The Virtual Brain Data Model
type: Ontology
version IRI: tvbo.owl
contributor: The Virtual Brain Ontology contributors
created: 2024-01-01
description: Metadata schema for simulation studies using The Virtual Brain neuroinformatics platform or other dynamic network models of large-scale brain activity.
license: EUPL-1.2
modified: 2026-04-30
publisher: www.thevirtualbrain.org
version: 0.4.0
label: tvb-datamodel
version info: 0.4.0

model_type (slot)
type: AnnotationProperty
definition: Coarse classification of this model (mean_field, neural_mass, phase_oscillator, phenomenological, spiking, generic, field). Used for filtering in Dynamics.list_db(model_type=...).
in scheme: tvbo
notation: model_type

unit (slot)
type: AnnotationProperty
range: UnitEnum
type: DatatypeProperty
definition: Physical unit of measurement. Values are drawn from the QUDT ontology (http://qudt.org/vocab/unit/) with UO cross-references where available.
in scheme: tvbo
notation: unit

center
type: ObjectProperty
definition: Add the center coordinate of this entity.
in scheme: BrainAtlas

coordinateSpace
type: ObjectProperty
range: CommonCoordinateSpace
definition: Common coordinate space (e.g. FSLMNI152, MNI152NLin2009cAsym). Reference by name; the CommonCoordinateSpace must be defined in tvbo/database/coordinate_spaces/ (or future equivalent location).
in scheme: BrainAtlas

entities
type: ObjectProperty
in scheme: BrainAtlas

hasParent
type: ObjectProperty
range: ParcellationEntity
definition: Add all anatomical parent structures for this entity as defined within the corresponding brain atlas.
in scheme: BrainAtlas

hemisphere
type: ObjectProperty
definition: Add the hemisphere of this entity.
in scheme: BrainAtlas

terminology
type: ObjectProperty
definition: Add the parcellation terminology version used for this brain atlas version.
in scheme: BrainAtlas

additional_equations (slot)
type: ObjectProperty
in scheme: tvbo
notation: additional_equations

affect (slot)
type: ObjectProperty
definition: Affect function: what happens when the event triggers. Can modify state variables and/or parameters. For stimulus type, this is the stimulus equation.
in scheme: tvbo
notation: affect

affect_negative (slot)
type: ObjectProperty
definition: Affect on downcrossing (continuous events only). If not specified, uses the same affect for both crossings.
in scheme: tvbo
notation: affect_negative

affect_parameters (slot)
type: ObjectProperty
type: DatatypeProperty
definition: Parameter symbols modifiable in the affect function.
in scheme: tvbo
notation: affect_parameters

affect_states (slot)
type: ObjectProperty
type: DatatypeProperty
definition: State variable symbols modifiable in the affect function.
in scheme: tvbo
notation: affect_states

algorithms (slot)
type: ObjectProperty
definition: Iterative parameter tuning algorithms (FIC, EIB, etc.)
in scheme: tvbo
notation: algorithms

axis (slot)
type: ObjectProperty
definition: Dimension along which the distribution is sampled. 'space' = per-node (default), 'time' = per-timestep (stochastic input).
in scheme: tvbo
notation: axis

bc_type (slot)
type: ObjectProperty
in scheme: tvbo
notation: bc_type

bids (slot)
type: ObjectProperty
definition: BIDS filename entities for this dataset
in scheme: tvbo
notation: bids

bifurcation parameter
type: ObjectProperty
domain: Bifurcation event
comment: Parameter (CURIE into the per-model parameter namespace) along which the bifurcation is observed.

bifurcation type
type: ObjectProperty
domain: Bifurcation event
comment: 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.

boundaries (slot)
type: ObjectProperty
in scheme: tvbo
notation: boundaries

bounds (slot)
type: ObjectProperty
definition: Constraints on parameter values after update
in scheme: tvbo
notation: bounds

branches (slot)
type: ObjectProperty
definition: Child branches to continue from detected bifurcation points (PO from Hopf, fold continuation, etc.).
in scheme: tvbo
notation: branches

call_args (slot)
type: ObjectProperty
definition: Arguments passed when calling the instance (__call__). Usually the input data from simulation result. Example: result (simulation output array).
in scheme: tvbo
notation: call_args

cases (slot)
type: ObjectProperty
in scheme: tvbo
notation: cases

class_call (slot)
type: ObjectProperty
definition: Class instantiation and call (alternative to callable/function). Use for external library classes that need __init__ then __call__. Example: Bold monitor from tvboptim.
in scheme: tvbo
notation: class_call

class_reference (slot)
type: ObjectProperty
definition: 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}]}
in scheme: tvbo
notation: class_reference

coefficient (slot)
type: ObjectProperty
in scheme: tvbo
notation: coefficient

condition_parameters (slot)
type: ObjectProperty
type: DatatypeProperty
definition: Parameter symbols accessible in the condition function.
in scheme: tvbo
notation: condition_parameters

condition_states (slot)
type: ObjectProperty
type: DatatypeProperty
definition: State variable symbols accessible in the condition function. For edges, can include source/destination vertex outputs.
in scheme: tvbo
notation: condition_states

conditionals (slot)
type: ObjectProperty
definition: Conditional logic for piecewise equations.
in scheme: tvbo
notation: conditionals

connectivity (slot)
type: ObjectProperty
in scheme: tvbo
notation: connectivity

constructor_args (slot)
type: ObjectProperty
definition: Arguments passed to __init__ when instantiating the class. Example: period=1000.0, downsample_period=4.0 for Bold monitor.
in scheme: tvbo
notation: constructor_args

continuation (slot)
type: ObjectProperty
definition: Override solver settings for this branch. Uses the same Continuation type — only explicitly set attributes override the parent's values.
in scheme: tvbo
notation: continuation

continuations (slot)
type: ObjectProperty
definition: 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
in scheme: tvbo
notation: continuations

coordinates (slot)
type: ObjectProperty
definition: Node coordinates (x,y,z) in the given coordinate space.
in scheme: tvbo
notation: coordinates

correlation (slot)
type: ObjectProperty
in scheme: tvbo
notation: correlation

coupling_function (slot)
type: ObjectProperty
definition: Mathematical function defining the coupling
in scheme: tvbo
notation: coupling_function

coupling_inputs (slot)
type: ObjectProperty
in scheme: tvbo
notation: coupling_inputs

coupling_terms (slot)
type: ObjectProperty
in scheme: tvbo
notation: coupling_terms

data (slot)
type: ObjectProperty
in scheme: tvbo
notation: data

dataset (slot)
type: ObjectProperty
definition: Multi-subject dataset for workflow rendering. When set, render_workflow() uses dataset.subjects/sessions to generate per-subject parallel jobs.
in scheme: tvbo
notation: dataset

derived_from_model (slot)
type: ObjectProperty
in scheme: tvbo
notation: derived_from_model

derived_observations (slot)
type: ObjectProperty
definition: Observations derived from combining other observations. Computed after all regular observations are available. Examples: fc_corr (from fc, fc_target), rmse, etc.
in scheme: tvbo
notation: derived_observations

description (slot)
type: ObjectProperty
range: string
type: DatatypeProperty
in scheme: tvbo
notation: description

distance_unit (slot)
type: ObjectProperty
definition: Unit for distances/lengths in the network
in scheme: tvbo
notation: distance_unit

domain (slot)
type: ObjectProperty
range: Range
in scheme: tvbo
notation: domain

edge_matrix_files (slot)
type: ObjectProperty
in scheme: tvbo
notation: edge_matrix_files

edges (slot)
type: ObjectProperty
definition: List of directed edges with coupling references (optional, for explicit edge definition)
in scheme: tvbo
notation: edges

element_type (slot)
type: ObjectProperty
in scheme: tvbo
notation: element_type

engine (slot)
type: ObjectProperty
definition: Primary engine (must appear in environment.requirements; migration target replacing deprecated 'software').
in scheme: tvbo
notation: engine

environment (slot)
type: ObjectProperty
range: SoftwareEnvironment (software)
definition: Execution environment (collection of requirements).
in scheme: tvbo
notation: environment

equation (slot)
type: ObjectProperty
range: Equation
in scheme: tvbo
notation: equation

event_type (slot)
type: ObjectProperty
definition: Type of event trigger mechanism.
in scheme: tvbo
notation: event_type

executable on
type: ObjectProperty
range: Backend

exhibits bifurcation
type: ObjectProperty
range: Bifurcation event
comment: Range is a reified BifurcationEvent that records the bifurcation type, the locus parameter, and (optionally) the critical value.

exhibits regime
type: ObjectProperty
comment: Object is a Regime class (open-world: model may admit additional regimes for parameter values not yet catalogued).

explorations (slot)
type: ObjectProperty
definition: Parameter exploration/grid search specifications
in scheme: tvbo
notation: explorations

field (slot)
type: ObjectProperty
definition: Primary field being solved for (deprecated; use state_variables).
in scheme: tvbo
notation: field

field_dynamics (slot)
type: ObjectProperty
in scheme: tvbo
notation: field_dynamics

freeze_parameters (slot)
type: ObjectProperty
definition: Parameters from previous stages to freeze (keep at optimized value but not update)
in scheme: tvbo
notation: freeze_parameters

graph_generator (slot)
type: ObjectProperty
definition: 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.
in scheme: tvbo
notation: graph_generator

has attractor
type: ObjectProperty

has model feature
type: ObjectProperty
range: Model feature

has stochasticity character
type: ObjectProperty
type: FunctionalProperty
comment: 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.

hi (slot)
type: ObjectProperty
definition: Upper bound or stopping value. Can be a number or argument name.
in scheme: tvbo
notation: hi

history (slot)
type: ObjectProperty
in scheme: tvbo
notation: history

imaging_modality (slot)
type: ObjectProperty
definition: Type of imaging modality (BOLD, EEG, MEG, etc.)
in scheme: tvbo
notation: imaging_modality

includes (slot)
type: ObjectProperty
definition: 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}]}]
in scheme: tvbo
notation: includes

incoming_states (slot)
type: ObjectProperty
definition: 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.
in scheme: tvbo
notation: incoming_states

initial_expression (slot)
type: ObjectProperty
definition: Analytic initial condition for the field.
in scheme: tvbo
notation: initial_expression

initial_state (slot)
type: ObjectProperty
definition: How to obtain the initial equilibrium. Default: time integration to steady state.
in scheme: tvbo
notation: initial_state

inner_coupling (slot)
type: ObjectProperty
definition: For hierarchical coupling: inner coupling applied at regional level
in scheme: tvbo
notation: inner_coupling

intensity (slot)
type: ObjectProperty
definition: Optional scalar or vector intensity parameter for noise.
in scheme: tvbo
notation: intensity

intermediate_expressions (slot)
type: ObjectProperty
in scheme: tvbo
notation: intermediate_expressions

label (slot)
type: ObjectProperty
range: string
type: DatatypeProperty
in scheme: tvbo
notation: label

linear_solver (slot)
type: ObjectProperty
definition: Linear solver for the Newton bordered system. E.g. COPBLS (collocation), MatrixBLS (shooting/poincaré).
in scheme: tvbo
notation: linear_solver

lo (slot)
type: ObjectProperty
definition: Lower bound or starting value. Can be a number or argument name.
in scheme: tvbo
notation: lo

loader (slot)
type: ObjectProperty
definition: Callable that loads the data (e.g., load_functional_connectivity)
in scheme: tvbo
notation: loader

local_coupling_term (slot)
type: ObjectProperty
in scheme: tvbo
notation: local_coupling_term

local_states (slot)
type: ObjectProperty
definition: References to state variables from the local (target) node. Used by name in pre_expression.
in scheme: tvbo
notation: local_states

loss (slot)
type: ObjectProperty
definition: 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.)
in scheme: tvbo
notation: loss

metric (slot)
type: ObjectProperty
definition: Metric equation for matching (e.g., correlation, rmse)
in scheme: tvbo
notation: metric

modality (slot)
type: ObjectProperty
definition: Imaging modality or simulation output type.
in scheme: tvbo
notation: modality

model (slot)
type: ObjectProperty
range: Dynamics
in scheme: tvbo
notation: model

models anatomical region
type: ObjectProperty
comment: Anatomical region(s) the Dynamics model is intended to represent. Range: UBERON terms.

