome of excitatory phenomenological threshold (order 9)"
notation ap "P6_e"

P6_i (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/P6_i

Polynome of inhibitory phenomenological threshold (order 9)
belongs to
Parameter c
has facts
description ap "Polynome of inhibitory phenomenological threshold (order 9)"
default Value ap "-0.01468669"^^double
definition ap "Polynome of inhibitory phenomenological threshold (order 9)"
notation ap "P6_i"

P7_e (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/P7_e

Polynome of excitatory phenomenological threshold (order 9)
belongs to
Parameter c
has facts
description ap "Polynome of excitatory phenomenological threshold (order 9)"
default Value ap "0.007437488"^^double
definition ap "Polynome of excitatory phenomenological threshold (order 9)"
notation ap "P7_e"

P7_i (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/P7_i

Polynome of inhibitory phenomenological threshold (order 9)
belongs to
Parameter c
has facts
description ap "Polynome of inhibitory phenomenological threshold (order 9)"
default Value ap "0.004502706"^^double
definition ap "Polynome of inhibitory phenomenological threshold (order 9)"
notation ap "P7_i"

P8_e (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/P8_e

Polynome of excitatory phenomenological threshold (order 9)
belongs to
Parameter c
has facts
description ap "Polynome of excitatory phenomenological threshold (order 9)"
default Value ap "0.001265065"^^double
definition ap "Polynome of excitatory phenomenological threshold (order 9)"
notation ap "P8_e"

P8_i (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/P8_i

Polynome of inhibitory phenomenological threshold (order 9)
belongs to
Parameter c
has facts
description ap "Polynome of inhibitory phenomenological threshold (order 9)"
default Value ap "0.002847219"^^double
definition ap "Polynome of inhibitory phenomenological threshold (order 9)"
notation ap "P8_i"

P9_e (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/P9_e

Polynome of excitatory phenomenological threshold (order 9)
belongs to
Parameter c
has facts
description ap "Polynome of excitatory phenomenological threshold (order 9)"
default Value ap "-0.04072161"^^double
definition ap "Polynome of excitatory phenomenological threshold (order 9)"
notation ap "P9_e"

P9_i (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/P9_i

Polynome of inhibitory phenomenological threshold (order 9)
belongs to
Parameter c
has facts
description ap "Polynome of inhibitory phenomenological threshold (order 9)"
default Value ap "-0.0153578"^^double
definition ap "Polynome of inhibitory phenomenological threshold (order 9)"
notation ap "P9_i"

p_connect_e (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/p_connect_e

connectivity probability
belongs to
Parameter c
has facts
description ap "connectivity probability"
default Value ap "0.05"^^double
definition ap "connectivity probability"
notation ap "p_connect_e"

p_connect_i (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/p_connect_i

connectivity probability
belongs to
Parameter c
has facts
description ap "connectivity probability"
default Value ap "0.05"^^double
definition ap "connectivity probability"
notation ap "p_connect_i"

P_e (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/P_e

Polynome of excitatory phenomenological threshold (order 9)
belongs to
Parameter c
has facts
description ap "Polynome of excitatory phenomenological threshold (order 9)"
default Value ap "-0.04983106"^^double
definition ap "Polynome of excitatory phenomenological threshold (order 9)"
notation ap "P_e"

p_i (StefanescuJirsa3D derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa3D/derived_variables/p_i

belongs to
DerivedVariable c
has facts
description ap "Per-mode quadratic coefficient for the inhibitory beta dynamics."
has Db Xref ap G O 0060080 ep
notation ap "p_i"
lhs ap "p_i"
rhs ap "d"

P_i (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/P_i

Polynome of inhibitory phenomenological threshold (order 9)
belongs to
Parameter c
has facts
description ap "Polynome of inhibitory phenomenological threshold (order 9)"
default Value ap "-0.05149122"^^double
definition ap "Polynome of inhibitory phenomenological threshold (order 9)"
notation ap "P_i"

Pang2011ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Pang2011

belongs to
Scholarly article c
has facts
issued ap "2011"
title ap "A new hyperchaotic system from the L"u system and its control"
author ap "Liu, Y."
author ap "Pang, S."
is Part Of ap "Journal of Computational and Applied Mathematics"
issue Number ap "8"
pagination ap "2775--2789"
volume Number ap "235"

Parameter explorationni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ParameterExploration

belongs to
Simulation task c

permeability (meg parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/observation_models/meg/parameters/permeability

belongs to
Parameter c
has facts
description ap "Magnetic constant (permeability of free space)"
default Value ap "1.256637E-6"^^double
notation ap "permeability"
unit (slot) dp "H_per_m"

phase (KuramotoModel2 derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KuramotoModel2/derived_variables/phase

belongs to
DerivedVariable c
has facts
description ap "Normalized phase output"
notation ap "phase"
rhs ap "theta / (2*pi)"

phi (LarterBreakspear parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/LarterBreakspear/parameters/phi

Temperature scaling factor.
belongs to
Parameter c
has facts
description ap "Temperature scaling factor"
default Value ap "0.7"^^double
definition ap "Temperature scaling factor."
notation ap "phi"

Proix2014ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Proix2014

belongs to
Scholarly article c
has facts
issued ap "2014"
title ap "A neural mass model of seizure initiation and propagation"
author ap "Proix, Timoth\'ee"
author ap "others"
is Part Of ap "Brain"

Proix2017ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Proix2017

belongs to
Scholarly article c
has facts
issued ap "2017"
title ap "Individual structural connectivity defines propagation networks in partial epilepsy"
author ap "Proix, Timoth\'ee"
author ap "others"
is Part Of ap "Brain"

PSICSni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/PSICS

belongs to
Software package c
has facts
description ap "Parallel Stochastic Ion Channel Simulator — a fast simulator for stochastic ion channel models in morphologically detailed neurons using efficient population-based algorithms."
license ap "MPL-2.0"
code Repository ap "https://github.com/BorgwardtLab/PSICS"

pyNeuroMLni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/pyNeuroML

belongs to
Software package c
has facts
description ap "Python API and command-line tools for NeuroML/LEMS model creation, validation, visualization, and simulation via jNeuroML and direct simulator backends."
license ap "LGPL-3.0-only"
code Repository ap "https://github.com/NeuroML/pyNeuroML"
url ap "https://docs.neuroml.org/Userdocs/Software/pyNeuroML.html"

PyNNni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/PyNN

belongs to
Software package c
has facts
description ap "A Python package for simulator-independent specification of spiking neuronal network models. Provides a common API for NEST, NEURON, Brian2, GeNN, and SpiNNaker backends."
license ap "CeCILL-2.0"
code Repository ap "https://github.com/NeuralEnsemble/PyNN"
identifier ap "10.3389/fninf.2008.00011"
url ap "https://neuralensemble.org/PyNN/"

pynn_gennni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/pynn_genn

belongs to
Software package c
has facts
description ap "PyNN interface for the GeNN GPU simulator, enabling PyNN models to run on NVIDIA GPUs via the GeNN backend."
license ap "GPL-2.0-only"
code Repository ap "https://github.com/genn-team/pynn_genn"

PyRatesni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/PyRates

belongs to
Software package c
has facts
description ap "A Python framework for rate-based and neural mass network simulations. Provides symbolic equation parsing, automatic code generation, and parameter continuation support."
license ap "BSD-3-Clause"
code Repository ap "https://github.com/pyrates-neuroscience/PyRates"
identifier ap "10.1371/journal.pone.0244637"
url ap "https://pyrates.readthedocs.io"

PyRhOni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/PyRhO

belongs to
Software package c
has facts
description ap "A Python module for fitting, simulating, and analyzing optogenetic rhodopsin photocurrent models. Integrates with NEURON and Brian2."
license ap "BSD-3-Clause"
code Repository ap "https://github.com/ProjectPyRhO/PyRhO"
identifier ap "10.3389/fninf.2016.00008"
url ap "https://pyrho.readthedocs.io"

q (CoombesByrne state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/CoombesByrne/state_variables/q

belongs to
StateVariable c
has facts
notation ap "q"
lhs ap "Derivative(q, t)"
rhs ap "alpha*(-g + pi*k*r - 2*q)"

Q (PreSigmoidal parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/coupling_functions/PreSigmoidal/parameters/Q

belongs to
Parameter c
has facts
description ap "Average"
default Value ap "1.0"^^double
notation ap "Q"

Q (WilsonCowan parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/WilsonCowan/parameters/Q

External stimulus to the inhibitory population (Wilson and Cowan, 1972).
belongs to
Parameter c
has facts
description ap "External stimulus to the inhibitory population (Wilson and Cowan, 1972)"
default Value ap "0.0"^^double
has Db Xref ap G O 0060080 ep
definition ap "External stimulus to the inhibitory population (Wilson and Cowan, 1972)."
notation ap "Q"

Q (ZetterbergJansen parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZetterbergJansen/parameters/Q

Maximum firing rate to the interneurons population [ms^-1]. (External stimulus. Constant intensity.Entry point for coupling.)
belongs to
Parameter c
has facts
description ap "Maximum firing rate to the interneurons population [ms^-1]"
default Value ap "0.12"^^double
has Db Xref ap C L 0000099 ni
has Db Xref ap G O 0099605 ep
definition ap "Maximum firing rate to the interneurons population [ms^-1]. (External stimulus. Constant intensity.Entry point for coupling.)"
notation ap "Q"

Q_e (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/Q_e

excitatory quantal conductance [nS]
belongs to
Parameter c
has facts
description ap "excitatory quantal conductance [nS]"
default Value ap "1.5"^^double
has Db Xref ap G O 0060079 ep
definition ap "excitatory quantal conductance [nS]"
notation ap "Q_e"

Q_i (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/Q_i

inhibitory quantal conductance [nS]
belongs to
Parameter c
has facts
description ap "inhibitory quantal conductance [nS]"
default Value ap "5.0"^^double
has Db Xref ap G O 0060080 ep
definition ap "inhibitory quantal conductance [nS]"
notation ap "Q_i"

Q_V (LarterBreakspear derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/LarterBreakspear/derived_variables/Q_V

belongs to
DerivedVariable c
has facts
description ap "Average firing rate of the population of PCs, V."
has Db Xref ap G O 0099605 ep
notation ap "Q_V"
lhs ap "Q_V"
rhs ap "0.5*Q_Vmax*(tanh((V - V_T)/delta_V) + 1)"

Q_Vmax (LarterBreakspear parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/LarterBreakspear/parameters/Q_Vmax

Maximal firing rate for excitatory populations.
belongs to
Parameter c
has facts
description ap "Maximal firing rate for excitatory populations"
default Value ap "1.0"^^double
has Db Xref ap G O 0098976 ep
has Db Xref ap G O 0099605 ep
definition ap "Maximal firing rate for excitatory populations."
notation ap "Q_Vmax"
unit (slot) dp "kHz"

Q_Z (LarterBreakspear derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/LarterBreakspear/derived_variables/Q_Z

belongs to
DerivedVariable c
has facts
description ap "Average firing rate of the population of IINs, Z."
has Db Xref ap G O 0099605 ep
notation ap "Q_Z"
lhs ap "Q_Z"
rhs ap "0.5*Q_Zmax*(tanh((Z - Z_T)/delta_Z) + 1)"

Q_Zmax (LarterBreakspear parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/LarterBreakspear/parameters/Q_Zmax

Maximal firing rate for inhibitory population.
belongs to
Parameter c
has facts
description ap "Maximal firing rate for inhibitory population"
default Value ap "1.0"^^double
has Db Xref ap G O 0099605 ep
definition ap "Maximal firing rate for inhibitory population."
notation ap "Q_Zmax"
unit (slot) dp "kHz"

Qi2008ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Qi2008

belongs to
Scholarly article c
has facts
issued ap "2008"
title ap "On a new hyperchaotic system"
author ap "Chen, G."
author ap "Qi, G."
author ap "van Wyk, B. J."
author ap "van Wyk, M. A."
is Part Of ap "Physics Letters A"
issue Number ap "2"
pagination ap "124--136"
volume Number ap "372"

r (CoombesByrne state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/CoombesByrne/state_variables/r

belongs to
StateVariable c
has facts
notation ap "r"
lhs ap "Derivative(r, t)"
rhs ap "Delta/pi + 2*V*r - g*r"

r (CoombesByrne2D state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/CoombesByrne2D/state_variables/r

belongs to
StateVariable c
has facts
notation ap "r"
lhs ap "Derivative(r, t)"
rhs ap "Delta/pi + 2*V*r - pi*k*r**2"

r (Epileptor2D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor2D/parameters/r

Temporal scaling in the slow state-variable, \ called :math:`1\tau_{0}` in Jirsa paper (see class Epileptor).
belongs to
Parameter c
has facts
description ap "Temporal scaling in the slow state-variable, \ called :math:`1\tau_{0}` in Jirsa paper (see class Epileptor)"
default Value ap "3.5E-4"^^double
definition ap "Temporal scaling in the slow state-variable, \ called :math:`1\tau_{0}` in Jirsa paper (see class Epileptor)."
notation ap "r"

r (Epileptor5D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor5D/parameters/r

Temporal scaling in the third state variable, called :math:`1/\tau_{0}` in Jirsa paper
belongs to
Parameter c
has facts
description ap "Temporal scaling in the third state variable, called :math:`1/\tau_{0}` in Jirsa paper"
default Value ap "3.5E-4"^^double
definition ap "Temporal scaling in the third state variable, called :math:`1/\tau_{0}` in Jirsa paper"
notation ap "r"

r (EpileptorRestingState parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/EpileptorRestingState/parameters/r

Temporal scaling in the third state-variable z, called :math:'1/ au_{0}' in Jirsa et al. (2014).
belongs to
Parameter c
has facts
description ap "Temporal scaling in the third state-variable z, called :math:'1/ au_{0}' in Jirsa et al"
default Value ap "3.5E-4"^^double
definition ap "Temporal scaling in the third state-variable z, called :math:'1/ au_{0}' in Jirsa et al. (2014)."
notation ap "r"

r (GastSchmidtKnosche_SD state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/GastSchmidtKnosche_SD/state_variables/r

belongs to
StateVariable c
has facts
notation ap "r"
lhs ap "Derivative(r, t)"
rhs ap "(Delta/(pi*tau) + 2*V*r)/tau"

r (GastSchmidtKnosche_SF state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/GastSchmidtKnosche_SF/state_variables/r

belongs to
StateVariable c
has facts
notation ap "r"
lhs ap "Derivative(r, t)"
rhs ap "(Delta/(pi*tau) + 2*V*r)/tau"

r (JansenRit parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/JansenRit/parameters/r

Steepness (or gain) parameter of the sigmoid function Sigm_JR.
belongs to
Parameter c
has facts
description ap "Steepness (or gain) parameter of the sigmoid function Sigm_JR"
default Value ap "0.56"^^double
definition ap "Steepness (or gain) parameter of the sigmoid function Sigm_JR."
notation ap "r"
unit (slot) dp "per_mV"

r (JansenRit1995 parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/JansenRit1995/parameters/r

belongs to
Parameter c
has facts
description ap "Steepness of sigmoid transformation"
default Value ap "0.56"^^double
notation ap "r"
unit (slot) dp "per_mV"

r (KIonEx derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/derived_variables/r

belongs to
DerivedVariable c
has facts
notation ap "r"
lhs ap "r"
rhs ap "R_minus*x/pi"

r (ModelJansen1995 parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ModelJansen1995/parameters/r

belongs to
Parameter c
has facts
default Value ap "0.56"^^double
notation ap "r"
unit (slot) dp "per_mV"

r (MontbrioPazoRoxin state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/MontbrioPazoRoxin/state_variables/r

belongs to
StateVariable c
has facts
notation ap "r"
lhs ap "Derivative(r, t)"
rhs ap "(Delta/(pi*tau) + 2*V*r)/tau"

r (SigmoidalJansenRit parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/coupling_functions/SigmoidalJansenRit/parameters/r

belongs to
Parameter c
has facts
description ap "The steepness of the sigmoidal transformation"
default Value ap "0.56"^^double
notation ap "r"

r (StefanescuJirsa3D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa3D/parameters/r

Adaptation parameter (Hindmarsh-Rose r).
belongs to
Parameter c
has facts
default Value ap "0.006"^^double
definition ap "Adaptation parameter (Hindmarsh-Rose r)."
notation ap "r"

r_E (CakanObermayer derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/CakanObermayer/derived_variables/r_E

belongs to
DerivedVariable c
has facts
description ap "Excitatory population firing rate. In full aLN this is ``Phi(mu_E_eff, s_EE)`` with ``Phi`` precomputed; here a sigmoid stand-in is used."
notation ap "r_E"
lhs ap "r_E"
rhs ap "r_max/(1 + exp(-k_phi*(mu_se - mu_th)))"

r_e (DumontGutkin state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/DumontGutkin/state_variables/r_e

belongs to
StateVariable c
has facts
notation ap "r_e"
lhs ap "Derivative(r_e, t)"
rhs ap "(Delta_e/(pi*tau_e) + 2*V_e*r_e)/tau_e"

r_e (WilsonCowan parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/WilsonCowan/parameters/r_e

Excitatory refractory period
belongs to
Parameter c
has facts
description ap "Excitatory refractory period"
default Value ap "1.0"^^double
has Db Xref ap G O 0098815 ep
definition ap "Excitatory refractory period"
notation ap "r_e"

r_I (CakanObermayer derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/CakanObermayer/derived_variables/r_I

belongs to
DerivedVariable c
has facts
description ap "Inhibitory population firing rate (sigmoid stand-in for aLN Phi)."
notation ap "r_I"
lhs ap "r_I"
rhs ap "r_max/(1 + exp(-k_phi*(mu_si - mu_th)))"

r_i (DumontGutkin state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/DumontGutkin/state_variables/r_i

belongs to
StateVariable c
has facts
notation ap "r_i"
lhs ap "Derivative(r_i, t)"
rhs ap "(Delta_i/(pi*tau_i) + 2*V_i*r_i)/tau_i"

r_i (WilsonCowan parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/WilsonCowan/parameters/r_i

Inhibitory refractory period
belongs to
Parameter c
has facts
description ap "Inhibitory refractory period"
default Value ap "1.0"^^double
has Db Xref ap G O 0098828 ep
definition ap "Inhibitory refractory period"
notation ap "r_i"

r_max (CakanObermayer parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/CakanObermayer/parameters/r_max

Asymptotic firing rate used in the sigmoid surrogate for the aLN transfer function (sigmoid stand-in for the precomputed lookup table).
belongs to
Parameter c
has facts
default Value ap "0.2"^^double
definition ap "Asymptotic firing rate used in the sigmoid surrogate for the aLN transfer function (sigmoid stand-in for the precomputed lookup table)."
notation ap "r_max"
unit (slot) dp "per_ms"

R_minus (KIonEx parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/parameters/R_minus

curvature left parabola
belongs to
Parameter c
has facts
description ap "curvature left parabola"
default Value ap "0.5"^^double
definition ap "curvature left parabola"
notation ap "R_minus"

r_NMDA (LarterBreakspear parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/LarterBreakspear/parameters/r_NMDA

Ratio of NMDA to AMPA receptors.
belongs to
Parameter c
has facts
description ap "Ratio of NMDA to AMPA receptors"
default Value ap "0.25"^^double
has Db Xref ap G O 0004971 ep
definition ap "Ratio of NMDA to AMPA receptors."
notation ap "r_NMDA"

R_ossler1976ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/R_ossler1976

belongs to
Scholarly article c
has facts
issued ap "1976"
title ap "An Equation for Continuous Chaos"
author ap "R"ossler, Otto E."
identifier ap "10.1016/0375-9601(76)90101-8"
is Part Of ap "Physics Letters A"
issue Number ap "5"
pagination ap "397--398"
volume Number ap "57"

R_plus (KIonEx parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/parameters/R_plus

curvature right parabola
belongs to
Parameter c
has facts
description ap "curvature right parabola"
default Value ap "-0.5"^^double
definition ap "curvature right parabola"
notation ap "R_plus"

RateML rwongwang ground truthni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/experiments/RateML_ReducedWongWang

belongs to
SimulationExperiment c

Rawni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/observation_models/raw

belongs to
Observation c
has facts
description ap "Records all state variables at every integration step without any transformation. Identity passthrough of the full simulation state."