models cell type
type: ObjectProperty
comment: Cell type(s) whose collective dynamics the model represents. Range: CL terms.

models neurotransmitter system
type: ObjectProperty
comment: Neurotransmitter system(s) whose synaptic dynamics the model represents. Range: GO biological-process terms.

modes (slot)
type: ObjectProperty
alternative label: components
in scheme: tvbo
notation: modes

module (slot)
type: ObjectProperty
type: DatatypeProperty
in scheme: tvbo
notation: module

name (slot)
type: ObjectProperty
range: string
type: DatatypeProperty
definition: Globally unique identifier for the entity.
definition: Optional step label; used in pipelines to key step outputs.
in scheme: tvbo
in scheme: common
notation: name

network (slot)
type: ObjectProperty
in scheme: tvbo
notation: network

nodes (slot)
type: ObjectProperty
definition: List of nodes with individual dynamics (optional, for heterogeneous networks)
in scheme: tvbo
notation: nodes

objective (slot)
type: ObjectProperty
definition: What the algorithm optimizes for
in scheme: tvbo
notation: objective

observable (slot)
type: ObjectProperty
definition: Observable to compute at each point. Use function: obs_name for simple observation, or function: func_name + arguments for FunctionCall.
in scheme: tvbo
notation: observable

ode_solver (slot)
type: ObjectProperty
definition: ODE solver for flow-based methods (shooting, poincaré). Specifies algorithm (e.g. Vern9, Rodas5) and tolerances. Not needed for collocation or trapezoid.
in scheme: tvbo
notation: ode_solver

operator_type (slot)
type: ObjectProperty
in scheme: tvbo
notation: operator_type

operators (slot)
type: ObjectProperty
in scheme: tvbo
notation: operators

optimizations (slot)
type: ObjectProperty
definition: Parameter optimization configurations
in scheme: tvbo
notation: optimizations

output_equation (slot)
type: ObjectProperty
definition: Output transformation equation (if equation-based)
in scheme: tvbo
notation: output_equation

outsym (slot)
type: ObjectProperty
type: DatatypeProperty
definition: Output symbol names for the edge model. E.g. ['P'] for a scalar power flow, ['Fx', 'Fy'] for 2D forces. Maps directly to outsym in ND.jl EdgeModel. If not specified, derived from coupling variables of the connected vertex dynamics.
in scheme: tvbo
notation: outsym

over (slot)
type: ObjectProperty
definition: Dimension to aggregate over (e.g., node, time, state)
in scheme: tvbo
notation: over

parameters (slot)
type: ObjectProperty
range: Parameter
in scheme: tvbo
notation: parameters

parcellation (slot)
type: ObjectProperty
definition: Brain parcellation/atlas reference
in scheme: tvbo
notation: parcellation

pipeline (slot)
type: ObjectProperty
definition: Ordered sequence of Functions. Each step has a unique `name` (used to key step outputs) and transforms input -> output. List form preserves execution order.
in scheme: tvbo
notation: pipeline

position (slot)
type: ObjectProperty
definition: Spatial coordinates (x, y, z) of the node
in scheme: tvbo
notation: position

post_expression (slot)
type: ObjectProperty
definition: Post-processing expression applied after coupling
in scheme: tvbo
notation: post_expression

pre_expression (slot)
type: ObjectProperty
definition: Pre-processing expression applied before coupling
in scheme: tvbo
notation: pre_expression

preprocessing (slot)
type: ObjectProperty
definition: Optional preprocessing to apply after loading
in scheme: tvbo
notation: preprocessing

provenance (slot)
type: ObjectProperty
definition: W3C PROV-O aligned provenance
in scheme: tvbo
notation: provenance

provides capability
type: ObjectProperty
domain: Backend
range: Backend capability

random_state (slot)
type: ObjectProperty
in scheme: tvbo
notation: random_state

region_mapping (slot)
type: ObjectProperty
definition: For hierarchical coupling: vertex-to-region mapping for aggregation
in scheme: tvbo
notation: region_mapping

regional_connectivity (slot)
type: ObjectProperty
definition: For hierarchical coupling: region-to-region connectivity with weights and delays
in scheme: tvbo
notation: regional_connectivity

requirements (slot)
type: ObjectProperty
range: SoftwareRequirement (software)
in scheme: tvbo
notation: requirements

requires (slot)
type: ObjectProperty
definition: Observables required by this update rule
in scheme: tvbo
notation: requires

sample (slot)
type: ObjectProperty
in scheme: tvbo
notation: sample

simulation_experiments (slot)
type: ObjectProperty
in scheme: tvbo
notation: simulation_experiments
preferred label: experiments

software_environment (slot)
type: ObjectProperty
definition: Software environment used to generate this data.
in scheme: tvbo
notation: software_environment

source (slot)
type: ObjectProperty
range: string
type: DatatypeProperty
in scheme: tvbo
notation: source

source_experiment (slot)
type: ObjectProperty
definition: Reference to the SimulationExperiment that generated this TimeSeries.
in scheme: tvbo
notation: source_experiment

source_observations (slot)
type: ObjectProperty
definition: 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.
in scheme: tvbo
notation: source_observations

sources (slot)
type: ObjectProperty
in scheme: tvbo
notation: sources

space (slot)
type: ObjectProperty
definition: 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.
in scheme: tvbo
notation: space

stages (slot)
type: ObjectProperty
definition: 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.
in scheme: tvbo
notation: stages

state (slot)
type: ObjectProperty
definition: Per-node initial state variable values, keyed by state variable name.
in scheme: tvbo
notation: state

step (slot)
type: ObjectProperty
definition: Step size. Can be: number, argument name, or expression.
in scheme: tvbo
notation: step

stimulation (slot)
type: ObjectProperty
in scheme: tvbo
notation: stimulation

stimulus (slot)
type: ObjectProperty
in scheme: tvbo
notation: stimulus

supports task
type: ObjectProperty
domain: Backend
range: Simulation task

symmetry (slot)
type: ObjectProperty
type: DatatypeProperty
definition: Edge symmetry type for NetworkDynamics.jl EdgeModel: 'directed' (default), 'antisymmetric', or 'symmetric'. AntiSymmetric edges flip sign for the reverse direction.
in scheme: tvbo
notation: symmetry

system_type (slot)
type: ObjectProperty
in scheme: tvbo
notation: system_type

target_component (slot)
type: ObjectProperty
type: DatatypeProperty
definition: Component to attach this event to. Can be a node label, edge label, or 'all_edges'/'all_vertices' for broadcast. If not specified, event is experiment-level.
in scheme: tvbo
notation: target_component

target_data (slot)
type: ObjectProperty
definition: Reference to empirical data observation for matching objectives
in scheme: tvbo
notation: target_data

target_parameter (slot)
type: ObjectProperty
definition: The parameter to update (e.g., J_i, wLRE)
in scheme: tvbo
notation: target_parameter

target_variable (slot)
type: ObjectProperty
definition: State variable for activity targets (e.g., S_e)
in scheme: tvbo
notation: target_variable

targets (slot)
type: ObjectProperty
definition: State variables this noise applies to; if omitted, applies globally.
in scheme: tvbo
notation: targets

tensor_coefficient (slot)
type: ObjectProperty
definition: Optional anisotropic tensor (e.g., diffusion).
in scheme: tvbo
notation: tensor_coefficient

time (slot)
type: ObjectProperty
in scheme: tvbo
notation: time

time_scale (slot)
type: ObjectProperty
range: UnitEnum
definition: Time unit for the integration / simulation. Determines the physical time meaning of one model time-step.
in scheme: tvbo
notation: time_scale

time_unit (slot)
type: ObjectProperty
definition: Default time unit for the network
in scheme: tvbo
notation: time_unit

tractogram (slot)
type: ObjectProperty
definition: Reference to tractography data
in scheme: tvbo
notation: tractogram

transforms (slot)
type: ObjectProperty
definition: 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.
in scheme: tvbo
notation: transforms

update_expression (slot)
type: ObjectProperty
in scheme: tvbo
notation: update_expression

update_rules (slot)
type: ObjectProperty
definition: How parameters are updated each iteration. When using 'includes', update_rules are inherited from included algorithms.
in scheme: tvbo
notation: update_rules

value (slot)
type: ObjectProperty
range: ScalarValue
type: DatatypeProperty
definition: Numeric, string, or boolean value. ScalarValue accepts any literal primitive type, allowing parameters to carry control flags (e.g., booleans) or symbolic placeholders alongside numeric defaults.
in scheme: tvbo
notation: value

warmup_from (slot)
type: ObjectProperty
definition: Previous stage to initialize from. Final values from that stage become initial values for this stage.
in scheme: tvbo
notation: warmup_from

x (slot)
type: ObjectProperty
in scheme: tvbo
notation: x

y (slot)
type: ObjectProperty
in scheme: tvbo
notation: y

amplitude (dbs)
type: ObjectProperty
in scheme: dbs
notation: amplitude

clinical_improvement (dbs)
type: ObjectProperty
definition: Observed improvement relative to baseline based on a defined score.
in scheme: dbs
notation: clinical_improvement

clinical_scores (dbs)
type: ObjectProperty
in scheme: dbs
notation: clinical_scores

contacts (dbs)
type: ObjectProperty
definition: List of physical contacts along the electrode
in scheme: dbs
notation: contacts

coordinate (dbs)
type: ObjectProperty
definition: 3D coordinate of the contact center in the defined coordinate space
in scheme: dbs
notation: coordinate

efield (dbs)
type: ObjectProperty
definition: Metadata about the E-field result for this setting
in scheme: dbs
notation: efield

electrode_reference (dbs)
type: ObjectProperty
in scheme: dbs
notation: electrode_reference

electrodes (dbs)
type: ObjectProperty
in scheme: dbs
notation: electrodes

frequency (dbs)
type: ObjectProperty
in scheme: dbs
notation: frequency

head (dbs)
type: ObjectProperty
in scheme: dbs
notation: head

mode (dbs)
type: ObjectProperty
type: DatatypeProperty
in scheme: dbs
notation: mode

parent_score (dbs)
type: ObjectProperty
definition: If this score is a subscore of a broader composite
in scheme: dbs
notation: parent_score

protocols (dbs)
type: ObjectProperty
definition: All DBS protocols assigned to this subject.
in scheme: dbs
notation: protocols

pulse_width (dbs)
type: ObjectProperty
in scheme: dbs
notation: pulse_width

scale (dbs)
type: ObjectProperty
definition: The scale this score belongs to, if applicable
in scheme: dbs
notation: scale

score (dbs)
type: ObjectProperty
in scheme: dbs
notation: score

settings (dbs)
type: ObjectProperty
in scheme: dbs
notation: settings

tail (dbs)
type: ObjectProperty
in scheme: dbs
notation: tail

target_structure (dbs)
type: ObjectProperty
definition: Anatomical target structure from a brain atlas
in scheme: dbs
notation: target_structure

trajectory (dbs)
type: ObjectProperty
definition: The planned trajectory for electrode implantation
in scheme: dbs
notation: trajectory

development_status (software)
type: ObjectProperty
definition: Development status (repostatus.org aligned).
in scheme: software
notation: development_status

ecosystem (software)
type: ObjectProperty
definition: Package ecosystem(s) through which the software is distributed.
in scheme: software
notation: ecosystem

environment_type (software)
type: ObjectProperty
definition: Category: conda, venv, docker, etc.
in scheme: software
notation: environment_type

interoperates_with (software)
type: ObjectProperty
definition: Tools this tool can exchange data with or delegate to.
in scheme: software
notation: interoperates_with

model_paradigm (software)
type: ObjectProperty
definition: Computational paradigms supported.
in scheme: software
notation: model_paradigm