RDE integrationni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/RDEIntegration

Forward integration of a random differential equation: parameters drawn from a distribution (Bayesian / ensemble simulation).
belongs to
Simulation task c

Reduced Wong-Wang (functional)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWangFunc

has facts
exhibits regime op Bistable ni
has attractor op Fixed point ni
has stochasticity character op Deterministic ni
models anatomical region op U B E R O N 0000956 ni
phase-space dimension dp "1"^^integer
pref Label ap "Reduced Wong-Wang (functional)"@en

ReducedWongWangni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWang

belongs to
Dynamics c
has facts
exhibits regime op Bistable ni
exhibits regime op Multistable ni
has attractor op Fixed point ni
has model feature op Excitatory/inhibitory subpopulations ni
has stochasticity character op Deterministic ni
models cell type op C L 0000099 ni
models cell type op C L 0000598 ni
models neurotransmitter system op G O 0007214 ni
models neurotransmitter system op G O 0035249 ni
has timescale separation dp "false"^^boolean
phase-space dimension dp "1"^^integer
description ap "Reduced WongWang (RWW) is a biologically-inspired one-dimensional (i.e., only one state-variable 'S') neural mass model that approximates the realistic temporal dynamics of a detailed spiking and conductance-based synaptic large-scale network (Deco et al., 2013). RWW is the dynamical mean-field (DMF) reduction of the Reduced WongWang Exc-Inh model, that consists in disentangling the contribution of the two neuronal populations (excitatory and inhibitory) in order to study the time evolution of just one pool of neurons for each network node (Wong & Wang, 2006). It results that the dynamics of each network node described the temporal evolution of the opening probability of the NMDA channels."
references ap Deco2013 ni
references ap Wong2006 ni
pref Label ap "Reduced Wong-Wang"@en
has Derived Variable ap H (ReducedWongWang derived variable) ni
has Derived Variable ap x (ReducedWongWang derived variable) ni
has Parameter ap I_o (ReducedWongWang parameter) ni
has Parameter ap J_N (ReducedWongWang parameter) ni
has Parameter ap a (ReducedWongWang parameter) ni
has Parameter ap b (ReducedWongWang parameter) ni
has Parameter ap d (ReducedWongWang parameter) ni
has Parameter ap gamma (ReducedWongWang parameter) ni
has Parameter ap tau_s (ReducedWongWang parameter) ni
has Parameter ap w (ReducedWongWang parameter) ni
has State Variable ap S (ReducedWongWang state variable) ni
model_type (slot) ap "mean_field"

ReducedWongWangExcInhni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWangExcInh

belongs to
Dynamics c
has facts
exhibits regime op Bistable ni
exhibits regime op Multistable ni
has attractor op Fixed point ni
has model feature op Excitatory/inhibitory subpopulations ni
has stochasticity character op Deterministic ni
models anatomical region op U B E R O N 0000956 ni
models cell type op C L 0000099 ni
models cell type op C L 0000598 ni
models neurotransmitter system op G O 0007214 ni
models neurotransmitter system op G O 0035249 ni
has timescale separation dp "false"^^boolean
phase-space dimension dp "2"^^integer
description ap "Reduced WongWang Exc-Inh (RWW_EI) is a biologically-inspired two-dimensional (i.e., two state-variables ('S_E','S_I')) neural mass model describing the dynamics of a cortical area consisting of local networks of excitatory (AMPA) and inhibitory (GABA-A) populations of spiking neurons interconnected via NMDA synapses. These neurons are organized into an inhibitory population accounting for 20% of the neurons and an excitatory population accounting for 80% of the neurons."
references ap Deco2014 ni
pref Label ap "Reduced Wong-Wang (E/I)"@en
has Derived Variable ap H_e (ReducedWongWangExcInh derived variable) ni
has Derived Variable ap H_i (ReducedWongWangExcInh derived variable) ni
has Derived Variable ap J_N_S_e (ReducedWongWangExcInh derived variable) ni
has Derived Variable ap coupling (ReducedWongWangExcInh derived variable) ni
has Derived Variable ap x_e (ReducedWongWangExcInh derived variable) ni
has Derived Variable ap x_i (ReducedWongWangExcInh derived variable) ni
has Parameter ap G (ReducedWongWangExcInh parameter) ni
has Parameter ap I_ext (ReducedWongWangExcInh parameter) ni
has Parameter ap I_o (ReducedWongWangExcInh parameter) ni
has Parameter ap J_N (ReducedWongWangExcInh parameter) ni
has Parameter ap J_i (ReducedWongWangExcInh parameter) ni
has Parameter ap W_e (ReducedWongWangExcInh parameter) ni
has Parameter ap W_i (ReducedWongWangExcInh parameter) ni
has Parameter ap a_e (ReducedWongWangExcInh parameter) ni
has Parameter ap a_i (ReducedWongWangExcInh parameter) ni
has Parameter ap b_e (ReducedWongWangExcInh parameter) ni
has Parameter ap b_i (ReducedWongWangExcInh parameter) ni
has Parameter ap d_e (ReducedWongWangExcInh parameter) ni
has Parameter ap d_i (ReducedWongWangExcInh parameter) ni
has Parameter ap gamma_e (ReducedWongWangExcInh parameter) ni
has Parameter ap gamma_i (ReducedWongWangExcInh parameter) ni
has Parameter ap lamda (ReducedWongWangExcInh parameter) ni
has Parameter ap tau_e (ReducedWongWangExcInh parameter) ni
has Parameter ap tau_i (ReducedWongWangExcInh parameter) ni
has Parameter ap w_p (ReducedWongWangExcInh parameter) ni
has State Variable ap S_e (ReducedWongWangExcInh state variable) ni
has State Variable ap S_i (ReducedWongWangExcInh state variable) ni
model_type (slot) ap "mean_field"

ReducedWongWangTvboptimni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWangTvboptim

belongs to
Dynamics c
has facts
exhibits regime op Bistable ni
has attractor op Fixed point ni
has stochasticity character op Deterministic ni
models anatomical region op U B E R O N 0000956 ni
phase-space dimension dp "1"^^integer
description ap "The Reduced Wong-Wang (RWW) model is a biophysically-based neural mass model that describes the dynamics of NMDA-mediated synaptic gating (Deco et al., 2013). It captures the slow dynamics relevant for resting-state fMRI and has been widely used for modeling whole-brain functional connectivity. RWW is the dynamical mean-field (DMF) reduction of the Wong & Wang (2006) spiking model. Each network node is described by a single state variable S representing the average NMDA synaptic gating (fraction of open channels). The total synaptic input x combines local excitatory recurrence (w), external input (I_o), and long-range network coupling (instant and delayed) scaled by the synaptic coupling strength J_N. The sigmoid transfer function H(x) maps the total input current to the average population firing rate. In a network setting, the global coupling strength G (a coupling parameter) scales the structural connectivity weights that modulate inter-regional communication."
references ap Deco2013 ni
references ap Wong2006 ni
pref Label ap "Reduced Wong-Wang (tvboptim)"@en
has Derived Variable ap H_x (ReducedWongWangTvboptim derived variable) ni
has Derived Variable ap x (ReducedWongWangTvboptim derived variable) ni
has Parameter ap I_o (ReducedWongWangTvboptim parameter) ni
has Parameter ap J_N (ReducedWongWangTvboptim parameter) ni
has Parameter ap a (ReducedWongWangTvboptim parameter) ni
has Parameter ap b (ReducedWongWangTvboptim parameter) ni
has Parameter ap d (ReducedWongWangTvboptim parameter) ni
has Parameter ap gamma (ReducedWongWangTvboptim parameter) ni
has Parameter ap tau_s (ReducedWongWangTvboptim parameter) ni
has Parameter ap w (ReducedWongWangTvboptim parameter) ni
has State Variable ap S (ReducedWongWangTvboptim state variable) ni
model_type (slot) ap "mean_field"

reference_electrode (eeg parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/observation_models/eeg/parameters/reference_electrode

belongs to
Parameter c
has facts
description ap "Re-referencing scheme. Options: - Electrode label (e.g. "Cz"): subtract that electrode signal - "average": subtract mean across all channels - null: ideal reference-free recording"
notation ap "reference_electrode"

rho (KIonEx parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/parameters/rho

maximal Na/K pump current
belongs to
Parameter c
has facts
description ap "maximal Na/K pump current"
default Value ap "250.0"^^double
definition ap "maximal Na/K pump current"
notation ap "rho"
unit (slot) dp "pA"

rho_1 (ZetterbergJansen parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZetterbergJansen/parameters/rho_1

Steepness of the sigmoidal transformation [mV^-1].
belongs to
Parameter c
has facts
description ap "Steepness of the sigmoidal transformation [mV^-1]"
default Value ap "0.56"^^double
definition ap "Steepness of the sigmoidal transformation [mV^-1]."
notation ap "rho_1"

rho_2 (ZetterbergJansen parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZetterbergJansen/parameters/rho_2

Firing threshold (PSP) for which a 50% firing rate is achieved. In other words, it is the value of the average membrane potential corresponding to the inflection point of the sigmoid [mV]. Population mean firing threshold.
belongs to
Parameter c
has facts
description ap "Firing threshold (PSP) for which a 50% firing rate is achieved"
default Value ap "6.0"^^double
definition ap "Firing threshold (PSP) for which a 50% firing rate is achieved. In other words, it is the value of the average membrane potential corresponding to the inflection point of the sigmoid [mV]. Population mean firing threshold."
notation ap "rho_2"

Rikitake1958ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Rikitake1958

belongs to
Scholarly article c
has facts
issued ap "1958"
title ap "Oscillations of a System of Disks"
author ap "Rikitake, Tsuneji"
identifier ap "10.1017/S0305004100033283"
is Part Of ap "Proceedings of the Cambridge Philosophical Society"
pagination ap "89--105"
volume Number ap "54"

Roessler1976ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Roessler1976

belongs to
Scholarly article c
has facts
issued ap "1976"
title ap "An Equation for Continuous Chaos"
author ap "Roessler, Otto E."
identifier ap "10.1016/0375-9601(76)90101-8"
is Part Of ap "Physics Letters A"
issue Number ap "5"
pagination ap "397--398"
volume Number ap "57"

Roessler1979ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Roessler1979

belongs to
Scholarly article c
has facts
issued ap "1979"
title ap "An equation for hyperchaos"
author ap "R"ossler, Otto E."
is Part Of ap "Physics Letters A"
issue Number ap "2--3"
pagination ap "155--157"
volume Number ap "71"

Roessler1979Aliasni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Roessler1979Alias

belongs to
Scholarly article c
has facts
title ap "Alias for Rossler1979"

Rossler1976ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Rossler1976

belongs to
Scholarly article c
has facts
issued ap "1976"
title ap "An Equation for Continuous Chaos"
author ap "R"ossler, Otto E."
identifier ap "10.1016/0375-9601(76)90101-8"
is Part Of ap "Physics Letters A"
issue Number ap "5"
pagination ap "397--398"
volume Number ap "57"

Rossler1979ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Rossler1979

belongs to
Scholarly article c
has facts
issued ap "1979"
title ap "An equation for hyperchaos"
author ap "R"ossler, O. E."
is Part Of ap "Physics Letters A"
issue Number ap "2--3"
pagination ap "155--157"
volume Number ap "71"

Ruelle1980ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Ruelle1980

belongs to
Scholarly article c
has facts
issued ap "1980"
title ap "Strange Attractors"
author ap "Ruelle, David"
identifier ap "10.1007/BF03024089"
is Part Of ap "The Mathematical Intelligencer"
issue Number ap "3"
pagination ap "126--137"
volume Number ap "2"

Rulkov2001ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Rulkov2001

belongs to
Scholarly article c
has facts
issued ap "2001"
title ap "Regularization of Synchronized Chaotic Bursts"
author ap "Abarbanel, Henry D. I."
author ap "Rulkov, Nikolai F."
author ap "Sushchik, M. M."
author ap "Tsimring, L. S."
is Part Of ap "Physical Review Letters"
pagination ap "183"
volume Number ap "86"

Rulkov2002ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Rulkov2002

belongs to
Scholarly article c
has facts
issued ap "2002"
title ap "Modeling of spiking-bursting neural behavior using two-dimensional map"
author ap "Rulkov, Nikolai F."
is Part Of ap "Physical Review E"
pagination ap "041922"
volume Number ap "65"

RungeKutta4thOrderni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/integrators/RungeKutta4thOrder

belongs to
Integrator c

RWW Functional Connectivity Fittingni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/experiments/RWW_BOLD_FC_Optimization

belongs to
SimulationExperiment c
has facts
description ap "Fitting functional connectivity using the Reduced Wong-Wang model. Two-stage optimization: global parameters first, then regional heterogeneity. Based on tvboptim RWW.qmd tutorial. "

s (Epileptor5D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor5D/parameters/s

Linear coefficient in the slow permittivity state-variable z_E5D in Epileptor5D (Jirsa et al.,2014).
belongs to
Parameter c
has facts
description ap "Linear coefficient in the slow permittivity state-variable z_E5D in Epileptor5D (Jirsa et al"
default Value ap "4.0"^^double
definition ap "Linear coefficient in the slow permittivity state-variable z_E5D in Epileptor5D (Jirsa et al.,2014)."
notation ap "s"

S (ReducedWongWang state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWang/state_variables/S

belongs to
StateVariable c
has facts
description ap "State-variable of the Reduced WongWang model, denoting the average, (NMDAR)-mediated synaptic gating, i"
notation ap "S"
lhs ap "Derivative(S, t)"
rhs ap "H*gamma*(1 - S) - S/tau_s"

S (ReducedWongWangTvboptim state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWangTvboptim/state_variables/S

belongs to
StateVariable c
has facts
description ap "Average NMDA synaptic gating variable, representing the fraction of open NMDA channels at each network node."
notation ap "S"
lhs ap "Derivative(S, t)"
rhs ap "-S/tau_s + (1 - S)*H(x)*gamma"

s (StefanescuJirsa3D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa3D/parameters/s

Adaptation feedback parameter.
belongs to
Parameter c
has facts
default Value ap "4.0"^^double
definition ap "Adaptation feedback parameter."
notation ap "s"

S_e (ReducedWongWangExcInh state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWangExcInh/state_variables/S_e

belongs to
StateVariable c
has facts
description ap "State-variable of the Reduced WongWang_EI model (Deco et al"
has Db Xref ap G O 0060079 ep
has Db Xref ap G O 0099536 ep
notation ap "S_e"
lhs ap "Derivative(S_e, t)"
rhs ap "H_e*gamma_e*(1 - S_e) - S_e/tau_e"

s_e (WilsonCowan derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/WilsonCowan/derived_variables/s_e

belongs to
DerivedVariable c
has facts
notation ap "s_e"
lhs ap "s_e"
rhs ap "c_e/(1.0 + exp(-a_e*(-b_e + x_e))) - 1.0*shift_sigmoid/(exp(a_e*b_e) + 1.0)"

S_e (ZerlautAdaptationFirstOrder derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/derived_variables/S_e

belongs to
DerivedVariable c
has facts
notation ap "S_e"
lhs ap "S_e"
rhs ap "(-sV0 + sigma_V_e)/DsV0"

s_EE (CakanObermayer parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/CakanObermayer/parameters/s_EE

Standard deviation of the random-coupling-driven membrane-potential fluctuations entering the E->E channel (sigmae_ext component).
belongs to
Parameter c
has facts
default Value ap "1.5"^^double
has Db Xref ap G O 0060079 ep
has Db Xref ap G O 0098815 ep
definition ap "Standard deviation of the random-coupling-driven membrane-potential fluctuations entering the E->E channel (sigmae_ext component)."
notation ap "s_EE"
unit (slot) dp "mV_per_ms"

s_ee (DumontGutkin state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/DumontGutkin/state_variables/s_ee

belongs to
StateVariable c
has facts
notation ap "s_ee"
lhs ap "Derivative(s_ee, t)"
rhs ap "(J_ee*r_e + c_pop0 - s_ee)/tau_s"

s_EI (CakanObermayer parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/CakanObermayer/parameters/s_EI

Standard deviation of the random-coupling-driven membrane-potential fluctuations entering the I->E channel.
belongs to
Parameter c
has facts
default Value ap "1.5"^^double
has Db Xref ap G O 0098815 ep
definition ap "Standard deviation of the random-coupling-driven membrane-potential fluctuations entering the I->E channel."
notation ap "s_EI"
unit (slot) dp "mV_per_ms"

s_ei (DumontGutkin state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/DumontGutkin/state_variables/s_ei

belongs to
StateVariable c
has facts
notation ap "s_ei"
lhs ap "Derivative(s_ei, t)"
rhs ap "(J_ei*r_i - s_ei)/tau_s"

S_i (ReducedWongWangExcInh state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWangExcInh/state_variables/S_i

belongs to
StateVariable c
has facts
description ap "State-variable of the Reduced WongWang_EI model (Deco et al"
has Db Xref ap G O 0060080 ep
has Db Xref ap G O 0099536 ep
notation ap "S_i"
lhs ap "Derivative(S_i, t)"
rhs ap "H_i*gamma_i - S_i/tau_i"

s_i (WilsonCowan derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/WilsonCowan/derived_variables/s_i

belongs to
DerivedVariable c
has facts
notation ap "s_i"
lhs ap "s_i"
rhs ap "c_i/(1.0 + exp(-a_i*(-b_i + x_i))) - 1.0*shift_sigmoid/(exp(a_i*b_i) + 1.0)"

S_i (ZerlautAdaptationFirstOrder derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/derived_variables/S_i

belongs to
DerivedVariable c
has facts
description ap "Scaling of the remote input for the inhibitory population with respect to the excitatory population."
notation ap "S_i"
lhs ap "S_i"
rhs ap "(-sV0 + sigma_V_i)/DsV0"

S_i (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/S_i

Scaling of the remote input for the inhibitory population with respect to the excitatory population.
belongs to
Parameter c
has facts
description ap "Scaling of the remote input for the inhibitory population with respect to the excitatory population"
default Value ap "1.0"^^double
has Db Xref ap G O 0060080 ep
definition ap "Scaling of the remote input for the inhibitory population with respect to the excitatory population."
notation ap "S_i"

s_IE (CakanObermayer parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/CakanObermayer/parameters/s_IE

Standard deviation of the random-coupling-driven membrane-potential fluctuations entering the E->I channel.
belongs to
Parameter c
has facts
default Value ap "1.5"^^double
has Db Xref ap G O 0098815 ep
definition ap "Standard deviation of the random-coupling-driven membrane-potential fluctuations entering the E->I channel."
notation ap "s_IE"
unit (slot) dp "mV_per_ms"

s_ie (DumontGutkin state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/DumontGutkin/state_variables/s_ie

belongs to
StateVariable c
has facts
notation ap "s_ie"
lhs ap "Derivative(s_ie, t)"
rhs ap "(Gamma*c_pop0 + J_ie*r_e - s_ie)/tau_s"

s_II (CakanObermayer parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/CakanObermayer/parameters/s_II

Standard deviation of the random-coupling-driven membrane-potential fluctuations entering the I->I channel.
belongs to
Parameter c
has facts
default Value ap "1.5"^^double
has Db Xref ap G O 0060080 ep
has Db Xref ap G O 0098828 ep
definition ap "Standard deviation of the random-coupling-driven membrane-potential fluctuations entering the I->I channel."
notation ap "s_II"
unit (slot) dp "mV_per_ms"

s_ii (DumontGutkin state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/DumontGutkin/state_variables/s_ii

belongs to
StateVariable c
has facts
notation ap "s_ii"
lhs ap "Derivative(s_ii, t)"
rhs ap "(J_ii*r_i - s_ii)/tau_s"

Scalingni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/coupling_functions/Scaling

belongs to
Coupling c
has facts
has Parameter ap a (Scaling parameter) ni

SDDE integrationni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/SDDEIntegration

Forward integration of a stochastic delay differential equation.
belongs to
Simulation task c

SDE integrationni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/SDEIntegration

Forward integration of a stochastic differential equation.
belongs to
Simulation task c

sensors_eeg_standard1005_fsaverage_aparc_projectionni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/sensors_eeg_standard1005_fsaverage_aparc_projection

belongs to
Network c
has facts
description ap "MNE standard_1005 EEG sensors (MNI, mm) with fsaverage aparc projection gain matrix (sensors x regions)."
alt Label ap "EEG standard_1005 fsaverage projection"
has Parameter ap conduction_speed (sensors_eeg_standard1005_fsaverage_aparc_projection parameter) ni

shift_sigmoid (WilsonCowan parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/WilsonCowan/parameters/shift_sigmoid

In order to have resting state (E=0 and I=0) in absence of external input, the logistic curve are translated downward S(0)=0
belongs to
Parameter c
has facts
description ap "In order to have resting state (E=0 and I=0) in absence of external input, the logistic curve are translated downward S(0)=0"
default Value ap "1.0"^^double
definition ap "In order to have resting state (E=0 and I=0) in absence of external input, the logistic curve are translated downward S(0)=0"
notation ap "shift_sigmoid"

sigma (HyperbolicTangent parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/coupling_functions/HyperbolicTangent/parameters/sigma

belongs to
Parameter c
has facts
description ap "Standard deviation of the coupling"
default Value ap "1.0"^^double
notation ap "sigma"

sigma (Sigmoidal parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/coupling_functions/Sigmoidal/parameters/sigma

belongs to
Parameter c
has facts
default Value ap "230.0"^^double
notation ap "sigma"

sigma (StefanescuJirsa2D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa2D/parameters/sigma

Standard deviation of the Gaussian heterogeneity distribution.
belongs to
Parameter c
has facts
default Value ap "0.35"^^double
has Db Xref ap G O 0060079 ep
definition ap "Standard deviation of the Gaussian heterogeneity distribution."
notation ap "sigma"

sigma (StefanescuJirsa3D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa3D/parameters/sigma

Standard deviation of the Gaussian heterogeneity distribution.
belongs to
Parameter c
has facts
default Value ap "0.3"^^double
has Db Xref ap G O 0042391 ep
definition ap "Standard deviation of the Gaussian heterogeneity distribution."
notation ap "sigma"

sigma_v1 (ZetterbergJansen derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZetterbergJansen/derived_variables/sigma_v1

belongs to
DerivedVariable c
has facts
notation ap "sigma_v1"
lhs ap "sigma_v1"
rhs ap "Piecewise((0, rho_1*(rho_2 - v1) > 709), (2*e0/(exp(rho_1*(rho_2 - v1)) + 1), True))"

sigma_v23 (ZetterbergJansen derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZetterbergJansen/derived_variables/sigma_v23

belongs to
DerivedVariable c
has facts
notation ap "sigma_v23"
lhs ap "sigma_v23"
rhs ap "Piecewise((0, rho_1*(rho_2 - (v2 - v3)) > 709), (2*e0/(exp(rho_1*(rho_2 - (v2 - v3))) + 1), True))"

sigma_v45 (ZetterbergJansen derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZetterbergJansen/derived_variables/sigma_v45

belongs to
DerivedVariable c
has facts
notation ap "sigma_v45"
lhs ap "sigma_v45"
rhs ap "Piecewise((0, rho_1*(rho_2 - (v4 - v5)) > 709), (2*e0/(exp(rho_1*(rho_2 - (v4 - v5))) + 1), True))"

sigma_V_e (ZerlautAdaptationFirstOrder derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/derived_variables/sigma_V_e

belongs to
DerivedVariable c
has facts
notation ap "sigma_V_e"
lhs ap "sigma_V_e"
rhs ap "sqrt(U_e_e**2*fe_e*tau_e**2/(2.0*T_m_e + 2.0*tau_e) + U_i_e**2*fi_e*tau_i**2/(2.0*T_m_e + 2.0*tau_i))"

sigma_V_i (ZerlautAdaptationFirstOrder derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/derived_variables/sigma_V_i

belongs to
DerivedVariable c
has facts
notation ap "sigma_V_i"
lhs ap "sigma_V_i"
rhs ap "sqrt(U_e_i**2*fe_i*tau_e**2/(2.0*T_m_i + 2.0*tau_e) + U_i_i**2*fi_i*tau_i**2/(2.0*T_m_i + 2.0*tau_i))"

sigma_y0_1 (JansenRit derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/JansenRit/derived_variables/sigma_y0_1

belongs to
DerivedVariable c
has facts
description ap "Sigmoid function that transforms the average membrane potential of the PCs populations (y0) into an average firing rate to the excitatory interneurons EINs."
notation ap "sigma_y0_1"
lhs ap "sigma_y0_1"
rhs ap "2.0*nu_max/(exp(r*(-J*a_1*y0 + v0)) + 1.0)"

sigma_y0_3 (JansenRit derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/JansenRit/derived_variables/sigma_y0_3

belongs to
DerivedVariable c
has facts
description ap "Sigmoid function that transforms the average membrane potential of the PCs populations (y0) into an average firing rate to the inhibitory interneurons IINs."
notation ap "sigma_y0_3"
lhs ap "sigma_y0_3"
rhs ap "2.0*nu_max/(exp(r*(-J*a_3*y0 + v0)) + 1.0)"

sigma_y1_y2 (JansenRit derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/JansenRit/derived_variables/sigma_y1_y2

belongs to
DerivedVariable c
has facts
description ap "Sigmoid function that transforms the average membrane potential of the interneurons populations (y1-y2) into an average firing rate to the PCs."
notation ap "sigma_y1_y2"
lhs ap "sigma_y1_y2"
rhs ap "2.0*nu_max/(exp(r*(v0 - y1 + y2)) + 1.0)"

Sigmoid activationni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/SigmoidActivation

belongs to
Model feature c

signal (KuramotoModel2 derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KuramotoModel2/derived_variables/signal

belongs to
DerivedVariable c
has facts
description ap "Sinusoidal signal output"
notation ap "signal"
rhs ap "sin(theta)"

Skiadas2008ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Skiadas2008

belongs to
Book c
has facts
issued ap "2008"
title ap "Chaotic Modelling and Simulation: Analysis of Chaotic Models, Attractors and Forms"
author ap "Skiadas, Christos H."
publisher ap "CRC Press"

slope (Epileptor2D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor2D/parameters/slope

Linear coefficient in the first state-variable x_E2D via the function f_E2D, in Epileptor2D (Proix et al.,2014).
belongs to
Parameter c
has facts
description ap "Linear coefficient in the first state-variable x_E2D via the function f_E2D, in Epileptor2D (Proix et al"
default Value ap "0.0"^^double
definition ap "Linear coefficient in the first state-variable x_E2D via the function f_E2D, in Epileptor2D (Proix et al.,2014)."
notation ap "slope"

slope (Epileptor5D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor5D/parameters/slope

Linear coefficient in the first state variable
belongs to
Parameter c
has facts
description ap "Linear coefficient in the first state variable"
default Value ap "0.0"^^double
definition ap "Linear coefficient in the first state variable"
notation ap "slope"

slope (EpileptorRestingState parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/EpileptorRestingState/parameters/slope

Linear coefficient in the first state-variable x1.
belongs to
Parameter c
has facts
description ap "Linear coefficient in the first state-variable x1"
default Value ap "0.0"^^double
definition ap "Linear coefficient in the first state-variable x1."
notation ap "slope"

SmileyNetworkni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/SmileyNetwork

belongs to
Network c
has facts
has Parameter ap conduction_speed (SmileyNetwork parameter) ni

Snuddani back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/Snudda

belongs to
Software package c
has facts
description ap "A Python tool for creating detailed neuronal network models with realistic 3D neuron placement, morphology, and connectivity using touch detection. Exports to NEURON via SONATA format."
license ap "GPL-3.0-only"
code Repository ap "https://github.com/Hjorthmedansen/Snudda"
url ap "https://snudda.readthedocs.io"

SONATAni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/SONATA

belongs to
Software package c
has facts
description ap "Scalable Open Network Architecture ToolKit and Application — a data format specification for storing large-scale neural network models and simulation results. Joint Allen Institute / Blue Brain standard."
license ap "BSD-3-Clause"
code Repository ap "https://github.com/AllenInstitute/sonata"
url ap "https://github.com/AllenInstitute/sonata/blob/master/docs/SONATA_DEVELOPER_GUIDE.md"

space-MNI152_atlas-Yeo17_res-1_dsegni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/atlases/space-MNI152_atlas-Yeo17_res-1_dseg

belongs to
BrainAtlas c
has facts
alt Label ap "Yeo17"

spatial_mask (spatial_average parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/observation_models/spatial_average/parameters/spatial_mask

belongs to
Parameter c
has facts
description ap "Vector of length N_nodes mapping each node to a region index (0-indexed). Inferred from network topology if not provided."
notation ap "spatial_mask"

SpatialAverageni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/observation_models/spatial_average

belongs to
Observation c
has facts
description ap "Computes spatially averaged signals within regions defined by a spatial mask (node-to-region assignment). The mask assigns each node to a region index, and the output is the mean signal per region."
has Parameter ap spatial_mask (spatial_average parameter) ni

SpikeInterfaceni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/SpikeInterface

belongs to
Software package c
has facts
description ap "A unified framework for spike sorting, providing a common interface to many spike sorting algorithms, preprocessing tools, and quality metrics."
license ap "MIT"
code Repository ap "https://github.com/SpikeInterface/spikeinterface"
identifier ap "10.7554/eLife.61834"
url ap "https://spikeinterface.readthedocs.io"

SpineCreatorni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/SpineCreator

belongs to
Software package c
has facts
description ap "A graphical tool for building neural network models using SpineML component-based descriptions, with export to multiple simulation engines."
license ap "GPL-3.0-only"
code Repository ap "https://github.com/SpineML/SpineCreator"
url ap "https://spineml.github.io/spinecreator/"

SpineMLni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/SpineML

belongs to
Software package c
has facts
description ap "A declarative XML-based language for describing spiking neural network models using a component-based approach. Designed for simulator independence."
license ap "BSD-3-Clause"
code Repository ap "https://github.com/SpineML"
url ap "https://spineml.github.io"

SPMni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/SPM

belongs to
Software package c
has facts
description ap "Statistical Parametric Mapping — software for the analysis of brain imaging data sequences (fMRI, PET, SPECT, EEG, MEG). Standard tool for voxel-based and DCM analyses."
license ap "GPL-2.0-or-later"
code Repository ap "https://github.com/spm/spm"
identifier ap "10.1016/B978-012372560-8/50002-4"
url ap "https://www.fil.ion.ucl.ac.uk/spm/"

Sprott2010ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Sprott2010

belongs to
Book c
has facts
issued ap "2010"
title ap "Elegant Chaos: Algebraically Simple Chaotic Flows"
author ap "Sprott, J. C."
identifier ap "10.1142/7434"
publisher ap "World Scientific"

Sprott2014ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Sprott2014

belongs to
Scholarly article c
has facts
issued ap "2014"
title ap "Simplest Chaotic Flows with Involutional Symmetries"
author ap "Sprott, J. C."
is Part Of ap "International Journal of Bifurcation and Chaos"
pagination ap "1450009"
volume Number ap "24"

Sprott2014bni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Sprott2014b

belongs to
Scholarly article c
has facts
issued ap "2014"
title ap "Physics Letters A"
author ap "Sprott, J. C."
is Part Of ap "Physics Letters A"
volume Number ap "378"

Sprott2020ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Sprott2020

belongs to
Scholarly article c
has facts
issued ap "2020"
title ap "Do We Need More Chaos Examples?"
author ap "Sprott, J. C."
is Part Of ap "Chaos Theory and Applications"
issue Number ap "2"
pagination ap "1--3"
volume Number ap "2"

SprottXiong2015ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/SprottXiong2015

belongs to
Scholarly article c
has facts
issued ap "2015"
title ap "Classifying and quantifying basins of attraction"
author ap "Sprott, J. C."
author ap "Xiong, A."
is Part Of ap "Chaos: An Interdisciplinary Journal of Nonlinear Science"
issue Number ap "8"
pagination ap "083101"
volume Number ap "25"

sPyNNakerni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/sPyNNaker

belongs to
Software package c
has facts
description ap "Software stack enabling PyNN models to execute on the SpiNNaker neuromorphic computing platform. Translates PyNN network descriptions into configurations for SpiNNaker's many-core ARM processors."
license ap "GPL-3.0-only"
code Repository ap "https://github.com/SpiNNakerManchester/sPyNNaker"
url ap "https://spinnakermanchester.github.io"

SS0 (TsodyksMarkram derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/TsodyksMarkram/derived_variables/SS0

belongs to
DerivedVariable c
has facts
description ap "Total synaptic input (recurrent + external)"
notation ap "SS0"
lhs ap "SS0"
rhs ap "J*u*x*E + E0"

SS1 (TsodyksMarkram derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/TsodyksMarkram/derived_variables/SS1

belongs to
DerivedVariable c
has facts
description ap "Softplus transfer function output"
notation ap "SS1"
lhs ap "SS1"
rhs ap "alpha*log(1 + exp(SS0/alpha))"

Stankevich2012ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Stankevich2012

belongs to
Creative work c
has facts
issued ap "2012"
title ap "Hyperchaotic dynamics in a R"ossler-like system"
author ap "Stankevich, N. V."

StefanescuJirsa2Dni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa2D

belongs to
Dynamics c
has facts
exhibits regime op Bistable ni
exhibits regime op Bursting ni
exhibits regime op Oscillatory ni
has attractor op Fixed point ni
has attractor op Limit cycle ni
has stochasticity character op Deterministic ni
models anatomical region op U B E R O N 0000956 ni
has timescale separation dp "true"^^boolean
phase-space dimension dp "4"^^integer
description ap "Reduced set of FitzHugh-Nagumo oscillators (Stefanescu & Jirsa 2008). A low-dimensional description of globally coupled heterogeneous excitatory and inhibitory FitzHugh-Nagumo populations. The reduction projects an infinite population onto `number_of_modes` modes and yields per-mode scalar state variables (xi, eta) for the excitatory and (alpha, beta) for the inhibitory subnetwork. The mode-coupling matrices Aik, Bik, Cik and the per-mode inputs IE_i, II_i, m_i, n_i, e_i, f_i are derived offline by Gaussian quadrature over the heterogeneity distribution N(mu, sigma^2); see TVB reference implementation `tvb.simulator.models.stefanescu_jirsa.ReducedSetFitzHughNagumo`."
pref Label ap "Stefanescu-Jirsa 2D"@en
has Derived Variable ap Aik (StefanescuJirsa2D derived variable) ni
has Derived Variable ap Bik (StefanescuJirsa2D derived variable) ni
has Derived Variable ap Cik (StefanescuJirsa2D derived variable) ni
has Derived Variable ap IE_i (StefanescuJirsa2D derived variable) ni
has Derived Variable ap II_i (StefanescuJirsa2D derived variable) ni
has Derived Variable ap e_i (StefanescuJirsa2D derived variable) ni
has Derived Variable ap f_i (StefanescuJirsa2D derived variable) ni
has Derived Variable ap m_i (StefanescuJirsa2D derived variable) ni
has Derived Variable ap n_i (StefanescuJirsa2D derived variable) ni
has Parameter ap K11 (StefanescuJirsa2D parameter) ni
has Parameter ap K12 (StefanescuJirsa2D parameter) ni
has Parameter ap K21 (StefanescuJirsa2D parameter) ni
has Parameter ap a (StefanescuJirsa2D parameter) ni
has Parameter ap b (StefanescuJirsa2D parameter) ni
has Parameter ap mu (StefanescuJirsa2D parameter) ni
has Parameter ap sigma (StefanescuJirsa2D parameter) ni
has Parameter ap tau (StefanescuJirsa2D parameter) ni
has State Variable ap alpha (StefanescuJirsa2D state variable) ni
has State Variable ap beta (StefanescuJirsa2D state variable) ni
has State Variable ap eta (StefanescuJirsa2D state variable) ni
has State Variable ap xi (StefanescuJirsa2D state variable) ni
model_type (slot) ap "neural_mass"

StefanescuJirsa3Dni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa3D

belongs to
Dynamics c
has facts
exhibits regime op Bursting ni
exhibits regime op Chaotic ni
exhibits regime op Oscillatory ni
has attractor op Limit cycle ni
has attractor op Strange attractor ni
has stochasticity character op Deterministic ni
models anatomical region op U B E R O N 0000956 ni
has timescale separation dp "true"^^boolean
phase-space dimension dp "6"^^integer
description ap "Reduced set of Hindmarsh-Rose oscillators (Stefanescu & Jirsa 2008). A low-dimensional description of globally coupled heterogeneous excitatory and inhibitory Hindmarsh-Rose populations. The reduction projects an infinite population onto `number_of_modes` modes and yields per-mode scalar state variables (xi, eta, tau) for the excitatory and (alpha, beta, gamma) for the inhibitory subnetwork. The mode-coupling matrices A_ik, B_ik, C_ik and the per-mode coefficients a_i, b_i, c_i, d_i, e_i, f_i, h_i, p_i, IE_i, II_i, m_i, n_i are derived offline by Gaussian quadrature over the heterogeneity distribution N(mu, sigma^2); see TVB reference implementation `tvb.simulator.models.stefanescu_jirsa.ReducedSetHindmarshRose`."
pref Label ap "Stefanescu-Jirsa 3D"@en
has Derived Variable ap A_ik (StefanescuJirsa3D derived variable) ni
has Derived Variable ap B_ik (StefanescuJirsa3D derived variable) ni
has Derived Variable ap C_ik (StefanescuJirsa3D derived variable) ni
has Derived Variable ap IE_i (StefanescuJirsa3D derived variable) ni
has Derived Variable ap II_i (StefanescuJirsa3D derived variable) ni
has Derived Variable ap a_i (StefanescuJirsa3D derived variable) ni
has Derived Variable ap b_i (StefanescuJirsa3D derived variable) ni
has Derived Variable ap c_i (StefanescuJirsa3D derived variable) ni
has Derived Variable ap d_i (StefanescuJirsa3D derived variable) ni
has Derived Variable ap e_i (StefanescuJirsa3D derived variable) ni
has Derived Variable ap f_i (StefanescuJirsa3D derived variable) ni
has Derived Variable ap h_i (StefanescuJirsa3D derived variable) ni
has Derived Variable ap m_i (StefanescuJirsa3D derived variable) ni
has Derived Variable ap n_i (StefanescuJirsa3D derived variable) ni
has Derived Variable ap p_i (StefanescuJirsa3D derived variable) ni
has Parameter ap K_11 (StefanescuJirsa3D parameter) ni
has Parameter ap K_12 (StefanescuJirsa3D parameter) ni
has Parameter ap K_21 (StefanescuJirsa3D parameter) ni
has Parameter ap a (StefanescuJirsa3D parameter) ni
has Parameter ap b (StefanescuJirsa3D parameter) ni
has Parameter ap c (StefanescuJirsa3D parameter) ni
has Parameter ap d (StefanescuJirsa3D parameter) ni
has Parameter ap mu (StefanescuJirsa3D parameter) ni
has Parameter ap r (StefanescuJirsa3D parameter) ni
has Parameter ap s (StefanescuJirsa3D parameter) ni
has Parameter ap sigma (StefanescuJirsa3D parameter) ni
has Parameter ap x_0 (StefanescuJirsa3D parameter) ni
has State Variable ap alpha (StefanescuJirsa3D state variable) ni
has State Variable ap beta (StefanescuJirsa3D state variable) ni
has State Variable ap eta (StefanescuJirsa3D state variable) ni
has State Variable ap gamma (StefanescuJirsa3D state variable) ni
has State Variable ap tau (StefanescuJirsa3D state variable) ni
has State Variable ap xi (StefanescuJirsa3D state variable) ni
model_type (slot) ap "neural_mass"

STEPSni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/STEPS

belongs to
Software package c
has facts
description ap "STochastic Engine for Pathway Simulation — a stochastic reaction-diffusion simulator for modeling biochemical signaling pathways in realistic 3D cellular morphologies."
license ap "GPL-3.0-only"
code Repository ap "https://github.com/CNS-OIST/STEPS"
identifier ap "10.3389/fninf.2014.00068"
url ap "https://steps.sourceforge.net"

Stiff solverni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StiffSolver

belongs to
Backend capability c

Stochastic solverni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StochasticSolver

belongs to
Backend capability c

Stommel1961ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Stommel1961

belongs to
Scholarly article c
has facts
issued ap "1961"
title ap "Thermohaline convection with two stable regimes of flow"
author ap "Stommel, Henry"
is Part Of ap "Tellus"
issue Number ap "2"
volume Number ap "13"

Strogatz2000ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Strogatz2000

belongs to
Scholarly article c
has facts
issued ap "2000"
title ap "From Kuramoto to Crawford: exploring the onset of synchronization in populations of coupled oscillators"
author ap "Strogatz, Steven H."
is Part Of ap "Physica D"

Strogatz2015ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Strogatz2015

belongs to
Book c
has facts
issued ap "2015"
title ap "Nonlinear Dynamics and Chaos: With Applications to Physics, Biology, Chemistry, and Engineering"
author ap "Strogatz, Steven H."
publisher ap "Westview Press"

SubSampleni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/observation_models/subsample

belongs to
Observation c
has facts
description ap "Temporal decimation of selected state variables. Records every N-th integration step without any averaging or smoothing."

SupHopfni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/SupHopf

belongs to
Dynamics c
has facts
exhibits bifurcation op ""
exhibits regime op Oscillatory ni
exhibits regime op Quiescent ni
has attractor op Fixed point ni
has attractor op Limit cycle ni
has stochasticity character op Deterministic ni
phase-space dimension dp "2"^^integer
description ap "Supercritical Hopf (SUPH) is an oscillatory/excitable neural mass model that describe the normal form of a supercritical Hopf bifurcation in Cartesian coordinates (Kuznetsov, 2013; Deco et al., 2017). This normal form has a supercritical bifurcation at 'a=0' with 'a' the bifurcation parameter in the model. So for 'a < 0', the local dynamics has a stable fixed point and the system corresponds to a damped oscillatory state, whereas for 'a > 0', the local dynamics enters in a stable limit cycle and the system switches to an oscillatory state."
references ap Deco2017 ni
pref Label ap "Supercritical Hopf"@en
has Derived Variable ap lc_0 (SupHopf derived variable) ni
has Parameter ap a (SupHopf parameter) ni
has Parameter ap omega (SupHopf parameter) ni
has State Variable ap x (SupHopf state variable) ni
has State Variable ap y (SupHopf state variable) ni
model_type (slot) ap "generic"

sV0 (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/sV0

Normalization factors page 48 after the equation 4 from [ZD_2018]
belongs to
Parameter c
has facts
description ap "Normalization factors page 48 after the equation 4 from [ZD_2018]"
default Value ap "4.0"^^double
definition ap "Normalization factors page 48 after the equation 4 from [ZD_2018]"
notation ap "sV0"

Symbolic code generationni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/CodeGeneration

Backend emits standalone simulator source code from a model specification.
belongs to
Backend capability c

T (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/T

Time scale of describing network activity
belongs to
Parameter c
has facts
description ap "Time scale of describing network activity"
default Value ap "20.0"^^double
definition ap "Time scale of describing network activity"
notation ap "T"

T_Ca (LarterBreakspear parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/LarterBreakspear/parameters/T_Ca

Threshold value for Ca channels.
belongs to
Parameter c
has facts
description ap "Threshold value for Ca channels"
default Value ap "-0.01"^^double
has Db Xref ap G O 0005262 ep
has Db Xref ap G O 1903233 ep
definition ap "Threshold value for Ca channels."
notation ap "T_Ca"

T_e (ZerlautAdaptationFirstOrder derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/derived_variables/T_e

belongs to
DerivedVariable c
has facts
notation ap "T_e"
lhs ap "T_e"
rhs ap "(-TvN0 + T_V_e*g_L/C_m)/DTvN0"

T_i (ZerlautAdaptationFirstOrder derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/derived_variables/T_i

belongs to
DerivedVariable c
has facts
notation ap "T_i"
lhs ap "T_i"
rhs ap "(-TvN0 + T_V_i*g_L/C_m)/DTvN0"

T_K (LarterBreakspear parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/LarterBreakspear/parameters/T_K

Threshold value for K channels.
belongs to
Parameter c
has facts
description ap "Threshold value for K channels"
default Value ap "0.0"^^double
has Db Xref ap G O 0005267 ep
definition ap "Threshold value for K channels."
notation ap "T_K"

T_m_e (ZerlautAdaptationFirstOrder derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/derived_variables/T_m_e

belongs to
DerivedVariable c
has facts
notation ap "T_m_e"
lhs ap "T_m_e"
rhs ap "C_m/mu_G_e"

T_m_i (ZerlautAdaptationFirstOrder derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/derived_variables/T_m_i

belongs to
DerivedVariable c
has facts
notation ap "T_m_i"
lhs ap "T_m_i"
rhs ap "C_m/mu_G_i"

T_Na (LarterBreakspear parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/LarterBreakspear/parameters/T_Na