package (software)
type: ObjectProperty
definition: Reference to the software package identity.
in scheme: software
notation: package

programming_language (software)
type: ObjectProperty
definition: Implementation languages.
in scheme: software
notation: programming_language

requirements (software)
type: ObjectProperty
definition: Constituent software requirements.
in scheme: software
notation: requirements

role (software)
type: ObjectProperty
in scheme: software
notation: role

scale (software)
type: ObjectProperty
definition: Spatial/organizational scales the tool operates at.
in scheme: software
notation: scale

tool_role (software)
type: ObjectProperty
definition: Primary function(s) in a simulation workflow.
in scheme: software
notation: tool_role

sessions (study)
type: ObjectProperty
definition: Data collection sessions for this subject. Each session can have its own network, empirical data, and conditions.
in scheme: study
notation: sessions

sex (study)
type: ObjectProperty
definition: Biological sex.
in scheme: study
notation: sex

subjects (study)
type: ObjectProperty
range: Subject (study)
definition: Subjects in a dataset.
in scheme: study
notation: subjects

abbreviation
type: DatatypeProperty
range: string
type: ObjectProperty
definition: Slot for the abbreviation of a resource.
in scheme: BrainAtlas

alternateName
type: DatatypeProperty
range: string
type: ObjectProperty
definition: Enter any alternate names, including abbreviations, for this entity.
in scheme: BrainAtlas

anatomicalAxesOrientation
type: DatatypeProperty
type: ObjectProperty
definition: Add the axes orientation in standard anatomical terms (XYZ).
in scheme: BrainAtlas

author
type: DatatypeProperty
range: string
type: ObjectProperty
in scheme: BrainAtlas

axesOrigin
type: DatatypeProperty
type: ObjectProperty
definition: Enter the origin (central point where all axes intersect).
in scheme: BrainAtlas

color
type: DatatypeProperty
type: ObjectProperty
definition: Add the color code used for visual representation of this entity.
in scheme: BrainAtlas

dataLocation
type: DatatypeProperty
range: string
type: ObjectProperty
definition: Add the location of the data file containing the parcellation terminology.
in scheme: BrainAtlas

defaultImage
type: DatatypeProperty
type: ObjectProperty
definition: Add all image files used as visual representation of this common coordinate space version.
in scheme: BrainAtlas

digitalIdentifier
type: DatatypeProperty
range: string
definition: Add the digital identifier of this brain atlas or coordinate space version.
in scheme: BrainAtlas

isVersionOf
type: DatatypeProperty
type: ObjectProperty
definition: Linked type for the version of a brain atlas or coordinate space.
in scheme: BrainAtlas

license
type: DatatypeProperty
type: ObjectProperty
definition: Linked type for the license of the brain atlas or coordinate space version.
in scheme: BrainAtlas

lookupLabel
type: DatatypeProperty
range: integer
definition: Enter the label used for looking up this entity in the parcellation terminology.
in scheme: BrainAtlas

nativeUnit
type: DatatypeProperty
type: ObjectProperty
definition: Add the native unit that is used for this common coordinate space version.
in scheme: BrainAtlas

ontologyIdentifier
type: DatatypeProperty
range: string
type: ObjectProperty
definition: Enter the internationalized resource identifier (IRI) to the related ontological terms.
in scheme: BrainAtlas

originalLookupLabel
type: DatatypeProperty
definition: Add the original label of this entity as defined in the parcellation terminology.
in scheme: BrainAtlas

relatedUBERONTerm
type: DatatypeProperty
type: ObjectProperty
definition: Add the related anatomical entity as defined by the UBERON ontology.
in scheme: BrainAtlas

versionIdentifier
type: DatatypeProperty
range: string
type: ObjectProperty
definition: Enter the version identifier of this brain atlas or coordinate space version.
in scheme: BrainAtlas

x
type: DatatypeProperty
definition: X coordinate
in scheme: BrainAtlas

y
type: DatatypeProperty
definition: Y coordinate
in scheme: BrainAtlas

z
type: DatatypeProperty
definition: Z coordinate
in scheme: BrainAtlas

accelerator (slot)
type: DatatypeProperty
type: ObjectProperty
definition: Hardware accelerator: 'cpu', 'gpu', 'tpu'
in scheme: tvbo
notation: accelerator

acronym (slot)
type: DatatypeProperty
range: string
type: ObjectProperty
in scheme: tvbo
notation: acronym

additive (slot)
type: DatatypeProperty
definition: Indicates whether the noise is additive
in scheme: tvbo
notation: additive

apply_every (slot)
type: DatatypeProperty
definition: Apply update every N iterations
in scheme: tvbo
notation: apply_every

autonomous (slot)
type: DatatypeProperty
definition: 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).
in scheme: tvbo
notation: autonomous

average (slot)
type: DatatypeProperty
type: ObjectProperty
definition: Averaging mode across trials. 'trials' = average over n_trials independent runs (evoked potential paradigm). None = return all trials.
in scheme: tvbo
notation: average

batch_size (slot)
type: DatatypeProperty
definition: Batch size for vectorized operations (None = auto)
in scheme: tvbo
notation: batch_size

bids_dir (slot)
type: DatatypeProperty
type: ObjectProperty
definition: Path to BEP017-compliant BIDS directory for loading connectivity matrices
in scheme: tvbo
notation: bids_dir

cohort (slot)
type: DatatypeProperty
type: ObjectProperty
definition: BIDS cohort- entity (e.g., HCPYA, PPMI85)
in scheme: tvbo
notation: cohort

comment (slot)
type: DatatypeProperty
type: ObjectProperty
in scheme: tvbo
notation: comment

conditional (slot)
type: DatatypeProperty
in scheme: tvbo
notation: conditional

connectivity_ref (slot)
type: DatatypeProperty
type: ObjectProperty
definition: Reference to connectivity data (_conndata-network_connectivity.tsv).
in scheme: tvbo
notation: connectivity_ref

correlated (slot)
type: DatatypeProperty
in scheme: tvbo
notation: correlated

coupling_variable (slot)
type: DatatypeProperty
definition: 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.
in scheme: tvbo
notation: coupling_variable

critical value
type: DatatypeProperty
type: FunctionalProperty
domain: Bifurcation event
range: double

dataLocation (slot)
type: DatatypeProperty
type: ObjectProperty
in scheme: tvbo
notation: dataLocation

data_file (slot)
type: DatatypeProperty
type: ObjectProperty
definition: Path to companion data file. Supported extensions: .h5 (HDF5), .zarr/ (Zarr), .csv (legacy single-matrix). Null if no companion data needed.
in scheme: tvbo
notation: data_file

dataset_path (slot)
type: DatatypeProperty
range: string
type: ObjectProperty
definition: Dataset path for array-valued parameters. When set, the parameter value is stored in the binary companion file (HDF5 or Zarr) at this path. The value slot is omitted.
in scheme: tvbo
notation: dataset_path

date_created (slot)
type: DatatypeProperty
type: ObjectProperty
definition: ISO 8601 (prov:generatedAtTime)
in scheme: tvbo
notation: date_created

default (slot)
type: DatatypeProperty
range: string
type: ObjectProperty
in scheme: tvbo
notation: default

definition (slot)
type: DatatypeProperty
range: string
type: ObjectProperty
in scheme: tvbo
notation: definition

degree (slot)
type: DatatypeProperty
definition: Polynomial degree per mesh interval for collocation. The m in PeriodicOrbitOCollProblem(N, m).
in scheme: tvbo
notation: degree

delay (slot)
type: DatatypeProperty
definition: Conduction delay (explicit edges, ms)
in scheme: tvbo
notation: delay

delta_p (slot)
type: DatatypeProperty
definition: Initial parameter offset from the bifurcation point.
in scheme: tvbo
notation: delta_p

derivative_initial_value (slot)
type: DatatypeProperty
definition: 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.
in scheme: tvbo
notation: derivative_initial_value

derived_from (slot)
type: DatatypeProperty
type: ObjectProperty
in scheme: tvbo
notation: derived_from

descriptor (slot)
type: DatatypeProperty
type: ObjectProperty
definition: Short alphanumeric identifier for the BIDS desc- filename entity (e.g., SC, FC, EC, SCFC). Classifies the connectivity modality of the network's edge measures.
in scheme: tvbo
notation: descriptor

detect_bifurcation (slot)
type: DatatypeProperty
definition: Bifurcation detection level. 0 = off, 1 = eigenvalues only, 2 = detect, 3 = locate precisely.
in scheme: tvbo
notation: detect_bifurcation

detect_fold (slot)
type: DatatypeProperty
definition: Enable fold (limit point) detection.
in scheme: tvbo
notation: detect_fold

dimension (slot)
type: DatatypeProperty
definition: Dimensionality of the coupling input (number of coupled values)
in scheme: tvbo
notation: dimension

dimension_labels (slot)
type: DatatypeProperty
type: ObjectProperty
definition: Ordered labels for the matrix columns (dim-1) when the matrix is non-square. Row labels (dim-0) are the parent Network's node labels. Stored as HDF5 dimension scales in the companion file.
in scheme: tvbo
notation: dimension_labels

distance (slot)
type: DatatypeProperty
definition: Edge length / tract distance (explicit edges, mm)
in scheme: tvbo
notation: distance

doi (slot)
type: DatatypeProperty
type: ObjectProperty
in scheme: tvbo
notation: doi

downsample_period (slot)
type: DatatypeProperty
definition: Intermediate downsampling period (ms). For BOLD: typically matches dt.
in scheme: tvbo
notation: downsample_period

ds (slot)
type: DatatypeProperty
definition: Initial arc-length step size.
in scheme: tvbo
notation: ds

ds_max (slot)
type: DatatypeProperty
definition: Maximum adaptive step size.
in scheme: tvbo
notation: ds_max

ds_min (slot)
type: DatatypeProperty
definition: Minimum adaptive step size.
in scheme: tvbo
notation: ds_min

dt (slot)
type: DatatypeProperty
definition: Time step (s).
in scheme: tvbo
notation: dt

duration (slot)
type: DatatypeProperty
range: float
in scheme: tvbo
notation: duration

element (slot)
type: DatatypeProperty
definition: 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.
in scheme: tvbo
notation: element

elements (slot)
type: DatatypeProperty
type: ObjectProperty
definition: Connectivity (indices) or file reference to topology.
in scheme: tvbo
notation: elements

equation_order (slot)
type: DatatypeProperty
definition: 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.
in scheme: tvbo
notation: equation_order

equation_type (slot)
type: DatatypeProperty
type: ObjectProperty
definition: Type of equation: 'differential' (default) means dx/dt = rhs, 'algebraic' means 0 = rhs or x ~ rhs (DAE constraint). Algebraic equations are used by ModelingToolkit.jl backend.
in scheme: tvbo
notation: equation_type

extension (slot)
type: DatatypeProperty
type: ObjectProperty
in scheme: tvbo
notation: extension

file (slot)
type: DatatypeProperty
range: string
in scheme: tvbo
notation: file

find_fixpoint (slot)
type: DatatypeProperty
definition: 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.
in scheme: tvbo
notation: find_fixpoint

free (slot)
type: DatatypeProperty
in scheme: tvbo
notation: free

gaussian (slot)
type: DatatypeProperty
definition: Indicates whether the noise is Gaussian
in scheme: tvbo
notation: gaussian

generated_at (slot)
type: DatatypeProperty
definition: Timestamp when this TimeSeries was generated.
in scheme: tvbo
notation: generated_at

generated_by (slot)
type: DatatypeProperty
type: ObjectProperty
definition: Software/agent identifier (prov:wasGeneratedBy)
in scheme: tvbo
notation: generated_by

geometry (slot)
type: DatatypeProperty
type: ObjectProperty
definition: Optional file for geometry/ROI mask (e.g., NIfTI, GIfTI).
in scheme: tvbo
notation: geometry

grounding (slot)
type: DatatypeProperty
range: anyURI
definition: 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)).
in scheme: tvbo
notation: grounding