Threshold value for sodium channels.
belongs to
Parameter c
has facts
description ap "Threshold value for sodium channels"
default Value ap "0.3"^^double
has Db Xref ap G O 0005272 ep
definition ap "Threshold value for sodium channels."
notation ap "T_Na"

t_scale (LarterBreakspear parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/LarterBreakspear/parameters/t_scale

Time scale factor
belongs to
Parameter c
has facts
description ap "Time scale factor"
default Value ap "1.0"^^double
definition ap "Time scale factor"
notation ap "t_scale"

T_V_e (ZerlautAdaptationFirstOrder derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/derived_variables/T_V_e

belongs to
DerivedVariable c
has facts
notation ap "T_V_e"
lhs ap "T_V_e"
rhs ap "(U_e_e**2*fe_e*tau_e**2 + U_i_e**2*fi_e*tau_i**2)/(U_e_e**2*fe_e*tau_e**2/(T_m_e + tau_e) + U_i_e**2*fi_e*tau_i**2/(T_m_e + tau_i))"

T_V_i (ZerlautAdaptationFirstOrder derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/derived_variables/T_V_i

belongs to
DerivedVariable c
has facts
notation ap "T_V_i"
lhs ap "T_V_i"
rhs ap "(U_e_i**2*fe_i*tau_e**2 + U_i_i**2*fi_i*tau_i**2)/(U_e_i**2*fe_i*tau_e**2/(T_m_i + tau_e) + U_i_i**2*fi_i*tau_i**2/(T_m_i + tau_i))"

tau (Epileptor5D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor5D/parameters/tau

Temporal scaling coefficient in fifth state variable
belongs to
Parameter c
has facts
description ap "Temporal scaling coefficient in fifth state variable"
default Value ap "10.0"^^double
definition ap "Temporal scaling coefficient in fifth state variable"
notation ap "tau"

tau (EpileptorRestingState parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/EpileptorRestingState/parameters/tau

Temporal scaling coefficient in the fifth state-variable y2.
belongs to
Parameter c
has facts
description ap "Temporal scaling coefficient in the fifth state-variable y2"
default Value ap "10.0"^^double
definition ap "Temporal scaling coefficient in the fifth state-variable y2."
notation ap "tau"

tau (GastSchmidtKnosche_SD parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/GastSchmidtKnosche_SD/parameters/tau

Characteristic time
belongs to
Parameter c
has facts
description ap "Characteristic time"
default Value ap "1.0"^^double
definition ap "Characteristic time"
notation ap "tau"

tau (GastSchmidtKnosche_SF parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/GastSchmidtKnosche_SF/parameters/tau

Characteristic time
belongs to
Parameter c
has facts
description ap "Characteristic time"
default Value ap "1.0"^^double
definition ap "Characteristic time"
notation ap "tau"

tau (Generic2dOscillator parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Generic2dOscillator/parameters/tau

A time-scale hierarchy can be introduced for the state variables :math:`V` and :math:`W`. Default parameter is 1, which means no time-scale hierarchy.
belongs to
Parameter c
has facts
description ap "A time-scale hierarchy can be introduced for the state variables :math:`V` and :math:`W`"
default Value ap "1.0"^^double
definition ap "A time-scale hierarchy can be introduced for the state variables :math:`V` and :math:`W`. Default parameter is 1, which means no time-scale hierarchy."
notation ap "tau"

tau (MontbrioPazoRoxin parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/MontbrioPazoRoxin/parameters/tau

Membrane time constant
belongs to
Parameter c
has facts
description ap "Membrane time constant"
default Value ap "1.0"^^double
definition ap "Membrane time constant"
notation ap "tau"

tau (StefanescuJirsa2D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa2D/parameters/tau

Timescale separation between fast (xi, alpha) and slow (eta, beta) variables.
belongs to
Parameter c
has facts
description ap "Timescale separation"
default Value ap "3.0"^^double
definition ap "Timescale separation between fast (xi, alpha) and slow (eta, beta) variables."
notation ap "tau"

tau (StefanescuJirsa3D state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa3D/state_variables/tau

belongs to
StateVariable c
has facts
description ap "Excitatory slow adaptation variable (per mode)."
has Db Xref ap G O 0060079 ep
notation ap "tau"
lhs ap "Derivative(tau, t)"
rhs ap "r*s*xi - r*tau - m_i"

tau (TsodyksMarkram parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/TsodyksMarkram/parameters/tau

belongs to
Parameter c
has facts
description ap "Membrane time constant (firing rate relaxation)"
default Value ap "0.013"^^double
notation ap "tau"

tau_A (CakanObermayer parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/CakanObermayer/parameters/tau_A

Time constant of the adaptation current.
belongs to
Parameter c
has facts
default Value ap "200.0"^^double
definition ap "Time constant of the adaptation current."
notation ap "tau_A"
unit (slot) dp "ms"

tau_A (GastSchmidtKnosche_SD parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/GastSchmidtKnosche_SD/parameters/tau_A

Adaptation time scale
belongs to
Parameter c
has facts
description ap "Adaptation time scale"
default Value ap "10.0"^^double
definition ap "Adaptation time scale"
notation ap "tau_A"

tau_A (GastSchmidtKnosche_SF parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/GastSchmidtKnosche_SF/parameters/tau_A

Adaptation time scale
belongs to
Parameter c
has facts
description ap "Adaptation time scale"
default Value ap "10.0"^^double
definition ap "Adaptation time scale"
notation ap "tau_A"

tau_e (DumontGutkin parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/DumontGutkin/parameters/tau_e

Characteristic time of excitatory population
belongs to
Parameter c
has facts
description ap "Characteristic time of excitatory population"
default Value ap "10.0"^^double
has Db Xref ap G O 0043179 ep
has Db Xref ap G O 0060079 ep
definition ap "Characteristic time of excitatory population"
notation ap "tau_e"

tau_e (ReducedWongWangExcInh parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWangExcInh/parameters/tau_e

Kinetic parameter that represents the decay times for NMDA synapses (Deco et al., 2014). Excitatory population NMDA decay time constant.
belongs to
Parameter c
has facts
description ap "Kinetic parameter that represents the decay times for NMDA synapses (Deco et al"
default Value ap "100.0"^^double
definition ap "Kinetic parameter that represents the decay times for NMDA synapses (Deco et al., 2014). Excitatory population NMDA decay time constant."
notation ap "tau_e"
unit (slot) dp "ms"

tau_e (WilsonCowan parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/WilsonCowan/parameters/tau_e

Excitatory population, membrane time-constant (Wilson and Cowan, 1972).
belongs to
Parameter c
has facts
description ap "Excitatory population, membrane time-constant (Wilson and Cowan, 1972)"
default Value ap "10.0"^^double
has Db Xref ap G O 0043179 ep
definition ap "Excitatory population, membrane time-constant (Wilson and Cowan, 1972)."
notation ap "tau_e"
unit (slot) dp "ms"

tau_e (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/tau_e

excitatory decay [ms]
belongs to
Parameter c
has facts
description ap "excitatory decay [ms]"
default Value ap "5.0"^^double
has Db Xref ap G O 0098815 ep
definition ap "excitatory decay [ms]"
notation ap "tau_e"

tau_i (DumontGutkin parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/DumontGutkin/parameters/tau_i

Characteristic time of inhibitory population
belongs to
Parameter c
has facts
description ap "Characteristic time of inhibitory population"
default Value ap "10.0"^^double
has Db Xref ap G O 0043180 ep
has Db Xref ap G O 0060080 ep
definition ap "Characteristic time of inhibitory population"
notation ap "tau_i"

tau_i (ReducedWongWangExcInh parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWangExcInh/parameters/tau_i

Kinetic parameter that represents the decay times for inhibitory GABA synapses (Deco et al., 2014).
belongs to
Parameter c
has facts
description ap "Kinetic parameter that represents the decay times for inhibitory GABA synapses (Deco et al"
default Value ap "10.0"^^double
has Db Xref ap G O 0016917 ep
definition ap "Kinetic parameter that represents the decay times for inhibitory GABA synapses (Deco et al., 2014)."
notation ap "tau_i"
unit (slot) dp "ms"

tau_i (WilsonCowan parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/WilsonCowan/parameters/tau_i

Inhibitory population, membrane time-constant (Wilson and Cowan, 1972).
belongs to
Parameter c
has facts
description ap "Inhibitory population, membrane time-constant (Wilson and Cowan, 1972)"
default Value ap "10.0"^^double
has Db Xref ap G O 0043180 ep
definition ap "Inhibitory population, membrane time-constant (Wilson and Cowan, 1972)."
notation ap "tau_i"
unit (slot) dp "ms"

tau_i (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/tau_i

inhibitory decay [ms]
belongs to
Parameter c
has facts
description ap "inhibitory decay [ms]"
default Value ap "5.0"^^double
has Db Xref ap G O 0098828 ep
definition ap "inhibitory decay [ms]"
notation ap "tau_i"

tau_K (LarterBreakspear parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/LarterBreakspear/parameters/tau_K

Time constant for K relaxation time (ms)
belongs to
Parameter c
has facts
description ap "Time constant for K relaxation time (ms)"
default Value ap "1.0"^^double
has Db Xref ap G O 0005267 ep
definition ap "Time constant for K relaxation time (ms)"
notation ap "tau_K"

tau_n (KIonEx parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/parameters/tau_n

time constant of gating variable
belongs to
Parameter c
has facts
description ap "time constant of gating variable"
default Value ap "4.0"^^double
definition ap "time constant of gating variable"
notation ap "tau_n"

tau_OU (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/tau_OU

time constant noise
belongs to
Parameter c
has facts
description ap "time constant noise"
default Value ap "5.0"^^double
definition ap "time constant noise"
notation ap "tau_OU"

tau_rs (EpileptorRestingState parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/EpileptorRestingState/parameters/tau_rs

Temporal scaling coefficient in the third population (x_rs, y_rs).
belongs to
Parameter c
has facts
description ap "Temporal scaling coefficient in the third population (x_rs, y_rs)"
default Value ap "1.0"^^double
definition ap "Temporal scaling coefficient in the third population (x_rs, y_rs)."
notation ap "tau_rs"

tau_s (DumontGutkin parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/DumontGutkin/parameters/tau_s

Synaptic time constant
belongs to
Parameter c
has facts
description ap "Synaptic time constant"
default Value ap "1.0"^^double
has Db Xref ap G O 0099536 ep
definition ap "Synaptic time constant"
notation ap "tau_s"

tau_s (ReducedWongWang parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWang/parameters/tau_s

Kinetic parameter. Decay time constant for the NMDA synapses of the neurons population (Deco et al., 2013).
belongs to
Parameter c
has facts
description ap "Kinetic parameter"
default Value ap "100.0"^^double
definition ap "Kinetic parameter. Decay time constant for the NMDA synapses of the neurons population (Deco et al., 2013)."
notation ap "tau_s"
unit (slot) dp "ms"

tau_s (ReducedWongWangTvboptim parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWangTvboptim/parameters/tau_s

NMDA decay time constant for the synaptic gating variable S.
belongs to
Parameter c
has facts
description ap "NMDA decay time constant"
default Value ap "100.0"^^double
definition ap "NMDA decay time constant for the synaptic gating variable S."
notation ap "tau_s"
unit (slot) dp "ms"

tau_se (CakanObermayer parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/CakanObermayer/parameters/tau_se

Synaptic time constant of excitatory PSCs (E->E and E->I).
belongs to
Parameter c
has facts
default Value ap "2.0"^^double
definition ap "Synaptic time constant of excitatory PSCs (E->E and E->I)."
notation ap "tau_se"
unit (slot) dp "ms"

tau_si (CakanObermayer parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/CakanObermayer/parameters/tau_si

Synaptic time constant of inhibitory PSCs (I->E and I->I).
belongs to
Parameter c
has facts
default Value ap "5.0"^^double
definition ap "Synaptic time constant of inhibitory PSCs (I->E and I->I)."
notation ap "tau_si"
unit (slot) dp "ms"

tau_w_e (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/tau_w_e

Adaptation time constant of excitatory neurons [ms]
belongs to
Parameter c
has facts
description ap "Adaptation time constant of excitatory neurons [ms]"
default Value ap "500.0"^^double
has Db Xref ap G O 0098815 ep
definition ap "Adaptation time constant of excitatory neurons [ms]"
notation ap "tau_w_e"

tau_w_i (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/tau_w_i

Adaptation time constant of inhibitory neurons [ms]
belongs to
Parameter c
has facts
description ap "Adaptation time constant of inhibitory neurons [ms]"
default Value ap "1.0"^^double
has Db Xref ap G O 0098828 ep
definition ap "Adaptation time constant of inhibitory neurons [ms]"
notation ap "tau_w_i"

tau_z (Epileptor3DStefanescuMcDonald parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor3DStefanescuMcDonald/parameters/tau_z

Slow timescale for the z permittivity variable.
belongs to
Parameter c
has facts
default Value ap "2857.0"^^double
definition ap "Slow timescale for the z permittivity variable."
notation ap "tau_z"
unit (slot) dp "ms"

tauD (TsodyksMarkram parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/TsodyksMarkram/parameters/tauD

belongs to
Parameter c
has facts
description ap "Synaptic depression recovery time constant"
default Value ap "0.2"^^double
notation ap "tauD"

tauF (TsodyksMarkram parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/TsodyksMarkram/parameters/tauF

belongs to
Parameter c
has facts
description ap "Synaptic facilitation decay time constant"
default Value ap "1.5"^^double
notation ap "tauF"

tauT (Hopfield parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Hopfield/parameters/tauT

The slow time-scale for threshold calculus :math:`\\theta`, state-variable of the model.
belongs to
Parameter c
has facts
description ap "The slow time-scale for threshold calculus :math:`\\theta`, state-variable of the model"
default Value ap "5.0"^^double
definition ap "The slow time-scale for threshold calculus :math:`\\theta`, state-variable of the model."
notation ap "tauT"

taux (Hopfield parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Hopfield/parameters/taux

The fast time-scale for potential calculus :math:`x`, state-variable of the model.
belongs to
Parameter c
has facts
description ap "The fast time-scale for potential calculus :math:`x`, state-variable of the model"
default Value ap "1.0"^^double
definition ap "The fast time-scale for potential calculus :math:`x`, state-variable of the model."
notation ap "taux"

TemporalAverageni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/observation_models/temporal_average

belongs to
Observation c
has facts
description ap "Running temporal mean over a sliding window of configurable length. Returns one averaged sample per period."

theta (Hopfield state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Hopfield/state_variables/theta

belongs to
StateVariable c
has facts
description ap "Slow state variable at node i"
notation ap "theta"
lhs ap "Derivative(theta, t)"
rhs ap "(c_pop1 - theta)/tauT"

theta (Kuramoto state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Kuramoto/state_variables/theta

belongs to
StateVariable c
has facts
description ap "The Kuramoto model has only one state variable representing oscillations in general"
notation ap "theta"
lhs ap "Derivative(theta, t)"
rhs ap "I + omega"

theta (KuramotoModel2 state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KuramotoModel2/state_variables/theta

belongs to
StateVariable c
has facts
description ap "The Kuramoto model has only one state variable representing oscillations in general"
notation ap "theta"
lhs ap "thetadot"
rhs ap "omega + I"

theta (PreSigmoidal parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/coupling_functions/PreSigmoidal/parameters/theta

belongs to
Parameter c
has facts
description ap "Threshold"
default Value ap "0.5"^^double
notation ap "theta"

theta_e (WilsonCowan parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/WilsonCowan/parameters/theta_e

Excitation threshold of excitatory population (Sanz-Leon et al., 2015).
belongs to
Parameter c
has facts
description ap "Excitation threshold of excitatory population (Sanz-Leon et al"
default Value ap "0.0"^^double
definition ap "Excitation threshold of excitatory population (Sanz-Leon et al., 2015)."
notation ap "theta_e"

theta_i (WilsonCowan parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/WilsonCowan/parameters/theta_i

Excitation threshold of inhibitory population (Sanz-Leon et al., 2015).
belongs to
Parameter c
has facts
description ap "Excitation threshold of inhibitory population (Sanz-Leon et al"
default Value ap "0.0"^^double
has Db Xref ap Inhibitory Threshold Variance ep
definition ap "Excitation threshold of inhibitory population (Sanz-Leon et al., 2015)."
notation ap "theta_i"

Thomas1999ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Thomas1999

belongs to
Scholarly article c
has facts
issued ap "1999"
title ap "Deterministic chaos seen in terms of feedback circuits: Analysis, synthesis, \& biological applications"
author ap "Thomas, Ren\'e"
is Part Of ap "International Journal of Bifurcation and Chaos"
issue Number ap "10"
pagination ap "1889--1905"
volume Number ap "9"

TimeScalingni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/TimeScaling

Time-constant or rate parameter that sets the temporal scale of a dynamical variable. No faithful upstream GO mapping (GO_0050789 was rejected as overly generic).
belongs to
SKOS Concept c
has facts
pref Label ap "TimeScaling"@en

tpl-fsaverage_acq-EEGstandard1005_atlas-DesikanKilliany_desc-projection_sensorsni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-fsaverage_acq-EEGstandard1005_atlas-DesikanKilliany_desc-projection_sensors

belongs to
Network c
has facts
description ap "MNE standard_1005 EEG sensors (MNI, mm) with fsaverage aparc projection gain matrix (sensors x regions)."
alt Label ap "EEG standard_1005 fsaverage projection"
has Parameter ap conduction_speed (tpl-fsaverage_acq-EEGstandard1005_atlas-DesikanKilliany_desc-projection_sensors parameter) ni

tpl-FSLMNI152_atlas-Schaefer2018_seg-17Networks_scale-1000_dsegni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/atlases/tpl-FSLMNI152_atlas-Schaefer2018_seg-17Networks_scale-1000_dseg

belongs to
BrainAtlas c
has facts
alt Label ap "Schaefer2018"

tpl-FSLMNI152_atlas-Schaefer2018_seg-17Networks_scale-100_dsegni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/atlases/tpl-FSLMNI152_atlas-Schaefer2018_seg-17Networks_scale-100_dseg

belongs to
BrainAtlas c
has facts
alt Label ap "Schaefer2018"

tpl-FSLMNI152_atlas-Schaefer2018_seg-17Networks_scale-200_dsegni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/atlases/tpl-FSLMNI152_atlas-Schaefer2018_seg-17Networks_scale-200_dseg

belongs to
BrainAtlas c
has facts
alt Label ap "Schaefer2018"

tpl-FSLMNI152_atlas-Schaefer2018_seg-17Networks_scale-300_dsegni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/atlases/tpl-FSLMNI152_atlas-Schaefer2018_seg-17Networks_scale-300_dseg

belongs to
BrainAtlas c
has facts
alt Label ap "Schaefer2018"

tpl-FSLMNI152_atlas-Schaefer2018_seg-17Networks_scale-400_dsegni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/atlases/tpl-FSLMNI152_atlas-Schaefer2018_seg-17Networks_scale-400_dseg

belongs to
BrainAtlas c
has facts
alt Label ap "Schaefer2018"

tpl-FSLMNI152_atlas-Schaefer2018_seg-17Networks_scale-500_dsegni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/atlases/tpl-FSLMNI152_atlas-Schaefer2018_seg-17Networks_scale-500_dseg

belongs to
BrainAtlas c
has facts
alt Label ap "Schaefer2018"

tpl-FSLMNI152_atlas-Schaefer2018_seg-17Networks_scale-600_dsegni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/atlases/tpl-FSLMNI152_atlas-Schaefer2018_seg-17Networks_scale-600_dseg

belongs to
BrainAtlas c
has facts
alt Label ap "Schaefer2018"

tpl-FSLMNI152_atlas-Schaefer2018_seg-17Networks_scale-700_dsegni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/atlases/tpl-FSLMNI152_atlas-Schaefer2018_seg-17Networks_scale-700_dseg

belongs to
BrainAtlas c
has facts
alt Label ap "Schaefer2018"

tpl-FSLMNI152_atlas-Schaefer2018_seg-17Networks_scale-800_dsegni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/atlases/tpl-FSLMNI152_atlas-Schaefer2018_seg-17Networks_scale-800_dseg

belongs to
BrainAtlas c
has facts
alt Label ap "Schaefer2018"

tpl-FSLMNI152_atlas-Schaefer2018_seg-17Networks_scale-900_dsegni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/atlases/tpl-FSLMNI152_atlas-Schaefer2018_seg-17Networks_scale-900_dseg

belongs to
BrainAtlas c
has facts
alt Label ap "Schaefer2018"

tpl-FSLMNI152_atlas-Schaefer2018_seg-7Networks_scale-1000_dsegni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/atlases/tpl-FSLMNI152_atlas-Schaefer2018_seg-7Networks_scale-1000_dseg

belongs to
BrainAtlas c
has facts
alt Label ap "Schaefer2018"

tpl-FSLMNI152_atlas-Schaefer2018_seg-7Networks_scale-100_dsegni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/atlases/tpl-FSLMNI152_atlas-Schaefer2018_seg-7Networks_scale-100_dseg

belongs to
BrainAtlas c
has facts
alt Label ap "Schaefer2018"

tpl-FSLMNI152_atlas-Schaefer2018_seg-7Networks_scale-200_dsegni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/atlases/tpl-FSLMNI152_atlas-Schaefer2018_seg-7Networks_scale-200_dseg

belongs to
BrainAtlas c
has facts
alt Label ap "Schaefer2018"

tpl-FSLMNI152_atlas-Schaefer2018_seg-7Networks_scale-300_dsegni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/atlases/tpl-FSLMNI152_atlas-Schaefer2018_seg-7Networks_scale-300_dseg

belongs to
BrainAtlas c
has facts
alt Label ap "Schaefer2018"

tpl-FSLMNI152_atlas-Schaefer2018_seg-7Networks_scale-400_dsegni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/atlases/tpl-FSLMNI152_atlas-Schaefer2018_seg-7Networks_scale-400_dseg