groups (slot)
type: DatatypeProperty
type: ObjectProperty
in scheme: tvbo
notation: groups

has conserved quantity
type: DatatypeProperty
range: boolean

has timescale separation
type: DatatypeProperty
range: boolean

has_reference (slot)
type: DatatypeProperty
range: string
type: ObjectProperty
in scheme: tvbo
notation: has_reference

hemi (slot)
type: DatatypeProperty
type: ObjectProperty
definition: BIDS hemi- entity (L or R) for hemisphere-specific surface/volume data
in scheme: tvbo
notation: hemi

id (slot)
type: DatatypeProperty
definition: Unique node identifier
in scheme: tvbo
notation: id

iri (slot)
type: DatatypeProperty
range: anyURI
definition: 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).
in scheme: tvbo
notation: iri

keys (slot)
type: DatatypeProperty
type: ObjectProperty
definition: Named keys for multi-dimensional coupling. When dimension > 1, provides symbolic names for each index (e.g., keys: [lre, ffi] for dimension: 2). Used in equations as variable names.
in scheme: tvbo
notation: keys

labels_dimensions (slot)
type: DatatypeProperty
type: ObjectProperty
definition: Mapping of dimension names to their labels (JSON-encoded dict).
in scheme: tvbo
notation: labels_dimensions

labels_ordering (slot)
type: DatatypeProperty
type: ObjectProperty
definition: Ordering of dimensions: Time, State Variable, Space, Mode.
in scheme: tvbo
notation: labels_ordering

latex (slot)
type: DatatypeProperty
in scheme: tvbo
notation: latex

learning_rate_schedule (slot)
type: DatatypeProperty
type: ObjectProperty
definition: Learning rate schedule: 'constant', 'linear', 'exponential'
in scheme: tvbo
notation: learning_rate_schedule

learning_rate_warmup (slot)
type: DatatypeProperty
definition: Linear warmup of learning rate from 0 to learning_rate over n_iterations. eta_effective = eta * (i+1) / n_iterations
in scheme: tvbo
notation: learning_rate_warmup

lefthandside (slot)
type: DatatypeProperty
type: ObjectProperty
in scheme: tvbo
notation: lefthandside
preferred label: lhs

license (slot)
type: DatatypeProperty
type: ObjectProperty
in scheme: tvbo
notation: license

log_scale (slot)
type: DatatypeProperty
definition: Whether to use logarithmic spacing.
in scheme: tvbo
notation: log_scale

max_bisection_steps (slot)
type: DatatypeProperty
definition: Maximum bisection steps for bifurcation point localization.
in scheme: tvbo
notation: max_bisection_steps

max_iterations (slot)
type: DatatypeProperty
in scheme: tvbo
notation: max_iterations

max_steps (slot)
type: DatatypeProperty
definition: Maximum continuation steps.
in scheme: tvbo
notation: max_steps

mesh_file (slot)
type: DatatypeProperty
type: ObjectProperty
definition: Path to external mesh file (GIFTI, VTK, MSH, FreeSurfer, etc.).
in scheme: tvbo
notation: mesh_file

mesh_format (slot)
type: DatatypeProperty
type: ObjectProperty
definition: Explicit format override (gifti, freesurfer, meshio, vtk, gmsh). Auto-detected from extension if null.
in scheme: tvbo
notation: mesh_format

mesh_intervals (slot)
type: DatatypeProperty
definition: Number of mesh intervals (time slices) for collocation or trapezoid methods. Collocation: N in PeriodicOrbitOCollProblem(N, m). Trapezoid: M in PeriodicOrbitTrapProblem(M=...).
in scheme: tvbo
notation: mesh_intervals

mode (slot)
type: DatatypeProperty
type: ObjectProperty
definition: Combination mode: 'product' (full grid), 'zip' (paired)
in scheme: tvbo
notation: mode

model_equation_ref (slot)
type: DatatypeProperty
type: ObjectProperty
definition: BIDS ModelEq reference: path to _eq.xml LEMS file.
in scheme: tvbo
notation: model_equation_ref

model_param_ref (slot)
type: DatatypeProperty
type: ObjectProperty
definition: BIDS ModelParam reference: path to _param.xml LEMS file.
in scheme: tvbo
notation: model_param_ref

modified (slot)
type: DatatypeProperty
in scheme: tvbo
notation: modified

n (slot)
type: DatatypeProperty
definition: Number of points (alternative to step for grid exploration).
in scheme: tvbo
notation: n

n_inversion (slot)
type: DatatypeProperty
definition: Number of eigenvalue sign inversions to flag a bifurcation. Must be even. Higher = fewer false positives.
in scheme: tvbo
notation: n_inversion

n_iterations (slot)
type: DatatypeProperty
definition: Number of iterations to run
in scheme: tvbo
notation: n_iterations

n_parallel (slot)
type: DatatypeProperty
definition: Parallel evaluations
in scheme: tvbo
notation: n_parallel

n_regions (slot)
type: DatatypeProperty
definition: Total number of regions
in scheme: tvbo
notation: n_regions

n_sections (slot)
type: DatatypeProperty
definition: Number of shooting sections for shooting or Poincaré methods.
in scheme: tvbo
notation: n_sections

n_threads (slot)
type: DatatypeProperty
definition: Number of CPU threads per worker (-1 = auto-detect)
in scheme: tvbo
notation: n_threads

n_trials (slot)
type: DatatypeProperty
definition: 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).
in scheme: tvbo
notation: n_trials

n_vertices (slot)
type: DatatypeProperty
definition: Total number of vertices
in scheme: tvbo
notation: n_vertices

n_workers (slot)
type: DatatypeProperty
definition: Number of parallel workers (maps to pmap devices in JAX, processes in multiprocessing)
in scheme: tvbo
notation: n_workers

nev (slot)
type: DatatypeProperty
definition: Number of eigenvalues to compute. Must be >= number of state variables for reliable Hopf detection.
in scheme: tvbo
notation: nev

newton_max_iterations (slot)
type: DatatypeProperty
definition: Maximum Newton corrector iterations per step.
in scheme: tvbo
notation: newton_max_iterations

newton_tol (slot)
type: DatatypeProperty
definition: Absolute tolerance for Newton corrector convergence.
in scheme: tvbo
notation: newton_tol

node_mapping (slot)
type: DatatypeProperty
type: ObjectProperty
definition: HDF5 dataset path for node-to-parent mapping. Int32 array of shape (N,) where entry i is the parent node ID. Required when parent_network is set.
in scheme: tvbo
notation: node_mapping

noise_type (slot)
type: DatatypeProperty
type: ObjectProperty
in scheme: tvbo
notation: noise_type

non_negative (slot)
type: DatatypeProperty
definition: All values >= 0
in scheme: tvbo
notation: non_negative

number_of_elements (slot)
type: DatatypeProperty
definition: Number of elements (triangles, quads, tetrahedra, etc.).
in scheme: tvbo
notation: number_of_elements

number_of_modes (slot)
type: DatatypeProperty
in scheme: tvbo
notation: number_of_modes

number_of_nodes (slot)
type: DatatypeProperty
alternative label: number_of_nodes
alternative label: number_of_regions
definition: Number of nodes in the network (derived from nodes if not set)
in scheme: tvbo
notation: number_of_nodes

number_of_stages (slot)
type: DatatypeProperty
in scheme: tvbo
notation: number_of_stages

number_of_subjects (slot)
type: DatatypeProperty
definition: Number of subjects in the tractography dataset
in scheme: tvbo
notation: number_of_subjects

number_of_vertices (slot)
type: DatatypeProperty
definition: Number of vertices in the mesh.
in scheme: tvbo
notation: number_of_vertices

observational_measures (slot)
type: DatatypeProperty
type: ObjectProperty
definition: BEP017 measure names for observational targets (e.g., BoldCorrelation)
in scheme: tvbo
notation: observational_measures

on_region (slot)
type: DatatypeProperty
type: ObjectProperty
definition: Mesh/atlas subset where BC applies.
in scheme: tvbo
notation: on_region

parent_network (slot)
type: DatatypeProperty
type: ObjectProperty
definition: Path/URI to parent (coarser) Network. When set, this network is a refinement where each node maps to exactly one parent node via node_mapping.
in scheme: tvbo
notation: parent_network

period (slot)
type: DatatypeProperty
definition: Sampling period for monitors (ms). For BOLD: TR in ms.
in scheme: tvbo
notation: period

phase-space dimension
type: DatatypeProperty
type: FunctionalProperty
range: positiveInteger

precision (slot)
type: DatatypeProperty
type: ObjectProperty
definition: Floating point precision: 'float32' or 'float64'
in scheme: tvbo
notation: precision

preconditioner (slot)
type: DatatypeProperty
type: ObjectProperty
in scheme: tvbo
notation: preconditioner

processing_pipeline (slot)
type: DatatypeProperty
type: ObjectProperty
definition: Processing pipeline used to generate the tractography
in scheme: tvbo
notation: processing_pipeline

quantity_kind (slot)
type: DatatypeProperty
type: ObjectProperty
definition: Scalar, vector, or tensor.
in scheme: tvbo
notation: quantity_kind

random_seed (slot)
type: DatatypeProperty
definition: Base random seed for reproducibility
in scheme: tvbo
notation: random_seed

reconstruction (slot)
type: DatatypeProperty
type: ObjectProperty
definition: BIDS rec- entity (e.g., dTOR)
in scheme: tvbo
notation: reconstruction

record (slot)
type: DatatypeProperty
range: boolean
definition: 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.
in scheme: tvbo
notation: record

reference (slot)
type: DatatypeProperty
type: ObjectProperty
definition: Publication or DOI reference for this tractography dataset
in scheme: tvbo
notation: reference

references (slot)
type: DatatypeProperty
range: string
type: ObjectProperty
in scheme: tvbo
notation: references

reported_optimum (slot)
type: DatatypeProperty
range: float
in scheme: tvbo
notation: reported_optimum

righthandside (slot)
type: DatatypeProperty
type: ObjectProperty
in scheme: tvbo
notation: righthandside
preferred label: rhs

run_id (slot)
type: DatatypeProperty
definition: BIDS run number.
in scheme: tvbo
notation: run_id

sampling_period (slot)
type: DatatypeProperty
definition: Time between samples (inverse of sampling_rate).
in scheme: tvbo
notation: sampling_period

sampling_period_unit (slot)
type: DatatypeProperty
type: ObjectProperty
definition: Unit of the sampling period (e.g., 'ms', 's').
in scheme: tvbo
notation: sampling_period_unit

sampling_rate (slot)
type: DatatypeProperty
definition: Sampling rate in Hz.
in scheme: tvbo
notation: sampling_rate

scale (slot)
type: DatatypeProperty
type: ObjectProperty
definition: BIDS scale- entity (BEP017, e.g., 1000)
in scheme: tvbo
notation: scale

scipy_ode_base (slot)
type: DatatypeProperty
in scheme: tvbo
notation: scipy_ode_base

segmentation (slot)
type: DatatypeProperty
type: ObjectProperty
definition: BIDS seg- entity (e.g., ordered, ranked, 17Networks)
in scheme: tvbo
notation: segmentation

session_id (slot)
type: DatatypeProperty
type: ObjectProperty
definition: BIDS session identifier.
in scheme: tvbo
notation: session_id

simulation_period (slot)
type: DatatypeProperty
definition: Duration of each simulation step (e.g., one BOLD TR)
in scheme: tvbo
notation: simulation_period

size (slot)
type: DatatypeProperty
in scheme: tvbo
notation: size

skip_t (slot)
type: DatatypeProperty
definition: Number of samples to skip at the start (transient removal). For FC: typically 10-20 TRs.
in scheme: tvbo
notation: skip_t

source_branch (slot)
type: DatatypeProperty
type: ObjectProperty
definition: Name of a previously computed branch (for from_branch method).
in scheme: tvbo
notation: source_branch