belongs to
BrainAtlas c
has facts
alt Label ap "Schaefer2018"

tpl-FSLMNI152_atlas-Schaefer2018_seg-7Networks_scale-500_dsegni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/atlases/tpl-FSLMNI152_atlas-Schaefer2018_seg-7Networks_scale-500_dseg

belongs to
BrainAtlas c
has facts
alt Label ap "Schaefer2018"

tpl-FSLMNI152_atlas-Schaefer2018_seg-7Networks_scale-600_dsegni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/atlases/tpl-FSLMNI152_atlas-Schaefer2018_seg-7Networks_scale-600_dseg

belongs to
BrainAtlas c
has facts
alt Label ap "Schaefer2018"

tpl-FSLMNI152_atlas-Schaefer2018_seg-7Networks_scale-700_dsegni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/atlases/tpl-FSLMNI152_atlas-Schaefer2018_seg-7Networks_scale-700_dseg

belongs to
BrainAtlas c
has facts
alt Label ap "Schaefer2018"

tpl-FSLMNI152_atlas-Schaefer2018_seg-7Networks_scale-800_dsegni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/atlases/tpl-FSLMNI152_atlas-Schaefer2018_seg-7Networks_scale-800_dseg

belongs to
BrainAtlas c
has facts
alt Label ap "Schaefer2018"

tpl-FSLMNI152_atlas-Schaefer2018_seg-7Networks_scale-900_dsegni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/atlases/tpl-FSLMNI152_atlas-Schaefer2018_seg-7Networks_scale-900_dseg

belongs to
BrainAtlas c
has facts
alt Label ap "Schaefer2018"

tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_scale-1000_desc-SC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_scale-1000_desc-SC_relmat

belongs to
Network c
has facts
alt Label ap "Schaefer1000 (dTOR)"
has Parameter ap conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_scale-1000_desc-SC_relmat parameter) ni

tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-1000_desc-SC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-1000_desc-SC_relmat

belongs to
Network c
has facts
alt Label ap "Schaefer2018_1000_17Networks_dTOR"
has Parameter ap conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-1000_desc-SC_relmat parameter) ni

tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-100_desc-SC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-100_desc-SC_relmat

belongs to
Network c
has facts
alt Label ap "Schaefer2018_100_17Networks_dTOR"
has Parameter ap conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-100_desc-SC_relmat parameter) ni

tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-200_desc-SC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-200_desc-SC_relmat

belongs to
Network c
has facts
alt Label ap "Schaefer2018_200_17Networks_dTOR"
has Parameter ap conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-200_desc-SC_relmat parameter) ni

tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-300_desc-SC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-300_desc-SC_relmat

belongs to
Network c
has facts
alt Label ap "Schaefer2018_300_17Networks_dTOR"
has Parameter ap conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-300_desc-SC_relmat parameter) ni

tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-400_desc-SC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-400_desc-SC_relmat

belongs to
Network c
has facts
alt Label ap "Schaefer2018_400_17Networks_dTOR"
has Parameter ap conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-400_desc-SC_relmat parameter) ni

tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-500_desc-SC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-500_desc-SC_relmat

belongs to
Network c
has facts
alt Label ap "Schaefer2018_500_17Networks_dTOR"
has Parameter ap conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-500_desc-SC_relmat parameter) ni

tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-600_desc-SC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-600_desc-SC_relmat

belongs to
Network c
has facts
alt Label ap "Schaefer2018_600_17Networks_dTOR"
has Parameter ap conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-600_desc-SC_relmat parameter) ni

tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-700_desc-SC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-700_desc-SC_relmat

belongs to
Network c
has facts
alt Label ap "Schaefer2018_700_17Networks_dTOR"
has Parameter ap conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-700_desc-SC_relmat parameter) ni

tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-800_desc-SC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-800_desc-SC_relmat

belongs to
Network c
has facts
alt Label ap "Schaefer2018_800_17Networks_dTOR"
has Parameter ap conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-800_desc-SC_relmat parameter) ni

tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-900_desc-SC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-900_desc-SC_relmat

belongs to
Network c
has facts
alt Label ap "Schaefer2018_900_17Networks_dTOR"
has Parameter ap conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-900_desc-SC_relmat parameter) ni

tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-1000_desc-SC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-1000_desc-SC_relmat

belongs to
Network c
has facts
alt Label ap "Schaefer2018_1000_7Networks_dTOR"
has Parameter ap conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-1000_desc-SC_relmat parameter) ni

tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-100_desc-SC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-100_desc-SC_relmat

belongs to
Network c
has facts
alt Label ap "Schaefer2018_100_7Networks_dTOR"
has Parameter ap conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-100_desc-SC_relmat parameter) ni

tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-200_desc-SC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-200_desc-SC_relmat

belongs to
Network c
has facts
alt Label ap "Schaefer2018_200_7Networks_dTOR"
has Parameter ap conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-200_desc-SC_relmat parameter) ni

tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-300_desc-SC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-300_desc-SC_relmat

belongs to
Network c
has facts
alt Label ap "Schaefer2018_300_7Networks_dTOR"
has Parameter ap conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-300_desc-SC_relmat parameter) ni

tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-400_desc-SC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-400_desc-SC_relmat

belongs to
Network c
has facts
alt Label ap "Schaefer2018_400_7Networks_dTOR"
has Parameter ap conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-400_desc-SC_relmat parameter) ni

tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-500_desc-SC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-500_desc-SC_relmat

belongs to
Network c
has facts
alt Label ap "Schaefer2018_500_7Networks_dTOR"
has Parameter ap conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-500_desc-SC_relmat parameter) ni

tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-600_desc-SC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-600_desc-SC_relmat

belongs to
Network c
has facts
alt Label ap "Schaefer2018_600_7Networks_dTOR"
has Parameter ap conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-600_desc-SC_relmat parameter) ni

tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-700_desc-SC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-700_desc-SC_relmat

belongs to
Network c
has facts
alt Label ap "Schaefer2018_700_7Networks_dTOR"
has Parameter ap conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-700_desc-SC_relmat parameter) ni

tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-800_desc-SC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-800_desc-SC_relmat

belongs to
Network c
has facts
alt Label ap "Schaefer2018_800_7Networks_dTOR"
has Parameter ap conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-800_desc-SC_relmat parameter) ni

tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-900_desc-SC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-900_desc-SC_relmat

belongs to
Network c
has facts
alt Label ap "Schaefer2018_900_7Networks_dTOR"
has Parameter ap conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-900_desc-SC_relmat parameter) ni

tpl-FSLMNI152_cohort-HCPYA_rec-Hansen2022_atlas-Schaefer2018_seg-7Networks_scale-100_desc-SCFC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-HCPYA_rec-Hansen2022_atlas-Schaefer2018_seg-7Networks_scale-100_desc-SCFC_relmat

belongs to
Network c
has facts
description ap "Schaefer2018 100-parcel 7Networks multi-graph network from Hansen et al. (2022). Contains structural connectivity (SC) from diffusion MRI tractography and functional connectivity (FC) from resting-state fMRI, both derived from the HCP Young Adult cohort. SC edge weights are log-transformed streamline counts normalized to [0, 1]. FC edge weights are Pearson correlations."
alt Label ap "Schaefer2018_100_7Networks_Hansen2022_SCFC"
has Parameter ap conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-Hansen2022_atlas-Schaefer2018_seg-7Networks_scale-100_desc-SCFC_relmat parameter) ni

tpl-FSLMNI152_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-Schaefer2018_scale-1000_desc-SC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-Schaefer2018_scale-1000_desc-SC_relmat

belongs to
Network c
has facts
alt Label ap "Schaefer1000 (MghUscHcp32)"
has Parameter ap conduction_speed (tpl-FSLMNI152_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-Schaefer2018_scale-1000_desc-SC_relmat parameter) ni

tpl-FSLMNI152_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-Schaefer2018_seg-17Networks_scale-1000_desc-SC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-Schaefer2018_seg-17Networks_scale-1000_desc-SC_relmat

belongs to
Network c
has facts
alt Label ap "Schaefer100017Networks (MghUscHcp32)"
has Parameter ap conduction_speed (tpl-FSLMNI152_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-Schaefer2018_seg-17Networks_scale-1000_desc-SC_relmat parameter) ni

tpl-FSLMNI152_cohort-PPMI85_rec-PPMI85_atlas-Schaefer2018_scale-1000_desc-SC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-PPMI85_rec-PPMI85_atlas-Schaefer2018_scale-1000_desc-SC_relmat

belongs to
Network c
has facts
alt Label ap "Schaefer1000 (PPMI85)"
has Parameter ap conduction_speed (tpl-FSLMNI152_cohort-PPMI85_rec-PPMI85_atlas-Schaefer2018_scale-1000_desc-SC_relmat parameter) ni

tpl-FSLMNI152_cohort-PPMI85_rec-PPMI85_atlas-Schaefer2018_seg-17Networks_scale-1000_desc-SC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-FSLMNI152_cohort-PPMI85_rec-PPMI85_atlas-Schaefer2018_seg-17Networks_scale-1000_desc-SC_relmat

belongs to
Network c
has facts
alt Label ap "Schaefer100017Networks (PPMI85)"
has Parameter ap conduction_speed (tpl-FSLMNI152_cohort-PPMI85_rec-PPMI85_atlas-Schaefer2018_seg-17Networks_scale-1000_desc-SC_relmat parameter) ni

tpl-MNI152NLin2009b_atlas-hcpmmp1_desc-ordered_dsegni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/atlases/tpl-MNI152NLin2009b_atlas-hcpmmp1_desc-ordered_dseg

belongs to
BrainAtlas c
has facts
alt Label ap "hcpmmp1"

tpl-MNI152NLin2009bAsym_cohort-HCPYA_rec-dTOR_atlas-HCPMMP1_desc-SC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009bAsym_cohort-HCPYA_rec-dTOR_atlas-HCPMMP1_desc-SC_relmat

belongs to
Network c
has facts
alt Label ap "hcpmmp1 (dTOR)"
has Parameter ap conduction_speed (tpl-MNI152NLin2009bAsym_cohort-HCPYA_rec-dTOR_atlas-HCPMMP1_desc-SC_relmat parameter) ni

tpl-MNI152NLin2009bAsym_cohort-HCPYA_rec-dTOR_atlas-HCPMMP1_seg-ordered_desc-SC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009bAsym_cohort-HCPYA_rec-dTOR_atlas-HCPMMP1_seg-ordered_desc-SC_relmat

belongs to
Network c
has facts
alt Label ap "hcpmmp1ordered (dTOR)"
has Parameter ap conduction_speed (tpl-MNI152NLin2009bAsym_cohort-HCPYA_rec-dTOR_atlas-HCPMMP1_seg-ordered_desc-SC_relmat parameter) ni

tpl-MNI152NLin2009bAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-HCPMMP1_desc-SC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009bAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-HCPMMP1_desc-SC_relmat

belongs to
Network c
has facts
alt Label ap "hcpmmp1 (MghUscHcp32)"
has Parameter ap conduction_speed (tpl-MNI152NLin2009bAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-HCPMMP1_desc-SC_relmat parameter) ni

tpl-MNI152NLin2009bAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-HCPMMP1_seg-ordered_desc-SC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009bAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-HCPMMP1_seg-ordered_desc-SC_relmat

belongs to
Network c
has facts
alt Label ap "hcpmmp1ordered (MghUscHcp32)"
has Parameter ap conduction_speed (tpl-MNI152NLin2009bAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-HCPMMP1_seg-ordered_desc-SC_relmat parameter) ni

tpl-MNI152NLin2009bAsym_cohort-PPMI85_rec-PPMI85_atlas-HCPMMP1_desc-SC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009bAsym_cohort-PPMI85_rec-PPMI85_atlas-HCPMMP1_desc-SC_relmat

belongs to
Network c
has facts
alt Label ap "hcpmmp1 (PPMI85)"
has Parameter ap conduction_speed (tpl-MNI152NLin2009bAsym_cohort-PPMI85_rec-PPMI85_atlas-HCPMMP1_desc-SC_relmat parameter) ni

tpl-MNI152NLin2009bAsym_cohort-PPMI85_rec-PPMI85_atlas-HCPMMP1_seg-ordered_desc-SC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009bAsym_cohort-PPMI85_rec-PPMI85_atlas-HCPMMP1_seg-ordered_desc-SC_relmat

belongs to
Network c
has facts
alt Label ap "hcpmmp1ordered (PPMI85)"
has Parameter ap conduction_speed (tpl-MNI152NLin2009bAsym_cohort-PPMI85_rec-PPMI85_atlas-HCPMMP1_seg-ordered_desc-SC_relmat parameter) ni

tpl-MNI152NLin2009c_atlas-DesikanKilliany_desc-ranked_dsegni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/atlases/tpl-MNI152NLin2009c_atlas-DesikanKilliany_desc-ranked_dseg

belongs to
BrainAtlas c
has facts
alt Label ap "DesikanKilliany"

tpl-MNI152Nlin2009c_atlas-Destrieux_desc-ranked_dsegni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/atlases/tpl-MNI152Nlin2009c_atlas-Destrieux_desc-ranked_dseg

belongs to
BrainAtlas c
has facts
alt Label ap "Destrieux"

tpl-MNI152NLin2009cAsym_cohort-HCPYA_atlas-Lobar8_desc-surf_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-HCPYA_atlas-Lobar8_desc-surf_relmat

belongs to
Network c
has facts
alt Label ap "Lobar8 surface (fsaverage 164k, 327684 vertices)"
has Parameter ap conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_atlas-Lobar8_desc-surf_relmat parameter) ni

tpl-MNI152NLin2009cAsym_cohort-HCPYA_atlas-Lobar8_hemi-L_desc-surf_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-HCPYA_atlas-Lobar8_hemi-L_desc-surf_relmat

belongs to
Network c
has facts
alt Label ap "Lobar8 LH surface (fsaverage 164k, 163842 vertices)"
has Parameter ap conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_atlas-Lobar8_hemi-L_desc-surf_relmat parameter) ni

tpl-MNI152NLin2009cAsym_cohort-HCPYA_atlas-Lobar8_hemi-R_desc-surf_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-HCPYA_atlas-Lobar8_hemi-R_desc-surf_relmat

belongs to
Network c
has facts
alt Label ap "Lobar8 RH surface (fsaverage 164k, 163842 vertices)"
has Parameter ap conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_atlas-Lobar8_hemi-R_desc-surf_relmat parameter) ni

tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-DesikanKilliany_desc-SC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-DesikanKilliany_desc-SC_relmat

belongs to
Network c
has facts
alt Label ap "DesikanKilliany (dTOR)"
has Parameter ap conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-DesikanKilliany_desc-SC_relmat parameter) ni

tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Destrieux_desc-SC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Destrieux_desc-SC_relmat

belongs to
Network c
has facts
alt Label ap "Destrieux (dTOR)"
has Parameter ap conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Destrieux_desc-SC_relmat parameter) ni

tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-HCPex_desc-SC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-HCPex_desc-SC_relmat

belongs to
Network c
has facts
alt Label ap "HCPex (dTOR)"
has Parameter ap conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-HCPex_desc-SC_relmat parameter) ni

tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Lobar8_desc-SCFC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Lobar8_desc-SCFC_relmat

belongs to
Network c
has facts
alt Label ap "Lobar8 (dTOR)"
has Parameter ap conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Lobar8_desc-SCFC_relmat parameter) ni

tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Lobar_desc-SC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Lobar_desc-SC_relmat

belongs to
Network c
has facts
alt Label ap "Lobar (dTOR)"
has Parameter ap conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Lobar_desc-SC_relmat parameter) ni

tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Lobar_desc-surf_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Lobar_desc-surf_relmat

belongs to
Network c
has facts
alt Label ap "Lobar surface (fsLR 32k, 64984 vertices)"
has Parameter ap conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Lobar_desc-surf_relmat parameter) ni

tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-virtualdbs_desc-SC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-virtualdbs_desc-SC_relmat

belongs to
Network c
has facts
alt Label ap "virtualdbs (dTOR)"
has Parameter ap conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-virtualdbs_desc-SC_relmat parameter) ni

tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Yeo17_desc-SC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Yeo17_desc-SC_relmat

belongs to
Network c
has facts
alt Label ap "Yeo17 (dTOR)"
has Parameter ap conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Yeo17_desc-SC_relmat parameter) ni

tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-DesikanKilliany_desc-SC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-DesikanKilliany_desc-SC_relmat

belongs to
Network c
has facts
alt Label ap "DesikanKilliany (MghUscHcp32)"
has Parameter ap conduction_speed (tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-DesikanKilliany_desc-SC_relmat parameter) ni

tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-Destrieux_desc-SC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-Destrieux_desc-SC_relmat

belongs to
Network c
has facts
alt Label ap "Destrieux (MghUscHcp32)"
has Parameter ap conduction_speed (tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-Destrieux_desc-SC_relmat parameter) ni

tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-HOCPA_desc-SC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-HOCPA_desc-SC_relmat

belongs to
Network c
has facts
alt Label ap "HOCPA (MghUscHcp32)"
has Parameter ap conduction_speed (tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-HOCPA_desc-SC_relmat parameter) ni

tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-virtualdbs_desc-SC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-virtualdbs_desc-SC_relmat

belongs to
Network c
has facts
alt Label ap "virtualdbs (MghUscHcp32)"
has Parameter ap conduction_speed (tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-virtualdbs_desc-SC_relmat parameter) ni

tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-Yeo17_desc-SC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-Yeo17_desc-SC_relmat

belongs to
Network c
has facts
alt Label ap "Yeo17 (MghUscHcp32)"
has Parameter ap conduction_speed (tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-Yeo17_desc-SC_relmat parameter) ni

tpl-MNI152NLin2009cAsym_cohort-PPMI85_rec-PPMI85_atlas-DesikanKilliany_desc-SC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-PPMI85_rec-PPMI85_atlas-DesikanKilliany_desc-SC_relmat

belongs to
Network c
has facts
alt Label ap "DesikanKilliany (PPMI85)"
has Parameter ap conduction_speed (tpl-MNI152NLin2009cAsym_cohort-PPMI85_rec-PPMI85_atlas-DesikanKilliany_desc-SC_relmat parameter) ni

tpl-MNI152NLin2009cAsym_cohort-PPMI85_rec-PPMI85_atlas-Destrieux_desc-SC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-PPMI85_rec-PPMI85_atlas-Destrieux_desc-SC_relmat

belongs to
Network c
has facts
alt Label ap "Destrieux (PPMI85)"
has Parameter ap conduction_speed (tpl-MNI152NLin2009cAsym_cohort-PPMI85_rec-PPMI85_atlas-Destrieux_desc-SC_relmat parameter) ni

tpl-MNI152NLin2009cAsym_cohort-PPMI85_rec-PPMI85_atlas-virtualdbs_desc-SC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-PPMI85_rec-PPMI85_atlas-virtualdbs_desc-SC_relmat

belongs to
Network c
has facts
alt Label ap "virtualdbs (PPMI85)"
has Parameter ap conduction_speed (tpl-MNI152NLin2009cAsym_cohort-PPMI85_rec-PPMI85_atlas-virtualdbs_desc-SC_relmat parameter) ni

tpl-MNI152NLin2009cAsym_cohort-PPMI85_rec-PPMI85_atlas-Yeo17_desc-SC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-PPMI85_rec-PPMI85_atlas-Yeo17_desc-SC_relmat

belongs to
Network c
has facts
alt Label ap "Yeo17 (PPMI85)"
has Parameter ap conduction_speed (tpl-MNI152NLin2009cAsym_cohort-PPMI85_rec-PPMI85_atlas-Yeo17_desc-SC_relmat parameter) ni

tpl-MNI152NLin2009cAsym_rec-avgMatrix_atlas-DesikanKilliany_desc-SCFC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_rec-avgMatrix_atlas-DesikanKilliany_desc-SCFC_relmat

belongs to
Network c
has facts
alt Label ap "DesikanKilliany (avgMatrix SC+FC)"
has Parameter ap conduction_speed (tpl-MNI152NLin2009cAsym_rec-avgMatrix_atlas-DesikanKilliany_desc-SCFC_relmat parameter) ni

tpl-MNI152NLin2009cAsym_rec-avgMatrix_atlas-Lobar8_desc-SCFC_relmatni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_rec-avgMatrix_atlas-Lobar8_desc-SCFC_relmat

belongs to
Network c
has facts
alt Label ap "Lobar8 (avgMatrix)"
has Parameter ap conduction_speed (tpl-MNI152NLin2009cAsym_rec-avgMatrix_atlas-Lobar8_desc-SCFC_relmat parameter) ni

TR (bold_double_exponential parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/observation_models/bold_double_exponential/parameters/TR

belongs to
Parameter c
has facts
default Value ap "2000.0"^^double
notation ap "TR"
unit (slot) dp "ms"

TR (bold_gamma parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/observation_models/bold_gamma/parameters/TR

belongs to
Parameter c
has facts
default Value ap "2000.0"^^double
notation ap "TR"
unit (slot) dp "ms"

TR (bold_mixture_of_gammas parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/observation_models/bold_mixture_of_gammas/parameters/TR

belongs to
Parameter c
has facts
default Value ap "2000.0"^^double
notation ap "TR"
unit (slot) dp "ms"

TR (bold_tvb parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/observation_models/bold_tvb/parameters/TR

belongs to
Parameter c
has facts
description ap "Repetition time (sampling period)"
default Value ap "720.0"^^double
notation ap "TR"
unit (slot) dp "ms"

TR (FC parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/observation_models/FC/parameters/TR

belongs to
Parameter c
has facts
description ap "Repetition time"
default Value ap "720.0"^^double
notation ap "TR"
unit (slot) dp "ms"