source_var (slot)
type: DatatypeProperty
type: ObjectProperty
definition: Output variable from source node to use (e.g., 'x_out'). If not specified, uses first output variable from source dynamics.
in scheme: tvbo
notation: source_var

sparse (slot)
type: DatatypeProperty
definition: Whether the coupling uses sparse representations
in scheme: tvbo
notation: sparse

state_wise_sigma (slot)
type: DatatypeProperty
in scheme: tvbo
notation: state_wise_sigma

step_size (slot)
type: DatatypeProperty
alternative label: dt
in scheme: tvbo
notation: step_size

steps (slot)
type: DatatypeProperty
in scheme: tvbo
notation: steps

stimulation_variable (slot)
type: DatatypeProperty
in scheme: tvbo
notation: stimulation_variable

structural_measures (slot)
type: DatatypeProperty
type: ObjectProperty
definition: BEP017 measure names for structural connectivity (e.g., streamlineCount, tractLength)
in scheme: tvbo
notation: structural_measures

subject_id (slot)
type: DatatypeProperty
type: ObjectProperty
definition: BIDS subject identifier.
in scheme: tvbo
notation: subject_id

symbol (slot)
type: DatatypeProperty
range: string
type: ObjectProperty
in scheme: tvbo
notation: symbol

tail_samples (slot)
type: DatatypeProperty
definition: Number of samples from the end to use. Takes the last N samples before aggregation. E.g., tail_samples: 500 means use data[-500:].
in scheme: tvbo
notation: tail_samples

target (slot)
type: DatatypeProperty
definition: Target node ID (set for explicit edges, absent for template edges)
in scheme: tvbo
notation: target

target_network (slot)
type: DatatypeProperty
type: ObjectProperty
definition: Path or name of the Network whose nodes define the columns of a non-square (projection) matrix. For example, a gain matrix with shape (n_sensors, n_regions) references the brain parcellation network here. Row labels come from the parent Network's own nodes.
in scheme: tvbo
notation: target_network

target_value (slot)
type: DatatypeProperty
definition: Target value for activity objectives
in scheme: tvbo
notation: target_value

target_var (slot)
type: DatatypeProperty
type: ObjectProperty
definition: Input variable on target node to connect to (e.g., 'c_in'). If not specified, uses first coupling input from target dynamics.
in scheme: tvbo
notation: target_var

task_name (slot)
type: DatatypeProperty
type: ObjectProperty
definition: BIDS task name for the simulation (e.g., 'rest', 'simulation').
in scheme: tvbo
notation: task_name

template (slot)
type: DatatypeProperty
type: ObjectProperty
definition: BIDS tpl- entity (e.g., FSLMNI152, MNI152NLin2009cAsym)
in scheme: tvbo
notation: template

time_integrator (slot)
type: DatatypeProperty
type: ObjectProperty
definition: e.g., implicit Euler, Crank-Nicolson.
in scheme: tvbo
notation: time_integrator

title (slot)
type: DatatypeProperty
type: ObjectProperty
in scheme: tvbo
notation: title

tol_stability (slot)
type: DatatypeProperty
definition: Tolerance on real part of eigenvalue for stability boundary.
in scheme: tvbo
notation: tol_stability

tolerances (slot)
type: DatatypeProperty
type: ObjectProperty
definition: Abs/rel tolerances.
in scheme: tvbo
notation: tolerances

transient_time (slot)
type: DatatypeProperty
in scheme: tvbo
notation: transient_time

trigger_times (slot)
type: DatatypeProperty
definition: Predetermined trigger times for preset_time events. The solver will step exactly to these times.
in scheme: tvbo
notation: trigger_times

valid_diagonal (slot)
type: DatatypeProperty
definition: Self-connections are meaningful
in scheme: tvbo
notation: valid_diagonal

variable_of_interest (slot)
type: DatatypeProperty
in scheme: tvbo
notation: variable_of_interest

vertex_to_region (slot)
type: DatatypeProperty
definition: Array mapping each vertex index to its parent region index. Can use dataLocation instead for large arrays.
in scheme: tvbo
notation: vertex_to_region

voi (slot)
type: DatatypeProperty
definition: Variable of interest index (which state variable to monitor). Default: 0.
in scheme: tvbo
notation: voi

warmup (slot)
type: DatatypeProperty
definition: Whether to apply learning rate warmup to this update rule. When true, the learning rate (eta) is scaled by (i+1)/n_iterations.
in scheme: tvbo
notation: warmup

weight (slot)
type: DatatypeProperty
definition: Connection weight (explicit edges)
in scheme: tvbo
notation: weight

weighted (slot)
type: DatatypeProperty
definition: Matrix entries carry weights (not just 0/1)
in scheme: tvbo
notation: weighted

window_size (slot)
type: DatatypeProperty
definition: Number of samples for windowed aggregation
in scheme: tvbo
notation: window_size

year (slot)
type: DatatypeProperty
in scheme: tvbo
notation: year

absolute_value (dbs)
type: DatatypeProperty
definition: Absolute value of the score at the time of assessment
in scheme: dbs
notation: absolute_value

acronym (dbs)
type: DatatypeProperty
type: ObjectProperty
definition: Short abbreviation (e.g., UPDRS)
in scheme: dbs
notation: acronym

active_contacts (dbs)
type: DatatypeProperty
in scheme: dbs
notation: active_contacts

baseline_value (dbs)
type: DatatypeProperty
definition: Preoperative baseline value of the score
in scheme: dbs
notation: baseline_value

contact_id (dbs)
type: DatatypeProperty
definition: Identifier (e.g., 0, 1, 2)
in scheme: dbs
notation: contact_id

description (dbs)
type: DatatypeProperty
type: ObjectProperty
in scheme: dbs
notation: description

diagnosis (dbs)
type: DatatypeProperty
type: ObjectProperty
in scheme: dbs
notation: diagnosis

electrode_id (dbs)
type: DatatypeProperty
type: ObjectProperty
definition: Unique identifier for this electrode
in scheme: dbs
notation: electrode_id

evaluator (dbs)
type: DatatypeProperty
type: ObjectProperty
definition: Who performed the rating (e.g., rater initials, clinician ID, or system)
in scheme: dbs
notation: evaluator

handedness (dbs)
type: DatatypeProperty
type: ObjectProperty
in scheme: dbs
notation: handedness

hemisphere (dbs)
type: DatatypeProperty
type: ObjectProperty
definition: Hemisphere of electrode (left/right)
in scheme: dbs
notation: hemisphere

id (dbs)
type: DatatypeProperty
range: integer
definition: Surrogate integer key.
in scheme: dbs
notation: id

label (dbs)
type: DatatypeProperty
type: ObjectProperty
definition: Optional human-readable label (e.g., "1a")
in scheme: dbs
notation: label

manufacturer (dbs)
type: DatatypeProperty
type: ObjectProperty
in scheme: dbs
notation: manufacturer

model (dbs)
type: DatatypeProperty
type: ObjectProperty
in scheme: dbs
notation: model

name (dbs)
type: DatatypeProperty
type: ObjectProperty
definition: Full name of the scale (e.g., Unified Parkinson’s Disease Rating Scale)
definition: Full name of the score (e.g., Unified Parkinson's Disease Rating Scale - Part III)
in scheme: dbs
notation: name

notes (dbs)
type: DatatypeProperty
type: ObjectProperty
in scheme: dbs
notation: notes

percent_change (dbs)
type: DatatypeProperty
definition: Percent change compared to preoperative baseline (positive = improvement)
in scheme: dbs
notation: percent_change

recon_path (dbs)
type: DatatypeProperty
type: ObjectProperty
in scheme: dbs
notation: recon_path

reference (dbs)
type: DatatypeProperty
type: ObjectProperty
definition: DOI, PMID or persistent identifier
definition: PubMed ID, DOI, or other reference to the score definition
in scheme: dbs
notation: reference

threshold_applied (dbs)
type: DatatypeProperty
definition: Threshold value applied to the E-field simulation
in scheme: dbs
notation: threshold_applied

time_post_surgery (dbs)
type: DatatypeProperty
definition: Timepoint of assessment in days or months after implantation
in scheme: dbs
notation: time_post_surgery

timepoint (dbs)
type: DatatypeProperty
type: ObjectProperty
definition: Timepoint of assessment (e.g., "1 month post-op", "6 months post-op")
in scheme: dbs
notation: timepoint

timing_info (dbs)
type: DatatypeProperty
type: ObjectProperty
in scheme: dbs
notation: timing_info

version (dbs)
type: DatatypeProperty
type: ObjectProperty
definition: Version of the instrument (e.g., 3.0)
in scheme: dbs
notation: version

volume_data (dbs)
type: DatatypeProperty
type: ObjectProperty
definition: Reference to raw or thresholded volume
in scheme: dbs
notation: volume_data

application_category (software)
type: DatatypeProperty
type: ObjectProperty
definition: High-level category (e.g., simulation, analysis, specification).
in scheme: software
notation: application_category

author (software)
type: DatatypeProperty
type: ObjectProperty
definition: Original author(s) or creating organization(s).
in scheme: software
notation: author

build_hash (software)
type: DatatypeProperty
type: ObjectProperty
definition: Deterministic hash of the resolved dependency set.
in scheme: software
notation: build_hash

citation (software)
type: DatatypeProperty
type: ObjectProperty
definition: Additional citation strings or DOIs.
in scheme: software
notation: citation

container_image (software)
type: DatatypeProperty
type: ObjectProperty
definition: Container image reference (e.g., ghcr.io/org/img:tag@sha256:...).
in scheme: software
notation: container_image

date_created (software)
type: DatatypeProperty
definition: Date the software was first released (YYYY-MM-DD).
in scheme: software
notation: date_created

date_modified (software)
type: DatatypeProperty
definition: Date of the most recent release or significant update.
in scheme: software
notation: date_modified

description (software)
type: DatatypeProperty
type: ObjectProperty
in scheme: software
notation: description

doi (software)
type: DatatypeProperty
type: ObjectProperty
definition: Digital Object Identifier for the software or its reference publication.
in scheme: software
notation: doi

funder (software)
type: DatatypeProperty
type: ObjectProperty
definition: Funding bodies or grants (e.g., 'EU H2020 945539', 'NIH R01...').
in scheme: software
notation: funder

hash (software)
type: DatatypeProperty
type: ObjectProperty
definition: Build or artifact hash for exact reproducibility.
in scheme: software
notation: hash

homepage (software)
type: DatatypeProperty
definition: Project homepage URL.
in scheme: software
notation: homepage

is_accessible_for_free (software)
type: DatatypeProperty
definition: Whether the tool is free/open-source.
in scheme: software
notation: is_accessible_for_free

issue_tracker (software)
type: DatatypeProperty
definition: URL of the bug tracker or issue board.
in scheme: software
notation: issue_tracker

keywords (software)
type: DatatypeProperty
type: ObjectProperty
definition: Tags for topic-based discovery and clustering.
in scheme: software
notation: keywords

label (software)
type: DatatypeProperty
type: ObjectProperty
in scheme: software
notation: label

license (software)
type: DatatypeProperty
type: ObjectProperty
definition: SPDX license identifier (e.g., MIT, GPL-3.0-only).
in scheme: software
notation: license

maintainer (software)
type: DatatypeProperty
type: ObjectProperty
definition: Current maintainer(s) or responsible organization(s).
in scheme: software
notation: maintainer

modules (software)
type: DatatypeProperty
type: ObjectProperty
definition: (Deprecated) Use environment.requirements list instead.
in scheme: software
notation: modules

operating_system (software)
type: DatatypeProperty
type: ObjectProperty
definition: Supported operating systems (e.g., Linux, macOS, Windows).
in scheme: software
notation: operating_system

optional (software)
type: DatatypeProperty
in scheme: software
notation: optional

platform (software)
type: DatatypeProperty
type: ObjectProperty
definition: OS / architecture (e.g., linux-64, macos-arm64).
in scheme: software
notation: platform

reference_publication (software)
type: DatatypeProperty
type: ObjectProperty
definition: DOI of the primary reference publication for this tool.
in scheme: software
notation: reference_publication

repository (software)
type: DatatypeProperty
definition: Source code repository URL.
in scheme: software
notation: repository

runtime_platform (software)
type: DatatypeProperty
type: ObjectProperty
definition: Execution backends or platforms (e.g., MPI, OpenMP, CUDA, JAX).
in scheme: software
notation: runtime_platform

same_as (software)
type: DatatypeProperty
definition: URIs that unambiguously identify this tool (Wikidata, bio.tools, RRID, SciCrunch).
in scheme: software
notation: same_as

source_url (software)
type: DatatypeProperty
type: ObjectProperty
definition: Canonical source or repository URL.
in scheme: software
notation: source_url

url (software)
type: DatatypeProperty
type: ObjectProperty
definition: (Deprecated) Use source_url.
in scheme: software
notation: url

version_spec (software)
type: DatatypeProperty
type: ObjectProperty
definition: Version or constraint specifier (e.g., '==2.7.3', '>=1.2,<2').
in scheme: software
notation: version_spec

age (study)
type: DatatypeProperty
definition: Age at time of study (years).
in scheme: study
notation: age

bids_root (study)
type: DatatypeProperty
type: ObjectProperty
definition: Path to BIDS dataset root directory. When set, subject networks and empirical data paths are resolved relative to this root.
in scheme: study
notation: bids_root

condition (study)
type: DatatypeProperty
type: ObjectProperty
definition: Experimental condition label (e.g., 'rest', 'task-nback'). Maps to BIDS 'task-' entity.
in scheme: study
notation: condition

conditions (study)
type: DatatypeProperty
type: ObjectProperty
definition: Global condition labels applied across all subjects (e.g., ['rest', 'task-nback', 'task-motor']).
in scheme: study
notation: conditions

dataset_id (study)
type: DatatypeProperty
range: string
type: ObjectProperty
definition: Unique identifier for the dataset.
in scheme: study
notation: dataset_id

description (study)
type: DatatypeProperty
type: ObjectProperty
in scheme: study
notation: description

empirical_data (study)
type: DatatypeProperty
type: ObjectProperty
definition: Paths to empirical recordings for this session (e.g., BOLD time series, MEG/EEG). Relative to dataset root.
in scheme: study
notation: empirical_data

group (study)
type: DatatypeProperty
type: ObjectProperty
definition: Group assignment (e.g., 'control', 'patient', 'healthy'). Maps to participants.tsv 'group' column in BIDS.
in scheme: study
notation: group

label (study)
type: DatatypeProperty
type: ObjectProperty
definition: Human-readable dataset name.
definition: Human-readable label for the subject.
definition: Human-readable session label.
in scheme: study
notation: label

metadata (study)
type: DatatypeProperty
type: ObjectProperty
definition: Additional subject metadata as key-value pairs or path to a sidecar JSON file.
in scheme: study
notation: metadata

reference (study)
type: DatatypeProperty
type: ObjectProperty
definition: DOI or citation for this dataset.
in scheme: study
notation: reference

session_id (study)
type: DatatypeProperty
range: string
type: ObjectProperty
definition: BIDS session identifier (without 'ses-' prefix). Examples: 'baseline', '6month', 'pre', 'post'.
in scheme: study
notation: session_id

subject_id (study)
type: DatatypeProperty
range: string
type: ObjectProperty
definition: BIDS-compatible subject identifier (without 'sub-' prefix). Examples: '01', 'ctrl03', 'patient17'.
in scheme: study
notation: subject_id

A
type: Class
subclass of: UnitEnum
definition: Ampere

cm
type: Class
subclass of: UnitEnum
definition: Centimetre

degC
type: Class
subclass of: UnitEnum
definition: Degree Celsius

H_per_m
type: Class
subclass of: UnitEnum
definition: Henry per metre (permeability)

Hz
type: Class
subclass of: UnitEnum
definition: Hertz (s⁻¹)

kg
type: Class
subclass of: UnitEnum
definition: Kilogram

kHz
type: Class
subclass of: UnitEnum
definition: Kilohertz

m
type: Class
subclass of: UnitEnum
definition: Metre

m_per_s
type: Class
subclass of: UnitEnum
definition: Metre per second

m_per_s2
type: Class
subclass of: UnitEnum
definition: Metre per second squared (acceleration)

mol_per_m3
type: Class
subclass of: UnitEnum
definition: Mole per cubic metre (mol/m³)

um3
type: Class
subclass of: UnitEnum
definition: Cubic micrometre (µm³)

uS
type: Class
subclass of: UnitEnum
definition: Microsiemens

us
type: Class
subclass of: UnitEnum
definition: Microsecond

mm
type: Class
subclass of: UnitEnum
definition: Millimetre

mm_per_ms
type: Class
subclass of: UnitEnum
definition: Millimetre per millisecond (= m/s)

mmol_per_m3
type: Class
subclass of: UnitEnum
alternative label: mM
definition: Millimole per cubic metre (mmol/m³ ≈ mM)

ms
type: Class
subclass of: UnitEnum
definition: Millisecond

mV
type: Class
subclass of: UnitEnum
definition: Millivolt

mV_per_ms
type: Class
subclass of: UnitEnum
definition: Millivolt per millisecond

mV_per_s
type: Class
subclass of: UnitEnum
definition: Millivolt per second

N_per_m
type: Class
subclass of: UnitEnum
definition: Newton per metre (spring constant)

nA
type: Class
subclass of: UnitEnum
definition: Nanoampere

nF
type: Class
subclass of: UnitEnum
definition: Nanofarad

nS
type: Class
subclass of: UnitEnum
definition: Nanosiemens

ohm
type: Class
subclass of: UnitEnum
definition: Ohm (Ω)

per_ms
type: Class
subclass of: UnitEnum
definition: Per millisecond (ms⁻¹)

per_mV
type: Class
subclass of: UnitEnum
definition: Reciprocal millivolt (mV⁻¹)

per_nC
type: Class
subclass of: UnitEnum
definition: Reciprocal nanocoulomb (nC⁻¹)

per_pC
type: Class
subclass of: UnitEnum
definition: Reciprocal picocoulomb (pC⁻¹)

per_s
type: Class
subclass of: UnitEnum
definition: Per second (s⁻¹)

percent
type: Class
subclass of: UnitEnum
definition: Percent (%)

pA
type: Class
subclass of: UnitEnum
definition: Picoampere

pF
type: Class
subclass of: UnitEnum
definition: Picofarad

pS
type: Class
subclass of: UnitEnum
definition: Picosiemens

rad
type: Class
subclass of: UnitEnum
definition: Radian

rad_per_s
type: Class
subclass of: UnitEnum
definition: Radian per second (angular velocity)

S_per_m
type: Class
subclass of: UnitEnum
definition: Siemens per metre (conductivity)

s
type: Class
subclass of: UnitEnum
definition: Second

s2
type: Class
subclass of: UnitEnum
definition: Second squared (inertia constant)

dimensionless
type: Class
subclass of: UnitEnum
definition: Dimensionless (unitless)

V
type: Class
subclass of: UnitEnum
definition: Volt

Book
type: Class
subclass of: Thing

Creative work
type: Class
subclass of: Thing

Report
type: Class
subclass of: Thing

Scholarly article
type: Class
subclass of: Thing

BrainAtlas
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: abbreviation
subclass of: Restriction
  all values from: string
  on property: author
subclass of: Restriction
  all values from: CommonCoordinateSpace
  on property: coordinateSpace
subclass of: Restriction
  all values from: string
  on property: isVersionOf
subclass of: Restriction
  all values from: ParcellationTerminology
  on property: terminology
subclass of: Restriction
  all values from: string
  on property: versionIdentifier
subclass of: Restriction
  all values from: string
  on property: name (slot)
subclass of: Restriction
  min cardinality: 0
  on property: coordinateSpace
subclass of: Restriction
  min cardinality: 0
  on property: terminology
subclass of: Restriction
  min cardinality: 1
  on property: name (slot)
subclass of: Restriction
  max cardinality: 1
  on property: coordinateSpace
subclass of: Restriction
  max cardinality: 1
  on property: terminology
subclass of: Restriction
  max cardinality: 1
  on property: name (slot)
subclass of: Restriction
  min cardinality: 0
  on property: abbreviation
subclass of: Restriction
  min cardinality: 0
  on property: author
subclass of: Restriction
  min cardinality: 0
  on property: isVersionOf
subclass of: Restriction
  min cardinality: 0
  on property: versionIdentifier
subclass of: Restriction
  max cardinality: 1
  on property: abbreviation
subclass of: Restriction
  max cardinality: 1
  on property: isVersionOf
subclass of: Restriction
  max cardinality: 1
  on property: versionIdentifier
definition: A schema for representing a version of a brain atlas.
in scheme: BrainAtlas

CommonCoordinateSpace
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: abbreviation
subclass of: Restriction
  all values from: string
  on property: alternateName
subclass of: Restriction
  all values from: string
  on property: anatomicalAxesOrientation
subclass of: Restriction
  all values from: string
  on property: axesOrigin
subclass of: Restriction
  all values from: string
  on property: defaultImage
subclass of: Restriction
  all values from: string
  on property: license
subclass of: Restriction
  all values from: string
  on property: nativeUnit
subclass of: Restriction
  all values from: string
  on property: name (slot)
subclass of: Restriction
  min cardinality: 1
  on property: name (slot)
subclass of: Restriction
  max cardinality: 1
  on property: name (slot)
subclass of: Restriction
  min cardinality: 0
  on property: abbreviation
subclass of: Restriction
  min cardinality: 0
  on property: alternateName
subclass of: Restriction
  min cardinality: 0
  on property: anatomicalAxesOrientation
subclass of: Restriction
  min cardinality: 0
  on property: axesOrigin
subclass of: Restriction
  min cardinality: 0
  on property: defaultImage
subclass of: Restriction
  min cardinality: 0
  on property: license
subclass of: Restriction
  min cardinality: 0
  on property: nativeUnit
subclass of: Restriction
  max cardinality: 1
  on property: abbreviation
subclass of: Restriction
  max cardinality: 1
  on property: anatomicalAxesOrientation
subclass of: Restriction
  max cardinality: 1
  on property: axesOrigin
subclass of: Restriction
  max cardinality: 1
  on property: license
subclass of: Restriction
  max cardinality: 1
  on property: nativeUnit
definition: A schema for representing a version of a common coordinate space.
in scheme: BrainAtlas

Coordinate
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: CommonCoordinateSpace
  on property: coordinateSpace
subclass of: Restriction
  min cardinality: 0
  on property: coordinateSpace
subclass of: Restriction
  max cardinality: 1
  on property: coordinateSpace
subclass of: Restriction
  all values from: float
  on property: x
subclass of: Restriction
  all values from: float
  on property: y
subclass of: Restriction
  all values from: float
  on property: z
subclass of: Restriction
  min cardinality: 0
  on property: x
subclass of: Restriction
  min cardinality: 0
  on property: y
subclass of: Restriction
  min cardinality: 0
  on property: z
subclass of: Restriction
  max cardinality: 1
  on property: x
subclass of: Restriction
  max cardinality: 1
  on property: y
subclass of: Restriction
  max cardinality: 1
  on property: z
definition: A 3D coordinate with X, Y, Z values.
in scheme: BrainAtlas