TsodyksMarkramni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/TsodyksMarkram

belongs to
Dynamics c
has facts
exhibits regime op Oscillatory ni
exhibits regime op Quiescent ni
has attractor op Fixed point ni
has attractor op Limit cycle ni
has stochasticity character op Deterministic ni
models anatomical region op U B E R O N 0000956 ni
models neurotransmitter system op G O 0035249 ni
phase-space dimension dp "3"^^integer
description ap "Tsodyks-Markram mean-field model of short-term synaptic plasticity. A three-variable neural mass model with firing rate E, synaptic depression variable x, and facilitation variable u. The transfer function uses a softplus nonlinearity α·log(1 + exp(s/α)). Reproduces the dynamics from BifurcationKit.jl/examples/TMModel.jl."
pref Label ap "Tsodyks-Markram"@en
has Derived Variable ap SS0 (TsodyksMarkram derived variable) ni
has Derived Variable ap SS1 (TsodyksMarkram derived variable) ni
has Parameter ap E0 (TsodyksMarkram parameter) ni
has Parameter ap J (TsodyksMarkram parameter) ni
has Parameter ap U0 (TsodyksMarkram parameter) ni
has Parameter ap alpha (TsodyksMarkram parameter) ni
has Parameter ap tau (TsodyksMarkram parameter) ni
has Parameter ap tauD (TsodyksMarkram parameter) ni
has Parameter ap tauF (TsodyksMarkram parameter) ni
has State Variable ap E (TsodyksMarkram state variable) ni
has State Variable ap u (TsodyksMarkram state variable) ni
has State Variable ap x (TsodyksMarkram state variable) ni
model_type (slot) ap "neural_mass"

tt (Epileptor2D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor2D/parameters/tt

Characteristic time scale of the whole-system Epileptor2D.
belongs to
Parameter c
has facts
description ap "Characteristic time scale of the whole-system Epileptor2D"
default Value ap "1.0"^^double
definition ap "Characteristic time scale of the whole-system Epileptor2D."
notation ap "tt"

tt (Epileptor5D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor5D/parameters/tt

Characteristic time scale of the whole-system Epileptor5D.
belongs to
Parameter c
has facts
description ap "Characteristic time scale of the whole-system Epileptor5D"
default Value ap "1.0"^^double
definition ap "Characteristic time scale of the whole-system Epileptor5D."
notation ap "tt"

tt (EpileptorRestingState parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/EpileptorRestingState/parameters/tt

Time scaling of the Epileptor.
belongs to
Parameter c
has facts
description ap "Time scaling of the Epileptor"
default Value ap "1.0"^^double
definition ap "Time scaling of the Epileptor."
notation ap "tt"

Tufillaro1984ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Tufillaro1984

belongs to
Scholarly article c
has facts
issued ap "1984"
title ap "Swinging Atwood's Machine"
author ap "Abbott, Tyler A."
author ap "Griffiths, David J."
author ap "Tufillaro, Nicholas B."
is Part Of ap "American Journal of Physics"
issue Number ap "10"
pagination ap "895--903"
volume Number ap "52"

Tufillaro1992ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Tufillaro1992

belongs to
Book c
has facts
issued ap "1992"
title ap "An Experimental Approach to Nonlinear Dynamics and Chaos"
author ap "Abbott, Tyler"
author ap "Reilly, James"
author ap "Tufillaro, Nicholas B."
identifier ap "10.1119/1.17380"
publisher ap "Addison-Wesley"

TVBni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/TVB

belongs to
Software package c
has facts
description ap "The Virtual Brain — a neuroinformatics platform for full-brain network simulation using neural mass and mean-field models on individual connectome data."
license ap "GPL-3.0-or-later"
code Repository ap "https://github.com/the-virtual-brain/tvb-root"
identifier ap "10.3389/fninf.2013.00010"
url ap "https://www.thevirtualbrain.org"

TVB-Oni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/TVB-O

belongs to
Software package c
has facts
description ap "The Virtual Brain Ontology — a Python library for knowledge representation, code generation, and simulation of large-scale brain network models. Integrates a LinkML-based ontology with JAX-accelerated numerical backends and interoperates with TVB, PyRates, NEURON, NEST, NeuroML, and NetworkDynamics.jl."
license ap "EUPL-1.2"
code Repository ap "https://github.com/virtual-twin/tvbo"
identifier ap "10.1101/2025.11.19.689211"
url ap "https://tvbo.charite.de"

TVB-Optimni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/software/TVB-Optim

belongs to
Software package c
has facts
description ap "Differentiable whole-brain simulation and optimization framework using JAX. Supports gradient-based fitting of neural mass models to empirical neuroimaging data."
license ap "EUPL-1.2"
code Repository ap "https://github.com/virtual-twin/tvboptim"
url ap "https://virtual-twin.github.io/tvboptim/"

TvN0 (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/TvN0

Normalization factors page 48 after the equation 4 from [ZD_2018]
belongs to
Parameter c
has facts
description ap "Normalization factors page 48 after the equation 4 from [ZD_2018]"
default Value ap "0.5"^^double
definition ap "Normalization factors page 48 after the equation 4 from [ZD_2018]"
notation ap "TvN0"

u (TsodyksMarkram state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/TsodyksMarkram/state_variables/u

belongs to
StateVariable c
has facts
description ap "Synaptic facilitation variable (release probability). Decays to U0 with time constant tauF and is enhanced proportionally to firing."
notation ap "u"
lhs ap "Derivative(u, t)"
rhs ap "(U0 - u)/tauF + U0*(1 - u)*E"

U (ZetterbergJansen parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZetterbergJansen/parameters/U

Maximum firing rate to the stellate population [ms^-1]. (External stimulus. Constant intensity.Entry point for coupling.)
belongs to
Parameter c
has facts
description ap "Maximum firing rate to the stellate population [ms^-1]"
default Value ap "0.12"^^double
has Db Xref ap G O 0099605 ep
definition ap "Maximum firing rate to the stellate population [ms^-1]. (External stimulus. Constant intensity.Entry point for coupling.)"
notation ap "U"

U0 (TsodyksMarkram parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/TsodyksMarkram/parameters/U0

belongs to
Parameter c
has facts
description ap "Baseline release probability"
default Value ap "0.3"^^double
notation ap "U0"

U_e_e (ZerlautAdaptationFirstOrder derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/derived_variables/U_e_e

belongs to
DerivedVariable c
has facts
notation ap "U_e_e"
lhs ap "U_e_e"
rhs ap "Q_e*(E_e - mu_V_e)/mu_G_e"

U_e_i (ZerlautAdaptationFirstOrder derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/derived_variables/U_e_i

belongs to
DerivedVariable c
has facts
notation ap "U_e_i"
lhs ap "U_e_i"
rhs ap "Q_e*(E_e - mu_V_i)/mu_G_i"

U_i_e (ZerlautAdaptationFirstOrder derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/derived_variables/U_i_e

belongs to
DerivedVariable c
has facts
notation ap "U_i_e"
lhs ap "U_i_e"
rhs ap "Q_i*(E_i - mu_V_e)/mu_G_e"

U_i_i (ZerlautAdaptationFirstOrder derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/derived_variables/U_i_i

belongs to
DerivedVariable c
has facts
notation ap "U_i_i"
lhs ap "U_i_i"
rhs ap "Q_i*(E_i - mu_V_i)/mu_G_i"

Ueda1961ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Ueda1961

belongs to
Scholarly article c
has facts
issued ap "1961"
title ap "Randomly Transitional Phenomena in the System Governed by Duffing's Equation"
author ap "Ueda, Yoshisuke"
is Part Of ap "Journal of Statistical Physics"

Ulam1960sni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Ulam1960s

belongs to
Creative work c
has facts
issued ap "1960"
title ap "Ulam coupled map on a ring"
author ap "Ulam, Stanislaw"

V (CoombesByrne state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/CoombesByrne/state_variables/V

belongs to
StateVariable c
has facts
notation ap "V"
lhs ap "Derivative(V, t)"
rhs ap "V**2 + c_pop0 + eta + g*(-V + v_syn) - pi**2*r**2"

V (CoombesByrne2D state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/CoombesByrne2D/state_variables/V

belongs to
StateVariable c
has facts
notation ap "V"
lhs ap "Derivative(V, t)"
rhs ap "V**2 + c_pop0 + eta + pi*k*r*(-V + v_syn) - pi**2*r**2"

V (GastSchmidtKnosche_SD state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/GastSchmidtKnosche_SD/state_variables/V

belongs to
StateVariable c
has facts
notation ap "V"
lhs ap "Derivative(V, t)"
rhs ap "(I + J*r*tau*(1 - A) + V**2 + c_pop0*cr + c_pop1*cv + eta - pi**2*r**2*tau**2)/tau"

V (GastSchmidtKnosche_SF state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/GastSchmidtKnosche_SF/state_variables/V

belongs to
StateVariable c
has facts
notation ap "V"
lhs ap "Derivative(V, t)"
rhs ap "(-A + I + J*r*tau + V**2 + c_pop0*cr + c_pop1*cv + eta - pi**2*r**2*tau**2)/tau"

V (Generic2dOscillator state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Generic2dOscillator/state_variables/V

belongs to
StateVariable c
has facts
description ap "V_G2D is the first state-variable of the Generic 2-Dimensional Oscillator model, that can be associated with membrane potentials and sodium activation (FitzHugh, 1961)"
has Db Xref ap G O 0005272 ep
notation ap "V"
lhs ap "Derivative(V, t)"
rhs ap "d*tau*(I*gamma - V**3*f + V**2*e + V*g + V*local_coupling + W*alpha + c_glob*gamma)"

V (KIonEx state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/state_variables/V

belongs to
StateVariable c
has facts
notation ap "V"
lhs ap "Derivative(V, t)"
rhs ap "Vcond"

V (LarterBreakspear state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/LarterBreakspear/state_variables/V

belongs to
StateVariable c
has facts
description ap "First state-variable of the Larter-Breakspear (Breakspear et al"
has Db Xref ap G O 0042391 ep
notation ap "V"
lhs ap "Derivative(V, t)"
rhs ap "t_scale*(I_ext*a_ne - Q_Z*Z*a_ie - W*g_K*(V - V_K) - g_L*(V - V_L) + m_Ca*(V - V_Ca)*(-C*a_ee*c_pop0*r_NMDA - a_ee*r_NMDA*(1.0 - C)*(Q_V + lc_0) - g_Ca) - (V - V_Na)*(C*a_ee*c_pop0 + a_ee*(1.0 - C)*(Q_V + lc_0) + g_Na*m_Na))"

V (MontbrioPazoRoxin state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/MontbrioPazoRoxin/state_variables/V

belongs to
StateVariable c
has facts
notation ap "V"
lhs ap "Derivative(V, t)"
rhs ap "(I + J*r*tau + V**2 + c_pop0*cr*tau + c_pop1*cv + eta - pi**2*r**2*tau**2)/tau"

v0 (JansenRit parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/JansenRit/parameters/v0

Average firing threshold (PSP) for which half of the firing rate is achieved. Note: - The usual value for this parameter is 6.0 (Jansen et al., 1993; Jansen & Rit, 1995).
belongs to
Parameter c
has facts
description ap "Average firing threshold (PSP) for which half of the firing rate is achieved"
default Value ap "5.52"^^double
has Db Xref ap G O 0099605 ep
definition ap "Average firing threshold (PSP) for which half of the firing rate is achieved. Note: - The usual value for this parameter is 6.0 (Jansen et al., 1993; Jansen & Rit, 1995)."
notation ap "v0"
unit (slot) dp "mV"

v0 (JansenRit1995 parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/JansenRit1995/parameters/v0

belongs to
Parameter c
has facts
description ap "PSP for 50% firing rate (sigmoid midpoint)"
default Value ap "6"^^integer
notation ap "v0"
unit (slot) dp "mV"

v0 (ModelJansen1995 parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ModelJansen1995/parameters/v0

belongs to
Parameter c
has facts
default Value ap "6"^^integer
notation ap "v0"
unit (slot) dp "mV"

v1 (ZetterbergJansen state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZetterbergJansen/state_variables/v1

belongs to
StateVariable c
has facts
notation ap "v1"
lhs ap "Derivative(v1, t)"
rhs ap "y1"

v2 (ZetterbergJansen state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZetterbergJansen/state_variables/v2

belongs to
StateVariable c
has facts
notation ap "v2"
lhs ap "Derivative(v2, t)"
rhs ap "y2"

v3 (ZetterbergJansen state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZetterbergJansen/state_variables/v3

belongs to
StateVariable c
has facts
notation ap "v3"
lhs ap "Derivative(v3, t)"
rhs ap "y3"

v4 (ZetterbergJansen state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZetterbergJansen/state_variables/v4

belongs to
StateVariable c
has facts
notation ap "v4"
lhs ap "Derivative(v4, t)"
rhs ap "y4"

v5 (ZetterbergJansen state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZetterbergJansen/state_variables/v5

belongs to
StateVariable c
has facts
notation ap "v5"
lhs ap "Derivative(v5, t)"
rhs ap "y5"

v6 (ZetterbergJansen state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZetterbergJansen/state_variables/v6

belongs to
StateVariable c
has facts
notation ap "v6"
lhs ap "Derivative(v6, t)"
rhs ap "y2 - y3"

v7 (ZetterbergJansen state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZetterbergJansen/state_variables/v7

belongs to
StateVariable c
has facts
notation ap "v7"
lhs ap "Derivative(v7, t)"
rhs ap "y4 - y5"

V_Ca (LarterBreakspear parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/LarterBreakspear/parameters/V_Ca

Calcium Nernst potential.
belongs to
Parameter c
has facts
description ap "Calcium Nernst potential"
default Value ap "1.0"^^double
has Db Xref ap G O 0005262 ep
definition ap "Calcium Nernst potential."
notation ap "V_Ca"

V_e (DumontGutkin state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/DumontGutkin/state_variables/V_e

belongs to
StateVariable c
has facts
notation ap "V_e"
lhs ap "Derivative(V_e, t)"
rhs ap "(I_e + V_e**2 + eta_e - pi**2*r_e**2*tau_e**2 + s_ee*tau_e - s_ei*tau_e)/tau_e"

V_e (ZerlautAdaptationFirstOrder derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/derived_variables/V_e

belongs to
DerivedVariable c
has facts
notation ap "V_e"
lhs ap "V_e"
rhs ap "(-muV0 + mu_V_e)/DmuV0"

V_i (DumontGutkin state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/DumontGutkin/state_variables/V_i

belongs to
StateVariable c
has facts
notation ap "V_i"
lhs ap "Derivative(V_i, t)"
rhs ap "(I_i + V_i**2 + eta_i - pi**2*r_i**2*tau_i**2 + s_ie*tau_i - s_ii*tau_i)/tau_i"

V_i (ZerlautAdaptationFirstOrder derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/derived_variables/V_i

belongs to
DerivedVariable c
has facts
notation ap "V_i"
lhs ap "V_i"
rhs ap "(-muV0 + mu_V_i)/DmuV0"

V_K (LarterBreakspear parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/LarterBreakspear/parameters/V_K

K Nernst potential.
belongs to
Parameter c
has facts
description ap "K Nernst potential"
default Value ap "-0.7"^^double
has Db Xref ap G O 0005267 ep
definition ap "K Nernst potential."
notation ap "V_K"

V_L (LarterBreakspear parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/LarterBreakspear/parameters/V_L

Nernst potential leak channels.
belongs to
Parameter c
has facts
description ap "Nernst potential leak channels"
default Value ap "-0.5"^^double
has Db Xref ap G O 0022840 ep
definition ap "Nernst potential leak channels."
notation ap "V_L"

V_Na (LarterBreakspear parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/LarterBreakspear/parameters/V_Na

Na Nernst potential.
belongs to
Parameter c
has facts
description ap "Na Nernst potential"
default Value ap "0.53"^^double
has Db Xref ap G O 0005272 ep
definition ap "Na Nernst potential."
notation ap "V_Na"

v_pyr (JansenRit1995 derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/JansenRit1995/derived_variables/v_pyr

belongs to
DerivedVariable c
has facts
description ap "Aggregate pyramidal PSP (EEG-like output)"
notation ap "v_pyr"
rhs ap "y1 - y2"

v_pyr (ModelJansen1995 derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ModelJansen1995/derived_variables/v_pyr

belongs to
DerivedVariable c
has facts
description ap "EEG-like output: pyramidal potential difference"
notation ap "v_pyr"
rhs ap "y1 - y2"

v_syn (CoombesByrne parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/CoombesByrne/parameters/v_syn

QIF membrane reversal potential
belongs to
Parameter c
has facts
description ap "QIF membrane reversal potential"
default Value ap "-10.0"^^double
has Db Xref ap G O 0042391 ep
definition ap "QIF membrane reversal potential"
notation ap "v_syn"

v_syn (CoombesByrne2D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/CoombesByrne2D/parameters/v_syn

QIF membrane reversal potential
belongs to
Parameter c
has facts
description ap "QIF membrane reversal potential"
default Value ap "-4.0"^^double
has Db Xref ap G O 0042391 ep
definition ap "QIF membrane reversal potential"
notation ap "v_syn"

V_T (LarterBreakspear parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/LarterBreakspear/parameters/V_T

Threshold potential for excitatory neurons. Describes the mean potential of the excitatory population.
belongs to
Parameter c
has facts
description ap "Threshold potential for excitatory neurons"
default Value ap "0.0"^^double
has Db Xref ap G O 0098815 ep
definition ap "Threshold potential for excitatory neurons. Describes the mean potential of the excitatory population."
notation ap "V_T"

V_temp (KIonEx derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/derived_variables/V_temp

belongs to
DerivedVariable c
has facts
notation ap "V_temp"
lhs ap "V_temp"
rhs ap "-1.0*(I_Cl + I_K + I_Na + I_pump)/Cm"

V_thre_e (ZerlautAdaptationFirstOrder derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/derived_variables/V_thre_e

belongs to
DerivedVariable c
has facts
notation ap "V_thre_e"
lhs ap "V_thre_e"
rhs ap "1000.0*P0_e + 1000.0*P1_e*V_e + 1000.0*P2_e*S_e + 1000.0*P3_e*T_e + 1000.0*P4_e*V_e**2 + 1000.0*P5_e*S_e**2 + 1000.0*P6_e*T_e**2 + 1000.0*P7_e*S_e*V_e + 1000.0*P8_e*T_e*V_e + 1000.0*P9_e*S_e*T_e"

V_thre_i (ZerlautAdaptationFirstOrder derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/derived_variables/V_thre_i

belongs to
DerivedVariable c
has facts
notation ap "V_thre_i"
lhs ap "V_thre_i"
rhs ap "1000.0*P0_i + 1000.0*P1_i*V_i + 1000.0*P2_i*S_i + 1000.0*P3_i*T_i + 1000.0*P4_i*V_i**2 + 1000.0*P5_i*S_i**2 + 1000.0*P6_i*T_i**2 + 1000.0*P7_i*S_i*V_i + 1000.0*P8_i*T_i*V_i + 1000.0*P9_i*S_i*T_i"

vanderpol1926ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/vanderpol1926

belongs to
Scholarly article c
has facts
issued ap "1926"
title ap "On relaxation-oscillations"
author ap "van der Pol, B."
is Part Of ap "The London, Edinburgh, and Dublin Philosophical Magazine and Journal of Science"
issue Number ap "11"
pagination ap "978--992"
volume Number ap "2"

Vcond (KIonEx derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/derived_variables/Vcond

belongs to
DerivedVariable c
has facts
notation ap "Vcond"
lhs ap "Vcond"
rhs ap "Piecewise((R_minus*c_pop0*(-V + E)/pi - R_minus*x**2 + V_temp + eta, V <= Vstar), (R_minus*c_pop0*(-V + E)/pi - R_plus*x**2 + V_temp + eta, True))"

Vectorised RNGni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/VectorizedRNG

belongs to
Backend capability c

VODEni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/integrators/VODE

belongs to
Integrator c

Volo2019ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Volo2019

belongs to
Scholarly article c
has facts
issued ap "2019"
title ap "Biophysical ingredients for a robust model of cortical dynamics"
author ap "di Volo, Matteo"
author ap "others"
is Part Of ap "PLOS Computational Biology"

Volo2019ani back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Volo2019a

belongs to
Scholarly article c
has facts
title ap "Alias for di Volo et al. 2019"

Vstar (KIonEx parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/parameters/Vstar

x-coordinate meeting point of parabolas
belongs to
Parameter c
has facts
description ap "x-coordinate meeting point of parabolas"
default Value ap "-31.0"^^double
definition ap "x-coordinate meeting point of parabolas"
notation ap "Vstar"

W (Generic2dOscillator state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Generic2dOscillator/state_variables/W

belongs to
StateVariable c
has facts
description ap "W_G2D is the second state-variable of the Generic 2-Dimensional Oscillator model, that can be associated with accommodation and refractoriness and considered to represent potassium activation, sodium inactivation, or both (FitzHugh, 1961)"
has Db Xref ap G O 0005272 ep
notation ap "W"
lhs ap "Derivative(W, t)"
rhs ap "d*(V**2*c + V*b - W*beta + a)/tau"

W (LarterBreakspear state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/LarterBreakspear/state_variables/W

belongs to
StateVariable c
has facts
description ap "Second state-variable of the Larter-Breakspear (Breakspear et al"
has Db Xref ap G O 0005267 ep
notation ap "W"
lhs ap "Derivative(W, t)"
rhs ap "phi*t_scale*(-W + m_K)/tau_K"

w (ReducedWongWang parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWang/parameters/w

Excitatory recurrence
belongs to
Parameter c
has facts
description ap "Excitatory recurrence"
default Value ap "0.6"^^double
definition ap "Excitatory recurrence"
notation ap "w"
unit (slot) dp "dimensionless"

w (ReducedWongWangTvboptim parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWangTvboptim/parameters/w

Local excitatory recurrence strength. Controls the positive feedback within each cortical population. Higher values increase local excitation and push the system toward higher firing rates.
belongs to
Parameter c
has facts
description ap "Excitatory recurrence strength (local feedback)"
default Value ap "0.5"^^double
definition ap "Local excitatory recurrence strength. Controls the positive feedback within each cortical population. Higher values increase local excitation and push the system toward higher firing rates."
notation ap "w"
unit (slot) dp "dimensionless"

W_e (ReducedWongWangExcInh parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWangExcInh/parameters/W_e

Excitatory population external input scaling weight
belongs to
Parameter c
has facts
description ap "Excitatory population external input scaling weight"
default Value ap "1.0"^^double
has Db Xref ap G O 0090394 ep
has Db Xref ap G O 2000463 ep
definition ap "Excitatory population external input scaling weight"
notation ap "W_e"

W_e (ZerlautAdaptationFirstOrder state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/state_variables/W_e

belongs to
StateVariable c
has facts
description ap "Level of adaptation of excitatory in pA"
notation ap "W_e"
lhs ap "Derivative(W_e, t)"
rhs ap "E*b_e - W_e/tau_w_e + a_e*(-E_L_e + mu_V_e)/tau_w_e"

w_i (KIonEx parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/parameters/w_i

intracellular volume
belongs to
Parameter c
has facts
description ap "intracellular volume"
default Value ap "2160.0"^^double
definition ap "intracellular volume"
notation ap "w_i"
unit (slot) dp "um3"

W_i (ReducedWongWangExcInh parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWangExcInh/parameters/W_i

Inhibitory population external input scaling weight
belongs to
Parameter c
has facts
description ap "Inhibitory population external input scaling weight"
default Value ap "0.7"^^double
has Db Xref ap G O 0060080 ep
definition ap "Inhibitory population external input scaling weight"
notation ap "W_i"

W_i (ZerlautAdaptationFirstOrder state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/state_variables/W_i

belongs to
StateVariable c
has facts
description ap "Level of adaptation of inhibitory in pA"
notation ap "W_i"
lhs ap "Derivative(W_i, t)"
rhs ap "I*b_i - W_i/tau_w_i + a_i*(-E_L_i + mu_V_i)/tau_w_i"

w_o (KIonEx parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/parameters/w_o

extracellular volume
belongs to
Parameter c
has facts
description ap "extracellular volume"
default Value ap "720.0"^^double
definition ap "extracellular volume"
notation ap "w_o"
unit (slot) dp "um3"

w_p (ReducedWongWangExcInh parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWangExcInh/parameters/w_p

Excitatory population recurrence weight
belongs to
Parameter c
has facts
description ap "Excitatory population recurrence weight"
default Value ap "1.4"^^double
has Db Xref ap G O 0060079 ep
definition ap "Excitatory population recurrence weight"
notation ap "w_p"

Wang2008ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Wang2008

belongs to
Scholarly article c
has facts
issued ap "2008"
title ap "A hyperchaos generated from Lorenz system"
author ap "Wang, M."
author ap "Wang, X."
is Part Of ap "Physica A: Statistical Mechanics and its Applications"
issue Number ap "14"
pagination ap "3751--3758"
volume Number ap "387"

Wang2009ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Wang2009

belongs to
Scholarly article c
has facts
issued ap "2009"
title ap "A 3-D four-wing attractor and its analysis"
author ap "Qi, G."
author ap "Sun, Y."
author ap "Wang, Z."
author ap "van Wyk, B. J."
author ap "van Wyk, M. A."
is Part Of ap "Brazilian Journal of Physics"
pagination ap "547--553"
volume Number ap "39"

weight_noise (ZerlautAdaptationFirstOrder parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder/parameters/weight_noise

weight noise
belongs to
Parameter c
has facts
description ap "weight noise"
default Value ap "10.5"^^double
definition ap "weight noise"
notation ap "weight_noise"

Weissteinni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Weisstein

belongs to
Creative work c
has facts
title ap "Lotka-Volterra Equations"
author ap "Weisstein, Eric W."
url ap "https://mathworld.wolfram.com/Lotka-VolterraEquations.html"

Wilson1972ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Wilson1972

belongs to
Scholarly article c
has facts
issued ap "1972"
title ap "Excitatory and inhibitory interactions in localized populations of model neurons"
author ap "Cowan, Jack D."
author ap "Wilson, Hugh R."
is Part Of ap "Biophysical Journal"

Wilson1973ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Wilson1973

belongs to
Scholarly article c
has facts
issued ap "1973"
title ap "A mathematical theory of the functional dynamics of cortical and thalamic nervous tissue"
author ap "Cowan, Jack D."
author ap "Wilson, Hugh R."
is Part Of ap "Biological Cybernetics"

WilsonCowanni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/WilsonCowan

belongs to
Dynamics c
has facts
exhibits bifurcation op ""
exhibits bifurcation op ""
exhibits regime op Bistable ni
exhibits regime op Oscillatory ni
exhibits regime op Quiescent ni
has attractor op Fixed point ni
has attractor op Limit cycle ni
has model feature op Excitatory/inhibitory subpopulations ni
has model feature op Sigmoid activation ni
has stochasticity character op Deterministic ni
models anatomical region op U B E R O N 0000956 ni
models cell type op C L 0000099 ni
models cell type op C L 0000598 ni
models neurotransmitter system op G O 0007214 ni
models neurotransmitter system op G O 0035249 ni
has timescale separation dp "false"^^boolean
phase-space dimension dp "2"^^integer
description ap "The Wilson and Cowan model consists of two populations or masses, one excitatory and one inhibitory, that are described by their mean firings rates E and I respectively (Wilson and Cowan, 1972, 1973). This model is the minimal representation of a NMM with a coarse-grained description of the overall activity of a large-scale neuronal network, as opposed to being a detailed biophysical model. While employing just two differential equations, it has been used to build various biophysically realistic models (Liley et al., 1999; Daffertshofer and van Wijk, 2011). Key parameters in the model are the strength of connectivity between each subtype of population (excitatory and inhibitory) and the strength of input to each subpopulation. The Input parameters P and Q also provide the entry point for local and long-range connectivity, that is, the activity coming from neighboring and distant populations respectively. Varying Input and connectivity generates a diversity of dynamical behaviors that are representative of observed activity in the brain, like multistability, oscillations, traveling waves and spatial patterns. We consider the transmission parameters of the excitatory population to be glutamatergic and therefore to be modified by glutamatergic receptors. The inhibitory population is considered as GABAergic. Note: - Equations and parameter names are taken from (Wilson and Cowan, 1972 and Sanz-Leon et al., 2015) - Default parameters are taken from Fig. 4 p.10 (Wilson and Cowan, 1972) - The model in Sanz-Leon et., 2015 includes more parameters than the original model, which can be traced in the description of the parameters."
references ap Wilson1972 ni
references ap Wilson1973 ni
pref Label ap "Wilson-Cowan"@en
has Derived Variable ap lc_0 (WilsonCowan derived variable) ni
has Derived Variable ap lc_1 (WilsonCowan derived variable) ni
has Derived Variable ap s_e (WilsonCowan derived variable) ni
has Derived Variable ap s_i (WilsonCowan derived variable) ni
has Derived Variable ap x_e (WilsonCowan derived variable) ni
has Derived Variable ap x_i (WilsonCowan derived variable) ni
has Parameter ap P (WilsonCowan parameter) ni
has Parameter ap Q (WilsonCowan parameter) ni
has Parameter ap a_e (WilsonCowan parameter) ni
has Parameter ap a_i (WilsonCowan parameter) ni
has Parameter ap alpha_e (WilsonCowan parameter) ni
has Parameter ap alpha_i (WilsonCowan parameter) ni
has Parameter ap b_e (WilsonCowan parameter) ni
has Parameter ap b_i (WilsonCowan parameter) ni
has Parameter ap c_e (WilsonCowan parameter) ni
has Parameter ap c_ee (WilsonCowan parameter) ni
has Parameter ap c_ei (WilsonCowan parameter) ni
has Parameter ap c_i (WilsonCowan parameter) ni
has Parameter ap c_ie (WilsonCowan parameter) ni
has Parameter ap c_ii (WilsonCowan parameter) ni
has Parameter ap k_e (WilsonCowan parameter) ni
has Parameter ap k_i (WilsonCowan parameter) ni
has Parameter ap r_e (WilsonCowan parameter) ni
has Parameter ap r_i (WilsonCowan parameter) ni
has Parameter ap shift_sigmoid (WilsonCowan parameter) ni
has Parameter ap tau_e (WilsonCowan parameter) ni
has Parameter ap tau_i (WilsonCowan parameter) ni
has Parameter ap theta_e (WilsonCowan parameter) ni
has Parameter ap theta_i (WilsonCowan parameter) ni
has State Variable ap E (WilsonCowan state variable) ni
has State Variable ap I (WilsonCowan state variable) ni
model_type (slot) ap "neural_mass"

Wong2006ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Wong2006

belongs to
Scholarly article c
has facts
issued ap "2006"
title ap "A Recurrent Network Mechanism of Time Integration in Perceptual Decisions"
author ap "Wang, Xiao-Jing"
author ap "Wong, Kong-Fatt"
identifier ap "10.1523/jneurosci.3733-05.2006"
is Part Of ap "The Journal of Neuroscience"
issue Number ap "4"
pagination ap "1314--1328"
publisher ap "Society for Neuroscience"
volume Number ap "26"

x (GenericLinear state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/GenericLinear/state_variables/x

belongs to
StateVariable c
has facts
description ap "State-variable of the Generic Linear model"
notation ap "x"
lhs ap "Derivative(x, t)"
rhs ap "c_pop0 + gamma*x + local_coupling*x"

x (Hopfield state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Hopfield/state_variables/x

belongs to
StateVariable c
has facts
notation ap "x"
lhs ap "Derivative(x, t)"
rhs ap "(c_pop0 - x)/taux"

x (KIonEx state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/state_variables/x

belongs to
StateVariable c
has facts
notation ap "x"
lhs ap "Derivative(x, t)"
rhs ap "xcond"

x (ReducedWongWang derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWang/derived_variables/x

belongs to
DerivedVariable c
has facts
description ap "(NMDAR)-mediated synaptic input current to the neurons population (Deco et al., 2013)."
notation ap "x"
lhs ap "x"
rhs ap "I_o + J_N*S*local_coupling + J_N*S*w + J_N*c_pop0"

x (ReducedWongWangTvboptim derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWangTvboptim/derived_variables/x

belongs to
DerivedVariable c
has facts
description ap "Total synaptic input current combining local recurrence, external input, and network coupling (instant and delayed) scaled by J_N."
notation ap "x"
lhs ap "x"
rhs ap "w*J_N*S + I_o + J_N*instant + J_N*delayed"

x (SupHopf state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/SupHopf/state_variables/x

belongs to
StateVariable c
has facts
description ap "First state-variable of the Supercritical Hopf model"
notation ap "x"
lhs ap "Derivative(x, t)"
rhs ap "c_pop0 + lc_0 - omega*y + x*(a - x**2 - y**2)"

x (TsodyksMarkram state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/TsodyksMarkram/state_variables/x

belongs to
StateVariable c
has facts
description ap "Synaptic depression variable (fraction of available neurotransmitter). Recovers to 1 with time constant tauD and is depleted proportionally to firing."
notation ap "x"
lhs ap "Derivative(x, t)"
rhs ap "(1 - x)/tauD - u*x*E"

x0 (Epileptor2D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor2D/parameters/x0

Degree of excitability or epileptogenicity in Epileptor2D (Proix et al.,2014). If x0 is greater than a critical value, x0,critic = −2.05 (i.e., in the supercritical regime), the system can trigger seizures autonomously; otherwise it is in its equilibrium state (i.e., in the subcritical regime). Note: - If modification_E2D: if x0 is smaller than a critical value, x0,critic = 2.91, can trigger seizures autonomously; otherwise it is in its equilibrium state (Proix et al., 2014).
belongs to
Parameter c
has facts
description ap "Degree of excitability or epileptogenicity in Epileptor2D (Proix et al"
default Value ap "-1.6"^^double
has Db Xref ap G O 0043179 ep
definition ap "Degree of excitability or epileptogenicity in Epileptor2D (Proix et al.,2014). If x0 is greater than a critical value, x0,critic = −2.05 (i.e., in the supercritical regime), the system can trigger seizures autonomously; otherwise it is in its equilibrium state (i.e., in the subcritical regime). Note: - If modification_E2D: if x0 is smaller than a critical value, x0,critic = 2.91, can trigger seizures autonomously; otherwise it is in its equilibrium state (Proix et al., 2014)."
notation ap "x0"

x0 (Epileptor5D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor5D/parameters/x0

Epileptogenicity Parameter. Degree of excitability or epileptogenicity in Epileptor5D (Jirsa et al.,2014). If x0 is greater than a critical value, x0,critic = −2.05, the system can trigger seizures autonomously; otherwise it is in its equilibrium state. Note: - If modification_E5D: if x0 is smaller than a critical value, x0,critic = 2.91, can trigger seizures autonomously; otherwise it is in its equilibrium state (Proix et al., 2014).
belongs to
Parameter c
has facts
description ap "Epileptogenicity Parameter"
default Value ap "-1.6"^^double
has Db Xref ap G O 0060079 ep
definition ap "Epileptogenicity Parameter. Degree of excitability or epileptogenicity in Epileptor5D (Jirsa et al.,2014). If x0 is greater than a critical value, x0,critic = −2.05, the system can trigger seizures autonomously; otherwise it is in its equilibrium state. Note: - If modification_E5D: if x0 is smaller than a critical value, x0,critic = 2.91, can trigger seizures autonomously; otherwise it is in its equilibrium state (Proix et al., 2014)."
notation ap "x0"

x0 (EpileptorRestingState parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/EpileptorRestingState/parameters/x0

Epileptogenicity parameter.
belongs to
Parameter c
has facts
description ap "Epileptogenicity parameter"
default Value ap "-1.6"^^double
definition ap "Epileptogenicity parameter."
notation ap "x0"

x1 (Epileptor2D state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor2D/state_variables/x1

belongs to
StateVariable c
has facts
description ap "First state-variable in the Epileptor2D (Proix et al"
notation ap "x1"
lhs ap "Derivative(x1, t)"
rhs ap "tt*(Iext + Kvf*c_pop0 + c + local_coupling*x1 - x1*x1cond - z)"

x1 (Epileptor3DStefanescuMcDonald state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor3DStefanescuMcDonald/state_variables/x1

belongs to
StateVariable c
has facts
description ap "Fast excitable variable (placeholder Epileptor-like dynamics)."
notation ap "x1"
lhs ap "Derivative(x1, t)"
rhs ap "N*(x1 - x1**3/3 - z + c_pop0)"

x1 (Epileptor5D state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor5D/state_variables/x1

belongs to
StateVariable c
has facts
description ap "First state-variable of the first Epileptor5D population (Jirsa et al"
notation ap "x1"
lhs ap "Derivative(x1, t)"
rhs ap "tt*(Iext + Kvf*c_pop0 + local_coupling*x1 + x1*x1cond + y1 - z)"

x1 (EpileptorRestingState state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/EpileptorRestingState/state_variables/x1

belongs to
StateVariable c
has facts
notation ap "x1"
lhs ap "Derivative(x1, t)"
rhs ap "tt*(Iext + Kvf*c_pop0 + local_coupling*x1 + x1*x1cond + y1 - z)"

x1cond (Epileptor2D derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor2D/derived_variables/x1cond

belongs to
DerivedVariable c
has facts
notation ap "x1cond"
lhs ap "x1cond"
rhs ap "Piecewise((a*x1**2 + x1*(-b + d), x1 < 0), (d*x1 - slope - 0.6*(z - 4.0)**2, True))"

x1cond (Epileptor5D derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor5D/derived_variables/x1cond

belongs to
DerivedVariable c
has facts
notation ap "x1cond"
lhs ap "x1cond"
rhs ap "Piecewise(((-a)*x1**2 + b*x1, x1 < 0), (slope - x2 + 0.6*(z - 4.0)**2, True))"

x1cond (EpileptorRestingState derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/EpileptorRestingState/derived_variables/x1cond

belongs to
DerivedVariable c
has facts
notation ap "x1cond"
lhs ap "x1cond"
rhs ap "Piecewise(((-a)*x1**2 + b*x1, x1 < 0), (slope - x2 + 0.6*(z - 4.0)**2, True))"

x2 (Epileptor5D state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor5D/state_variables/x2

belongs to
StateVariable c
has facts
description ap "First state-variable of the second Epileptor5D sub-population (Jirsa et al"
notation ap "x2"
lhs ap "Derivative(x2, t)"
rhs ap "tt*(Iext2 + Kf*c_pop1 + bb*g - x2**3 + x2 - y2 - 0.3*z + 1.05)"

x2 (EpileptorRestingState state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/EpileptorRestingState/state_variables/x2

belongs to
StateVariable c
has facts
notation ap "x2"
lhs ap "Derivative(x2, t)"
rhs ap "tt*(Iext2 + Kf*c_pop1 + bb*g - x2**3 + x2 - y2 - 0.3*z + 1.05)"

x_0 (Epileptor3DStefanescuMcDonald parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor3DStefanescuMcDonald/parameters/x_0

Excitability parameter (Epileptor convention).
belongs to
Parameter c
has facts
default Value ap "-1.6"^^double
definition ap "Excitability parameter (Epileptor convention)."
notation ap "x_0"

x_0 (StefanescuJirsa3D parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa3D/parameters/x_0

Leftmost equilibrium point of x in the Hindmarsh-Rose oscillator.
belongs to
Parameter c
has facts
default Value ap "-1.6"^^double
has Db Xref ap G O 0042391 ep
definition ap "Leftmost equilibrium point of x in the Hindmarsh-Rose oscillator."
notation ap "x_0"

x_e (ReducedWongWangExcInh derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWangExcInh/derived_variables/x_e

belongs to
DerivedVariable c
has facts
description ap "Input current to the excitatory population (Deco et al., 2014)."
has Db Xref ap G O 0098815 ep
notation ap "x_e"
lhs ap "x_e"
rhs ap "a_e*(I_ext + I_o*W_e + J_N_S_e*w_p - J_i*S_i + coupling) - b_e"

x_e (WilsonCowan derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/WilsonCowan/derived_variables/x_e

belongs to
DerivedVariable c
has facts
description ap "Average level of excitation in excitatory neuron at time t. Can be interpreted as membrane potential (Sanz-Leon et al., 2015)."
has Db Xref ap G O 0042391 ep
notation ap "x_e"
lhs ap "x_e"
rhs ap "alpha_e*(-I*c_ei + P + c_ee*E + c_pop0 + lc_0 + lc_1 - theta_e)"

x_i (ReducedWongWangExcInh derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ReducedWongWangExcInh/derived_variables/x_i

belongs to
DerivedVariable c
has facts
description ap "Input current to the inhibitory population (Deco et al., 2014)."
has Db Xref ap G O 0060080 ep
notation ap "x_i"
lhs ap "x_i"
rhs ap "a_i*(I_o*W_i + J_N_S_e - S_i + coupling*lamda) - b_i"

x_i (WilsonCowan derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/WilsonCowan/derived_variables/x_i

belongs to
DerivedVariable c
has facts
description ap "Average level of excitation in inhibitory neuron at time t. Can be interpreted as membrane potential. (Sanz-Leon et al., 2015)."
has Db Xref ap G O 0042391 ep
notation ap "x_i"
lhs ap "x_i"
rhs ap "alpha_i*(-I*c_ii + Q + c_ie*E + lc_0 + lc_1 - theta_i)"

x_rs (EpileptorRestingState state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/EpileptorRestingState/state_variables/x_rs

belongs to
StateVariable c
has facts
notation ap "x_rs"
lhs ap "Derivative(x_rs, t)"
rhs ap "d_rs*tau_rs*(I_rs*gamma_rs + K_rs*c_pop2*gamma_rs + alpha_rs*y_rs + e_rs*x_rs**2 - f_rs*x_rs**3 + lc_1)"

xcond (KIonEx derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/KIonEx/derived_variables/xcond

belongs to
DerivedVariable c
has facts
notation ap "xcond"
lhs ap "xcond"
rhs ap "Piecewise((Delta - J*r*x + 2*R_minus*x*(V - c_minus), V <= Vstar), (Delta - J*r*x + 2*R_plus*x*(V - c_plus), True))"

xi (StefanescuJirsa2D state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa2D/state_variables/xi

belongs to
StateVariable c
has facts
description ap "Excitatory fast variable (per mode)."
has Db Xref ap G O 0060079 ep
notation ap "xi"
lhs ap "Derivative(xi, t)"
rhs ap "tau*(xi - e_i*xi**3/3 - eta) + K11*(Aik*xi - xi) - K12*(Bik*alpha - xi) + tau*(IE_i + c_pop0 + local_coupling*xi)"

xi (StefanescuJirsa3D state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/StefanescuJirsa3D/state_variables/xi

belongs to
StateVariable c
has facts
description ap "Excitatory fast variable (per mode)."
has Db Xref ap G O 0042391 ep
notation ap "xi"
lhs ap "Derivative(xi, t)"
rhs ap "eta - a_i*xi**3 + b_i*xi**2 - tau + K_11*(A_ik*xi - xi) - K_12*(B_ik*alpha - xi) + IE_i + c_pop0 + local_coupling*xi"

y (SupHopf state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/SupHopf/state_variables/y

belongs to
StateVariable c
has facts
description ap "Second state-variable of the Supercritical Hopf model"
notation ap "y"
lhs ap "Derivative(y, t)"
rhs ap "c_pop1 + omega*x + y*(a - x**2 - y**2)"