ParcellationEntity
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: abbreviation
subclass of: Restriction
  all values from: string
  on property: alternateName
subclass of: Restriction
  all values from: Coordinate
  on property: center
subclass of: Restriction
  all values from: string
  on property: color
subclass of: Restriction
  all values from: ParcellationEntity
  on property: hasParent
subclass of: Restriction
  all values from: Hemisphere
  on property: hemisphere
subclass of: Restriction
  all values from: string
  on property: ontologyIdentifier
subclass of: Restriction
  all values from: string
  on property: relatedUBERONTerm
subclass of: Restriction
  all values from: string
  on property: versionIdentifier
subclass of: Restriction
  all values from: string
  on property: name (slot)
subclass of: Restriction
  min cardinality: 0
  on property: center
subclass of: Restriction
  min cardinality: 0
  on property: hasParent
subclass of: Restriction
  min cardinality: 0
  on property: hemisphere
subclass of: Restriction
  min cardinality: 1
  on property: name (slot)
subclass of: Restriction
  max cardinality: 1
  on property: center
subclass of: Restriction
  max cardinality: 1
  on property: hemisphere
subclass of: Restriction
  max cardinality: 1
  on property: name (slot)
subclass of: Restriction
  all values from: integer
  on property: lookupLabel
subclass of: Restriction
  all values from: integer
  on property: originalLookupLabel
subclass of: Restriction
  min cardinality: 0
  on property: abbreviation
subclass of: Restriction
  min cardinality: 0
  on property: alternateName
subclass of: Restriction
  min cardinality: 0
  on property: color
subclass of: Restriction
  min cardinality: 0
  on property: lookupLabel
subclass of: Restriction
  min cardinality: 0
  on property: ontologyIdentifier
subclass of: Restriction
  min cardinality: 0
  on property: originalLookupLabel
subclass of: Restriction
  min cardinality: 0
  on property: relatedUBERONTerm
subclass of: Restriction
  min cardinality: 0
  on property: versionIdentifier
subclass of: Restriction
  max cardinality: 1
  on property: abbreviation
subclass of: Restriction
  max cardinality: 1
  on property: color
subclass of: Restriction
  max cardinality: 1
  on property: lookupLabel
subclass of: Restriction
  max cardinality: 1
  on property: originalLookupLabel
subclass of: Restriction
  max cardinality: 1
  on property: relatedUBERONTerm
subclass of: Restriction
  max cardinality: 1
  on property: versionIdentifier
subject: anatomicalLocation
subject: studyTarget
definition: A schema for representing a parcellation entity, which is an anatomical location or study target.
in scheme: BrainAtlas

ParcellationTerminology
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: dataLocation
subclass of: Restriction
  all values from: ParcellationEntity
  on property: entities
subclass of: Restriction
  all values from: string
  on property: ontologyIdentifier
subclass of: Restriction
  all values from: string
  on property: versionIdentifier
subclass of: Restriction
  all values from: string
  on property: label (slot)
subclass of: Restriction
  min cardinality: 0
  on property: entities
subclass of: Restriction
  min cardinality: 0
  on property: label (slot)
subclass of: Restriction
  max cardinality: 1
  on property: label (slot)
subclass of: Restriction
  min cardinality: 0
  on property: dataLocation
subclass of: Restriction
  min cardinality: 0
  on property: ontologyIdentifier
subclass of: Restriction
  min cardinality: 0
  on property: versionIdentifier
subclass of: Restriction
  max cardinality: 1
  on property: dataLocation
subclass of: Restriction
  max cardinality: 1
  on property: versionIdentifier
definition: A schema for representing a parcellation terminology, which consists of parcellation entities.
in scheme: BrainAtlas

string
type: Class
subclass of: Thing

SKOS Concept
type: Class
subclass of: Thing

conda_forge
type: Class
subclass of: EcosystemEnum
definition: Conda-Forge community channel.

network_system
type: Class
subclass of: SimulationScale
definition: Whole-brain or large-scale network of regions.

mean_field
type: Class
subclass of: ModelParadigm
definition: Mean-field reductions of spiking networks.

simulator
type: Class
subclass of: ToolRole
definition: Core numerical simulator.

C
type: Class
subclass of: ProgrammingLanguageEnum

MATLAB
type: Class
subclass of: ProgrammingLanguageEnum

multiscale
type: Class
subclass of: ModelParadigm
definition: Bridging multiple spatial/temporal scales.

JavaScript
type: Class
subclass of: ProgrammingLanguageEnum

R
type: Class
subclass of: ProgrammingLanguageEnum

XML
type: Class
subclass of: ProgrammingLanguageEnum

C#
type: Class
subclass of: ProgrammingLanguageEnum

C++
type: Class
subclass of: ProgrammingLanguageEnum

Java
type: Class
subclass of: ProgrammingLanguageEnum

specification_language
type: Class
subclass of: ToolRole
definition: Model description language or data standard.

framework
type: Class
subclass of: ToolRole
definition: Multi-paradigm simulation framework.

Python
type: Class
subclass of: ProgrammingLanguageEnum

pypi
type: Class
subclass of: EcosystemEnum
definition: Python Package Index.

data_standard
type: Class
subclass of: ModelParadigm
definition: Data format or exchange standard.

Haskell
type: Class
subclass of: ProgrammingLanguageEnum

rate_based
type: Class
subclass of: ModelParadigm
definition: Firing-rate models.

Julia
type: Class
subclass of: ProgrammingLanguageEnum

neuron
type: Class
subclass of: SimulationScale
definition: Single neuron (compartmental or point).

neural_network
type: Class
subclass of: SimulationScale
definition: Microcircuit / local network of neurons.

compartmental
type: Class
subclass of: ModelParadigm
definition: Multi-compartment morphologically detailed models.

Rust
type: Class
subclass of: ProgrammingLanguageEnum

HOC
type: Class
subclass of: ProgrammingLanguageEnum
definition: NEURON's high-level interpreted language.

phase_oscillator
type: Class
subclass of: ModelParadigm
definition: Phase-reduced or Kuramoto-type oscillator models.

maven
type: Class
subclass of: EcosystemEnum
definition: Maven Central Repository (Java).

neural_mass
type: Class
subclass of: ModelParadigm
subclass of: SimulationScale
definition: Phenomenological population-rate / neural-mass models.
definition: Population-level neural mass or mean-field model.

npm
type: Class
subclass of: EcosystemEnum
definition: Node Package Manager registry.

conductance_based
type: Class
subclass of: ModelParadigm
definition: Conductance-based / Hodgkin-Huxley-type models.

model_repository
type: Class
subclass of: ToolRole
definition: Database or repository of published models.

plasticity
type: Class
subclass of: ModelParadigm
definition: Synaptic plasticity (STDP, homeostatic, etc.).

spiking
type: Class
subclass of: ModelParadigm
definition: Spiking neuron models (LIF, AdEx, Izhikevich, etc.).

optimization_framework
type: Class
subclass of: ToolRole
definition: Parameter optimization / fitting tool.

Fortran
type: Class
subclass of: ProgrammingLanguageEnum

reaction_diffusion
type: Class
subclass of: ModelParadigm
definition: Stochastic or deterministic reaction-diffusion.

bifurcation_analysis
type: Class
subclass of: ModelParadigm
subclass of: ToolRole
alternative label: continuation_tool
definition: Dynamical systems bifurcation / continuation analysis.
definition: Numerical continuation / bifurcation analysis.

channel
type: Class
subclass of: SimulationScale
definition: Ion channel / sub-cellular molecular dynamics.

cran
type: Class
subclass of: EcosystemEnum
definition: Comprehensive R Archive Network.

visualization_tool
type: Class
subclass of: ToolRole
definition: Visualization or graphical user interface.

analysis_tool
type: Class
subclass of: ToolRole
definition: Post-processing, signal analysis, or statistics.

Additive noise
type: Class
subclass of: Stochasticity character

Aggregation
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: DimensionType
  on property: over (slot)
subclass of: Restriction
  all values from: ReductionType
  on property: type
subclass of: Restriction
  min cardinality: 0
  on property: over (slot)
subclass of: Restriction
  min cardinality: 0
  on property: type
subclass of: Restriction
  max cardinality: 1
  on property: over (slot)
subclass of: Restriction
  max cardinality: 1
  on property: type
definition: Specifies how to aggregate values across a dimension. Used for loss functions to define per-element loss with reduction.
in scheme: tvbo

AggregationType
type: Class
equivalent class: Class
  union of: first (AggregationType)
  union of: last (AggregationType)
  union of: mean (AggregationType)
  union of: none (AggregationType)
  union of: window (AggregationType)
subclass of: Thing
definition: How to aggregate time series data
in scheme: tvbo
permissible values: first (AggregationType)
permissible values: last (AggregationType)
permissible values: mean (AggregationType)
permissible values: none (AggregationType)
permissible values: window (AggregationType)

Algorithm
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: Algorithm
  on property: depends on
subclass of: Restriction
  all values from: string
  on property: description (slot)
subclass of: Restriction
  all values from: ExecutionConfig
  on property: execution
subclass of: Restriction
  all values from: FunctionCall
  on property: functions
subclass of: Restriction
  all values from: Parameter
  on property: hyperparameters
subclass of: Restriction
  all values from: AlgorithmInclude
  on property: includes (slot)
subclass of: Restriction
  all values from: string
  on property: learning_rate_schedule (slot)
subclass of: Restriction
  all values from: string
  on property: name (slot)
subclass of: Restriction
  all values from: TuningObjective
  on property: objective (slot)
subclass of: Restriction
  all values from: Observation
  on property: observations
subclass of: Restriction
  all values from: string
  on property: type
subclass of: Restriction
  all values from: UpdateRule
  on property: update_rules (slot)
subclass of: Restriction
  min cardinality: 0
  on property: depends on
subclass of: Restriction
  min cardinality: 0
  on property: description (slot)
subclass of: Restriction
  min cardinality: 0
  on property: execution
subclass of: Restriction
  min cardinality: 0
  on property: functions
subclass of: Restriction
  min cardinality: 0
  on property: hyperparameters
subclass of: Restriction
  min cardinality: 0
  on property: includes (slot)
subclass of: Restriction
  min cardinality: 1
  on property: name (slot)
subclass of: Restriction
  min cardinality: 0
  on property: objective (slot)
subclass of: Restriction
  min cardinality: 0
  on property: observations
subclass of: Restriction
  min cardinality: 0
  on property: type
subclass of: Restriction
  min cardinality: 0
  on property: update_rules (slot)
subclass of: Restriction
  max cardinality: 1
  on property: description (slot)
subclass of: Restriction
  max cardinality: 1
  on property: execution
subclass of: Restriction
  max cardinality: 1
  on property: name (slot)
subclass of: Restriction
  max cardinality: 1
  on property: objective (slot)
subclass of: Restriction
  max cardinality: 1
  on property: type
subclass of: Restriction
  all values from: integer
  on property: apply_every (slot)
subclass of: Restriction
  all values from: float
  on property: learning rate
subclass of: Restriction
  all values from: boolean
  on property: learning_rate_warmup (slot)
subclass of: Restriction
  all values from: integer
  on property: n_iterations (slot)
subclass of: Restriction
  all values from: float
  on property: simulation_period (slot)
subclass of: Restriction
  min cardinality: 0
  on property: apply_every (slot)
subclass of: Restriction
  min cardinality: 0
  on property: learning rate
subclass of: Restriction
  min cardinality: 0
  on property: learning_rate_schedule (slot)
subclass of: Restriction
  min cardinality: 0
  on property: learning_rate_warmup (slot)
subclass of: Restriction
  min cardinality: 0
  on property: n_iterations (slot)
subclass of: Restriction
  min cardinality: 0
  on property: simulation_period (slot)
subclass of: Restriction
  max cardinality: 1
  on property: apply_every (slot)
subclass of: Restriction
  max cardinality: 1
  on property: learning rate
subclass of: Restriction
  max cardinality: 1
  on property: learning_rate_schedule (slot)
subclass of: Restriction
  max cardinality: 1
  on property: learning_rate_warmup (slot)
subclass of: Restriction
  max cardinality: 1
  on property: n_iterations (slot)
subclass of: Restriction
  max cardinality: 1
  on property: simulation_period (slot)
definition: A complete specification of an iterative parameter tuning algorithm. Combines update rules, objectives, observations, and hyperparameters.
in scheme: tvbo

AlgorithmInclude
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: Algorithm
  on property: algorithm
subclass of: Restriction
  all values from: Parameter
  on property: arguments
subclass of: Restriction
  min cardinality: 1
  on property: algorithm
subclass of: Restriction
  min cardinality: 0
  on property: arguments
subclass of: Restriction
  max cardinality: 1
  on property: algorithm
definition: Reference to an included algorithm with optional argument overrides. Allows combining algorithms with different hyperparameter values.
in scheme: tvbo

Argument
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: description (slot)
subclass of: Restriction
  all values from: string
  on property: name (slot)
subclass of: Restriction
  all values from: ScalarValue
  on property: value (slot)
subclass of: Restriction
  min cardinality: 0
  on property: description (slot)
subclass of: Restriction
  min cardinality: 1
  on property: name (slot)
subclass of: Restriction
  min cardinality: 0
  on property: value (slot)
subclass of: Restriction
  max cardinality: 1
  on property: description (slot)
subclass of: Restriction
  max cardinality: 1
  on property: name (slot)
subclass of: Restriction
  max cardinality: 1
  on property: value (slot)
definition: 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).
in scheme: tvbo

Attractor
type: Class
subclass of: Dynamical property

Backend
type: Class
subclass of: Thing
comment: A code-generation or simulation backend (JAX, TVB, PyRates, tvboptim, NetworkDynamics.jl, BifurcationKit.jl).