y0 (JansenRit state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/JansenRit/state_variables/y0

belongs to
StateVariable c
has facts
description ap "First state-variable of the first Jansen-Rit population"
has Db Xref ap C L 0000598 ni
has Db Xref ap G O 0060079 ep
notation ap "y0"
lhs ap "Derivative(y0, t)"
rhs ap "y3"

y0 (JansenRit1995 state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/JansenRit1995/state_variables/y0

belongs to
StateVariable c
has facts
notation ap "y0"
rhs ap "y3"

y0 (ModelJansen1995 state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ModelJansen1995/state_variables/y0

belongs to
StateVariable c
has facts
notation ap "y0"
rhs ap "y3"

y1 (Epileptor5D state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor5D/state_variables/y1

belongs to
StateVariable c
has facts
description ap "Second state-variable of the first Epileptor5D sub-population (Jirsa et al"
notation ap "y1"
lhs ap "Derivative(y1, t)"
rhs ap "tt*(c - d*x1**2 - y1)"

y1 (EpileptorRestingState state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/EpileptorRestingState/state_variables/y1

belongs to
StateVariable c
has facts
notation ap "y1"
lhs ap "Derivative(y1, t)"
rhs ap "tt*(c - d*x1**2 - y1)"

y1 (JansenRit state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/JansenRit/state_variables/y1

belongs to
StateVariable c
has facts
description ap "First state-variable of the second Jansen-Rit population (EINs)"
has Db Xref ap C L 0000099 ni
has Db Xref ap G O 0060076 ep
has Db Xref ap G O 0060079 ep
notation ap "y1"
lhs ap "Derivative(y1, t)"
rhs ap "y4"

y1 (JansenRit1995 state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/JansenRit1995/state_variables/y1

belongs to
StateVariable c
has facts
notation ap "y1"
rhs ap "y4"

y1 (ModelJansen1995 state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ModelJansen1995/state_variables/y1

belongs to
StateVariable c
has facts
notation ap "y1"
rhs ap "y4"

y1 (ZetterbergJansen state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZetterbergJansen/state_variables/y1

belongs to
StateVariable c
has facts
notation ap "y1"
lhs ap "Derivative(y1, t)"
rhs ap "He*ke*(gamma_1*sigma_v23 + gamma_1T*(U + coupled_input)) - ke**2*v1 - 2*ke*y1"

y2 (Epileptor5D state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor5D/state_variables/y2

belongs to
StateVariable c
has facts
description ap "Second state-variable of the second Epileptor5D population (Jirsa et al"
notation ap "y2"
lhs ap "Derivative(y2, t)"
rhs ap "tt*(-y2 + y2cond)/tau"

y2 (EpileptorRestingState state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/EpileptorRestingState/state_variables/y2

belongs to
StateVariable c
has facts
notation ap "y2"
lhs ap "Derivative(y2, t)"
rhs ap "tt*(-y2 + y2cond)/tau"

y2 (JansenRit state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/JansenRit/state_variables/y2

belongs to
StateVariable c
has facts
description ap "First state-variable of the third Jansen-Rit population (IINs)"
has Db Xref ap C L 0000099 ni
has Db Xref ap G O 0060077 ep
notation ap "y2"
lhs ap "Derivative(y2, t)"
rhs ap "y5"

y2 (JansenRit1995 state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/JansenRit1995/state_variables/y2

belongs to
StateVariable c
has facts
notation ap "y2"
rhs ap "y5"

y2 (ModelJansen1995 state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ModelJansen1995/state_variables/y2

belongs to
StateVariable c
has facts
notation ap "y2"
rhs ap "y5"

y2 (ZetterbergJansen state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZetterbergJansen/state_variables/y2

belongs to
StateVariable c
has facts
notation ap "y2"
lhs ap "Derivative(y2, t)"
rhs ap "He*ke*(gamma_2*sigma_v1 + gamma_2T*(P + coupled_input)) - ke**2*v2 - 2*ke*y2"

y2cond (Epileptor5D derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor5D/derived_variables/y2cond

belongs to
DerivedVariable c
has facts
notation ap "y2cond"
lhs ap "y2cond"
rhs ap "Piecewise((0.0, x2 < -0.25), (aa*(x2 + 0.25), True))"

y2cond (EpileptorRestingState derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/EpileptorRestingState/derived_variables/y2cond

belongs to
DerivedVariable c
has facts
notation ap "y2cond"
lhs ap "y2cond"
rhs ap "Piecewise((0.0, x2 < -0.25), (aa*(x2 + 0.25), True))"

y3 (JansenRit state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/JansenRit/state_variables/y3

belongs to
StateVariable c
has facts
description ap "Second state-variable of the first Jansen-Rit population (excitatory PCs)"
has Db Xref ap C L 0000598 ni
notation ap "y3"
lhs ap "Derivative(y3, t)"
rhs ap "A*a*sigma_y1_y2 - a**2*y0 - 2.0*a*y3"

y3 (JansenRit1995 state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/JansenRit1995/state_variables/y3

belongs to
StateVariable c
has facts
notation ap "y3"
rhs ap "A*a*Sigm(y1 - y2) - 2*a*y3 - a**2*y0"

y3 (ModelJansen1995 state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ModelJansen1995/state_variables/y3

belongs to
StateVariable c
has facts
notation ap "y3"
rhs ap "A*a*Sigm(y1 - y2) - 2*a*y3 - a**2*y0"

y3 (ZetterbergJansen state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZetterbergJansen/state_variables/y3

belongs to
StateVariable c
has facts
notation ap "y3"
lhs ap "Derivative(y3, t)"
rhs ap "Hi*gamma_4*ki*sigma_v45 - ki**2*v3 - 2*ki*y3"

y4 (JansenRit state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/JansenRit/state_variables/y4

belongs to
StateVariable c
has facts
description ap "Second state-variable of the second excitatory Jansen-Rit population (excitatory EINs)"
has Db Xref ap C L 0000099 ni
notation ap "y4"
lhs ap "Derivative(y4, t)"
rhs ap "A*a*(J*a_2*sigma_y0_1 + c_pop0 + local_coupling*(y1 - y2) + mu) - a**2*y1 - 2.0*a*y4"

y4 (JansenRit1995 state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/JansenRit1995/state_variables/y4

belongs to
StateVariable c
has facts
notation ap "y4"
rhs ap "A*a*(p + C2*Sigm(C1*y0) + c_intercolumn) - 2*a*y4 - a**2*y1"

y4 (ModelJansen1995 state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ModelJansen1995/state_variables/y4

belongs to
StateVariable c
has facts
notation ap "y4"
rhs ap "A*a*(p + C2*Sigm(C1*y0) + c_glob) - 2*a*y4 - a**2*y1"

y4 (ZetterbergJansen state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZetterbergJansen/state_variables/y4

belongs to
StateVariable c
has facts
notation ap "y4"
lhs ap "Derivative(y4, t)"
rhs ap "He*ke*(gamma_3*sigma_v23 + gamma_3T*(Q + coupled_input)) - ke**2*v4 - 2*ke*y4"

y5 (JansenRit state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/JansenRit/state_variables/y5

belongs to
StateVariable c
has facts
description ap "Second state-variable of the third (inhibitory) Jansen-Rit population (IINs)"
has Db Xref ap C L 0000099 ni
notation ap "y5"
lhs ap "Derivative(y5, t)"
rhs ap "B*J*a_4*b*sigma_y0_3 - b**2*y2 - 2.0*b*y5"

y5 (JansenRit1995 state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/JansenRit1995/state_variables/y5

belongs to
StateVariable c
has facts
notation ap "y5"
rhs ap "B*b*(C4*Sigm(C3*y0)) - 2*b*y5 - b**2*y2"

y5 (ModelJansen1995 state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ModelJansen1995/state_variables/y5

belongs to
StateVariable c
has facts
notation ap "y5"
rhs ap "B*b*(C4*Sigm(C3*y0)) - 2*b*y5 - b**2*y2"

y5 (ZetterbergJansen state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZetterbergJansen/state_variables/y5

belongs to
StateVariable c
has facts
notation ap "y5"
lhs ap "Derivative(y5, t)"
rhs ap "Hi*gamma_5*ki*sigma_v45 - ke**2*v5 - 2*ki*y5"

y_rs (EpileptorRestingState state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/EpileptorRestingState/state_variables/y_rs

belongs to
StateVariable c
has facts
notation ap "y_rs"
lhs ap "Derivative(y_rs, t)"
rhs ap "d_rs*(a_rs + b_rs*x_rs - beta_rs*y_rs)/tau_rs"

z (Epileptor2D state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor2D/state_variables/z

belongs to
StateVariable c
has facts
description ap "Slow permittivity state-variable of the Epileptor2D (Proix et al"
notation ap "z"
lhs ap "Derivative(z, t)"
rhs ap "r*tt*(Ks*c_pop0 + h - z)"

z (Epileptor3DStefanescuMcDonald state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor3DStefanescuMcDonald/state_variables/z

belongs to
StateVariable c
has facts
description ap "Slow permittivity / excitability variable."
notation ap "z"
lhs ap "Derivative(z, t)"
rhs ap "(4*(x1 - x_0) - z)/tau_z"

z (Epileptor5D state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor5D/state_variables/z

belongs to
StateVariable c
has facts
description ap "Slow permittivity state-variable of the Epileptor5D (Jirsa et al"
notation ap "z"
lhs ap "Derivative(z, t)"
rhs ap "r*tt*(Ks*c_pop0 + h - z)"

z (EpileptorRestingState state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/EpileptorRestingState/state_variables/z

belongs to
StateVariable c
has facts
notation ap "z"
lhs ap "Derivative(z, t)"
rhs ap "r*tt*(Ks*c_pop0 - 4*x0 + 4*x1 - z + zcond)"

Z (LarterBreakspear state variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/LarterBreakspear/state_variables/Z

belongs to
StateVariable c
has facts
description ap "Third state-variable of the Larter-Breakspear (Breakspear et al"
has Db Xref ap C L 0000099 ni
has Db Xref ap G O 0060080 ep
notation ap "Z"
lhs ap "Derivative(Z, t)"
rhs ap "b*t_scale*(I_ext*a_ni + Q_V*V*a_ei)"

Z_T (LarterBreakspear parameter)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/LarterBreakspear/parameters/Z_T

Threshold potential (mean) for inihibtory neurons.
belongs to
Parameter c
has facts
description ap "Threshold potential (mean) for inihibtory neurons"
default Value ap "0.0"^^double
has Db Xref ap G O 0060080 ep
definition ap "Threshold potential (mean) for inihibtory neurons."
notation ap "Z_T"

Zaslavskii1978ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Zaslavskii1978

belongs to
Scholarly article c
has facts
issued ap "1978"
title ap "The simplest case of a strange attractor"
author ap "Chernikov, A. A."
author ap "Sagdeev, R. Z."
author ap "Usikov, D. A."
author ap "Zaslavskii, G. M."
is Part Of ap "Physics Letters A"
issue Number ap "3"
pagination ap "145--147"
volume Number ap "69"

zcond (Epileptor2D derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor2D/derived_variables/zcond

belongs to
DerivedVariable c
has facts
notation ap "zcond"
lhs ap "zcond"
rhs ap "Piecewise((-0.1*z**7, z < 0), (0, True))"

zcond (Epileptor5D derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/Epileptor5D/derived_variables/zcond

belongs to
DerivedVariable c
has facts
notation ap "zcond"
lhs ap "zcond"
rhs ap "Piecewise((-0.1*z**7, z < 0), (0.0, True))"

zcond (EpileptorRestingState derived variable)ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/EpileptorRestingState/derived_variables/zcond

belongs to
DerivedVariable c
has facts
notation ap "zcond"
lhs ap "zcond"
rhs ap "Piecewise((-0.1*z**7, z < 0), (0.0, True))"

Zerlaut2018ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Zerlaut2018

belongs to
Scholarly article c
has facts
issued ap "2018"
title ap "A mean-field model of conductance-based networks of adaptive exponential integrate-and-fire neurons"
author ap "Destexhe, Alain"
author ap "Zerlaut, Yann"
is Part Of ap "Neural Computation"

ZerlautAdaptationFirstOrderni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZerlautAdaptationFirstOrder

belongs to
Dynamics c
has facts
exhibits bifurcation op ""
exhibits regime op Oscillatory ni
exhibits regime op Quiescent ni
has attractor op Fixed point ni
has attractor op Limit cycle ni
has model feature op Excitatory/inhibitory subpopulations ni
has stochasticity character op Deterministic ni
models anatomical region op U B E R O N 0000956 ni
models cell type op C L 0000099 ni
models cell type op C L 0000598 ni
models neurotransmitter system op G O 0007214 ni
models neurotransmitter system op G O 0035249 ni
has timescale separation dp "true"^^boolean
phase-space dimension dp "5"^^integer
references ap Volo2019 ni
references ap Zerlaut2018 ni
pref Label ap "Zerlaut (first-order adaptation)"@en
has Derived Variable ap Fe_ext (ZerlautAdaptationFirstOrder derived variable) ni
has Derived Variable ap Fi_ext (ZerlautAdaptationFirstOrder derived variable) ni
has Derived Variable ap S_e (ZerlautAdaptationFirstOrder derived variable) ni
has Derived Variable ap S_i (ZerlautAdaptationFirstOrder derived variable) ni
has Derived Variable ap T_V_e (ZerlautAdaptationFirstOrder derived variable) ni
has Derived Variable ap T_V_i (ZerlautAdaptationFirstOrder derived variable) ni
has Derived Variable ap T_e (ZerlautAdaptationFirstOrder derived variable) ni
has Derived Variable ap T_i (ZerlautAdaptationFirstOrder derived variable) ni
has Derived Variable ap T_m_e (ZerlautAdaptationFirstOrder derived variable) ni
has Derived Variable ap T_m_i (ZerlautAdaptationFirstOrder derived variable) ni
has Derived Variable ap U_e_e (ZerlautAdaptationFirstOrder derived variable) ni
has Derived Variable ap U_e_i (ZerlautAdaptationFirstOrder derived variable) ni
has Derived Variable ap U_i_e (ZerlautAdaptationFirstOrder derived variable) ni
has Derived Variable ap U_i_i (ZerlautAdaptationFirstOrder derived variable) ni
has Derived Variable ap V_e (ZerlautAdaptationFirstOrder derived variable) ni
has Derived Variable ap V_i (ZerlautAdaptationFirstOrder derived variable) ni
has Derived Variable ap V_thre_e (ZerlautAdaptationFirstOrder derived variable) ni
has Derived Variable ap V_thre_i (ZerlautAdaptationFirstOrder derived variable) ni
has Derived Variable ap f_out_e (ZerlautAdaptationFirstOrder derived variable) ni
has Derived Variable ap f_out_i (ZerlautAdaptationFirstOrder derived variable) ni
has Derived Variable ap fe_e (ZerlautAdaptationFirstOrder derived variable) ni
has Derived Variable ap fe_i (ZerlautAdaptationFirstOrder derived variable) ni
has Derived Variable ap fi_e (ZerlautAdaptationFirstOrder derived variable) ni
has Derived Variable ap fi_i (ZerlautAdaptationFirstOrder derived variable) ni
has Derived Variable ap lc_E (ZerlautAdaptationFirstOrder derived variable) ni
has Derived Variable ap lc_I (ZerlautAdaptationFirstOrder derived variable) ni
has Derived Variable ap mu_G_e (ZerlautAdaptationFirstOrder derived variable) ni
has Derived Variable ap mu_G_i (ZerlautAdaptationFirstOrder derived variable) ni
has Derived Variable ap mu_Ge_e (ZerlautAdaptationFirstOrder derived variable) ni
has Derived Variable ap mu_Ge_i (ZerlautAdaptationFirstOrder derived variable) ni
has Derived Variable ap mu_Gi_e (ZerlautAdaptationFirstOrder derived variable) ni
has Derived Variable ap mu_Gi_i (ZerlautAdaptationFirstOrder derived variable) ni
has Derived Variable ap mu_V_e (ZerlautAdaptationFirstOrder derived variable) ni
has Derived Variable ap mu_V_i (ZerlautAdaptationFirstOrder derived variable) ni
has Derived Variable ap sigma_V_e (ZerlautAdaptationFirstOrder derived variable) ni
has Derived Variable ap sigma_V_i (ZerlautAdaptationFirstOrder derived variable) ni
has Parameter ap C_m (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap DTvN0 (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap DmuV0 (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap DsV0 (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap E_L_e (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap E_L_i (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap E_e (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap E_i (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap K_ext_e (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap K_ext_i (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap N_tot (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap P0_e (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap P0_i (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap P1_e (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap P1_i (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap P2_e (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap P2_i (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap P3_e (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap P3_i (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap P4_e (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap P4_i (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap P5_e (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap P5_i (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap P6_e (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap P6_i (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap P7_e (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap P7_i (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap P8_e (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap P8_i (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap P9_e (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap P9_i (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap P_e (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap P_i (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap Q_e (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap Q_i (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap S_i (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap T (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap TvN0 (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap a_e (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap a_i (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap b_e (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap b_i (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap external_input_ex_ex (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap external_input_ex_in (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap external_input_in_ex (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap external_input_in_in (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap g (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap g_L (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap muV0 (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap p_connect_e (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap p_connect_i (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap sV0 (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap tau_OU (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap tau_e (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap tau_i (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap tau_w_e (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap tau_w_i (ZerlautAdaptationFirstOrder parameter) ni
has Parameter ap weight_noise (ZerlautAdaptationFirstOrder parameter) ni
has State Variable ap E (ZerlautAdaptationFirstOrder state variable) ni
has State Variable ap I (ZerlautAdaptationFirstOrder state variable) ni
has State Variable ap W_e (ZerlautAdaptationFirstOrder state variable) ni
has State Variable ap W_i (ZerlautAdaptationFirstOrder state variable) ni
has State Variable ap ou_drift (ZerlautAdaptationFirstOrder state variable) ni
model_type (slot) ap "mean_field"

Zetterberg1978ni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/studies/Zetterberg1978

belongs to
Scholarly article c
has facts
issued ap "1978"
title ap "A model for the interrelationship between EEG and evoked potentials"
author ap "Jansen, B. H."
author ap "Zetterberg, L. H."
is Part Of ap "Biological Cybernetics"

ZetterbergJansenni back to ToC or Named Individual ToC

IRI: https://w3id.org/tvbo/ZetterbergJansen

belongs to
Dynamics c
has facts
exhibits bifurcation op ""
exhibits regime op Oscillatory ni
has attractor op Fixed point ni
has attractor op Limit cycle ni
has model feature op Sigmoid activation ni
has stochasticity character op Deterministic ni
models anatomical region op U B E R O N 0000956 ni
phase-space dimension dp "6"^^integer
references ap Zetterberg1978 ni
pref Label ap "Zetterberg-Jansen"@en
has Derived Variable ap coupled_input (ZetterbergJansen derived variable) ni
has Derived Variable ap sigma_v1 (ZetterbergJansen derived variable) ni
has Derived Variable ap sigma_v23 (ZetterbergJansen derived variable) ni
has Derived Variable ap sigma_v45 (ZetterbergJansen derived variable) ni
has Parameter ap He (ZetterbergJansen parameter) ni
has Parameter ap Hi (ZetterbergJansen parameter) ni
has Parameter ap P (ZetterbergJansen parameter) ni
has Parameter ap Q (ZetterbergJansen parameter) ni
has Parameter ap U (ZetterbergJansen parameter) ni
has Parameter ap e0 (ZetterbergJansen parameter) ni
has Parameter ap gamma_1 (ZetterbergJansen parameter) ni
has Parameter ap gamma_1T (ZetterbergJansen parameter) ni
has Parameter ap gamma_2 (ZetterbergJansen parameter) ni
has Parameter ap gamma_2T (ZetterbergJansen parameter) ni
has Parameter ap gamma_3 (ZetterbergJansen parameter) ni
has Parameter ap gamma_3T (ZetterbergJansen parameter) ni
has Parameter ap gamma_4 (ZetterbergJansen parameter) ni
has Parameter ap gamma_5 (ZetterbergJansen parameter) ni
has Parameter ap ke (ZetterbergJansen parameter) ni
has Parameter ap ki (ZetterbergJansen parameter) ni
has Parameter ap rho_1 (ZetterbergJansen parameter) ni
has Parameter ap rho_2 (ZetterbergJansen parameter) ni
has State Variable ap v1 (ZetterbergJansen state variable) ni
has State Variable ap v2 (ZetterbergJansen state variable) ni
has State Variable ap v3 (ZetterbergJansen state variable) ni
has State Variable ap v4 (ZetterbergJansen state variable) ni
has State Variable ap v5 (ZetterbergJansen state variable) ni
has State Variable ap v6 (ZetterbergJansen state variable) ni
has State Variable ap v7 (ZetterbergJansen state variable) ni
has State Variable ap y1 (ZetterbergJansen state variable) ni
has State Variable ap y2 (ZetterbergJansen state variable) ni
has State Variable ap y3 (ZetterbergJansen state variable) ni
has State Variable ap y4 (ZetterbergJansen state variable) ni
has State Variable ap y5 (ZetterbergJansen state variable) ni
model_type (slot) ap "neural_mass"

Legend back to ToC

c: Classes
op: Object Properties
dp: Data Properties
ni: Named Individuals
ep: External Properties

References back to ToC

Add your references here. It is recommended to have them as a list.

Acknowledgments back to ToC

The authors would like to thank Silvio Peroni for developing LODE, a Live OWL Documentation Environment, which is used for representing the Cross Referencing Section of this document and Daniel Garijo for developing Widoco, the program used to create the template used in this documentation.