Backend capability
type: Class
subclass of: Thing
comment: 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.

BidsEntities
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: acquisition
subclass of: Restriction
  all values from: string
  on property: atlas
subclass of: Restriction
  all values from: string
  on property: cohort (slot)
subclass of: Restriction
  all values from: string
  on property: hemi (slot)
subclass of: Restriction
  all values from: string
  on property: reconstruction (slot)
subclass of: Restriction
  all values from: string
  on property: scale (slot)
subclass of: Restriction
  all values from: string
  on property: segmentation (slot)
subclass of: Restriction
  all values from: string
  on property: template (slot)
subclass of: Restriction
  min cardinality: 0
  on property: atlas
subclass of: Restriction
  max cardinality: 1
  on property: atlas
subclass of: Restriction
  min cardinality: 0
  on property: acquisition
subclass of: Restriction
  min cardinality: 0
  on property: cohort (slot)
subclass of: Restriction
  min cardinality: 0
  on property: hemi (slot)
subclass of: Restriction
  min cardinality: 0
  on property: reconstruction (slot)
subclass of: Restriction
  min cardinality: 0
  on property: scale (slot)
subclass of: Restriction
  min cardinality: 0
  on property: segmentation (slot)
subclass of: Restriction
  min cardinality: 0
  on property: template (slot)
subclass of: Restriction
  max cardinality: 1
  on property: acquisition
subclass of: Restriction
  max cardinality: 1
  on property: cohort (slot)
subclass of: Restriction
  max cardinality: 1
  on property: hemi (slot)
subclass of: Restriction
  max cardinality: 1
  on property: reconstruction (slot)
subclass of: Restriction
  max cardinality: 1
  on property: scale (slot)
subclass of: Restriction
  max cardinality: 1
  on property: segmentation (slot)
subclass of: Restriction
  max cardinality: 1
  on property: template (slot)
definition: BIDS filename entities (BEP017-aligned) for provenance and data discovery. Reusable on Network, BrainAtlas, Tractogram, or any dataset with BIDS-conformant naming.
in scheme: tvbo

Bifurcation
type: Class
subclass of: Dynamical property

Bifurcation event
type: Class
subclass of: Thing
comment: Reified record of a bifurcation in a specific model along a specific parameter.

Bistable
type: Class
subclass of: Dynamical regime
type: NamedIndividual

Bogdanov-Takens
type: Class
subclass of: Bifurcation

BoundaryCondition
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: BoundaryConditionType
  on property: bc_type (slot)
subclass of: Restriction
  all values from: string
  on property: description (slot)
subclass of: Restriction
  all values from: string
  on property: label (slot)
subclass of: Restriction
  all values from: string
  on property: on_region (slot)
subclass of: Restriction
  all values from: Equation
  on property: value (slot)
subclass of: Restriction
  min cardinality: 0
  on property: bc_type (slot)
subclass of: Restriction
  min cardinality: 0
  on property: description (slot)
subclass of: Restriction
  min cardinality: 0
  on property: label (slot)
subclass of: Restriction
  min cardinality: 0
  on property: value (slot)
subclass of: Restriction
  max cardinality: 1
  on property: bc_type (slot)
subclass of: Restriction
  max cardinality: 1
  on property: description (slot)
subclass of: Restriction
  max cardinality: 1
  on property: label (slot)
subclass of: Restriction
  max cardinality: 1
  on property: value (slot)
subclass of: Restriction
  all values from: boolean
  on property: time dependent
subclass of: Restriction
  min cardinality: 0
  on property: on_region (slot)
subclass of: Restriction
  min cardinality: 0
  on property: time dependent
subclass of: Restriction
  max cardinality: 1
  on property: on_region (slot)
subclass of: Restriction
  max cardinality: 1
  on property: time dependent
in scheme: tvbo

BoundaryConditionType
type: Class
equivalent class: Class
  union of: Dirichlet (BoundaryConditionType)
  union of: Neumann (BoundaryConditionType)
  union of: Periodic (BoundaryConditionType)
  union of: Robin (BoundaryConditionType)
subclass of: Thing
in scheme: tvbo
permissible values: Dirichlet (BoundaryConditionType)
permissible values: Neumann (BoundaryConditionType)
permissible values: Periodic (BoundaryConditionType)
permissible values: Robin (BoundaryConditionType)

BrainRegionSeries
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: values
subclass of: Restriction
  min cardinality: 0
  on property: values
definition: A series whose values represent latitude
in scheme: tvbo

BranchSwitch
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: Continuation
  on property: continuation (slot)
subclass of: Restriction
  all values from: string
  on property: description (slot)
subclass of: Restriction
  all values from: Discretization
  on property: discretization
subclass of: Restriction
  all values from: string
  on property: name (slot)
subclass of: Restriction
  all values from: Option
  on property: options
subclass of: Restriction
  all values from: Parameter
  on property: parameters (slot)
subclass of: Restriction
  all values from: string
  on property: source point
subclass of: Restriction
  min cardinality: 0
  on property: continuation (slot)
subclass of: Restriction
  min cardinality: 0
  on property: description (slot)
subclass of: Restriction
  min cardinality: 0
  on property: discretization
subclass of: Restriction
  min cardinality: 1
  on property: name (slot)
subclass of: Restriction
  min cardinality: 0
  on property: options
subclass of: Restriction
  min cardinality: 0
  on property: parameters (slot)
subclass of: Restriction
  max cardinality: 1
  on property: continuation (slot)
subclass of: Restriction
  max cardinality: 1
  on property: description (slot)
subclass of: Restriction
  max cardinality: 1
  on property: discretization
subclass of: Restriction
  max cardinality: 1
  on property: name (slot)
subclass of: Restriction
  all values from: boolean
  on property: bothside
subclass of: Restriction
  all values from: float
  on property: delta_p (slot)
subclass of: Restriction
  min cardinality: 0
  on property: bothside
subclass of: Restriction
  min cardinality: 0
  on property: delta_p (slot)
subclass of: Restriction
  min cardinality: 0
  on property: source point
subclass of: Restriction
  max cardinality: 1
  on property: bothside
subclass of: Restriction
  max cardinality: 1
  on property: delta_p (slot)
subclass of: Restriction
  max cardinality: 1
  on property: source point
definition: 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.
in scheme: tvbo

Bursting
type: Class
subclass of: Dynamical regime
type: NamedIndividual

Callable
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: description (slot)
subclass of: Restriction
  all values from: string
  on property: module (slot)
subclass of: Restriction
  all values from: string
  on property: name (slot)
subclass of: Restriction
  all values from: SoftwareRequirement (software)
  on property: software
subclass of: Restriction
  min cardinality: 0
  on property: description (slot)
subclass of: Restriction
  min cardinality: 0
  on property: module (slot)
subclass of: Restriction
  min cardinality: 1
  on property: name (slot)
subclass of: Restriction
  min cardinality: 0
  on property: software
subclass of: Restriction
  max cardinality: 1
  on property: description (slot)
subclass of: Restriction
  max cardinality: 1
  on property: module (slot)
subclass of: Restriction
  max cardinality: 1
  on property: name (slot)
subclass of: Restriction
  max cardinality: 1
  on property: software
in scheme: tvbo

Case
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: condition
subclass of: Restriction
  all values from: Equation
  on property: equation (slot)
subclass of: Restriction
  min cardinality: 0
  on property: condition
subclass of: Restriction
  min cardinality: 0
  on property: equation (slot)
subclass of: Restriction
  max cardinality: 1
  on property: condition
subclass of: Restriction
  max cardinality: 1
  on property: equation (slot)
in scheme: tvbo

Chaotic
type: Class
subclass of: Dynamical regime
type: NamedIndividual

ClassReference
type: Class
subclass of: Callable
subclass of: Restriction
  all values from: Argument
  on property: call_args (slot)
subclass of: Restriction
  all values from: Argument
  on property: constructor_args (slot)
subclass of: Restriction
  all values from: string
  on property: warmup source
subclass of: Restriction
  min cardinality: 0
  on property: call_args (slot)
subclass of: Restriction
  min cardinality: 0
  on property: constructor_args (slot)
subclass of: Restriction
  min cardinality: 0
  on property: warmup source
subclass of: Restriction
  max cardinality: 1
  on property: warmup source
definition: 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.
in scheme: tvbo

Coloured noise
type: Class
subclass of: Stochasticity character

ConditionalBlock
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: condition
subclass of: Restriction
  all values from: string
  on property: expression
subclass of: Restriction
  min cardinality: 0
  on property: condition
subclass of: Restriction
  min cardinality: 0
  on property: expression
subclass of: Restriction
  max cardinality: 1
  on property: condition
subclass of: Restriction
  max cardinality: 1
  on property: expression
definition: A single condition and its corresponding equation segment.
in scheme: tvbo

Continuation
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: ContinuationAlgorithm
  on property: algorithm
subclass of: Restriction
  all values from: BranchSwitch
  on property: branches (slot)
subclass of: Restriction
  all values from: string
  on property: description (slot)
subclass of: Restriction
  all values from: Dynamics
  on property: dynamics
subclass of: Restriction
  all values from: ExecutionConfig
  on property: execution
subclass of: Restriction
  all values from: Parameter
  on property: free parameters
subclass of: Restriction
  all values from: InitialState
  on property: initial_state (slot)
subclass of: Restriction
  all values from: string
  on property: label (slot)
subclass of: Restriction
  all values from: string
  on property: name (slot)
subclass of: Restriction
  all values from: Option
  on property: options
subclass of: Restriction
  all values from: SoftwareRequirement (software)
  on property: software
subclass of: Restriction
  min cardinality: 0
  on property: algorithm
subclass of: Restriction
  min cardinality: 0
  on property: branches (slot)
subclass of: Restriction
  min cardinality: 0
  on property: description (slot)
subclass of: Restriction
  min cardinality: 0
  on property: dynamics
subclass of: Restriction
  min cardinality: 0
  on property: execution
subclass of: Restriction
  min cardinality: 0
  on property: free parameters
subclass of: Restriction
  min cardinality: 0
  on property: initial_state (slot)
subclass of: Restriction
  min cardinality: 0
  on property: label (slot)
subclass of: Restriction
  min cardinality: 1
  on property: name (slot)
subclass of: Restriction
  min cardinality: 0
  on property: options
subclass of: Restriction
  min cardinality: 0
  on property: software
subclass of: Restriction
  max cardinality: 1
  on property: algorithm
subclass of: Restriction
  max cardinality: 1
  on property: description (slot)
subclass of: Restriction
  max cardinality: 1
  on property: dynamics
subclass of: Restriction
  max cardinality: 1
  on property: execution
subclass of: Restriction
  max cardinality: 1
  on property: initial_state (slot)
subclass of: Restriction
  max cardinality: 1
  on property: label (slot)
subclass of: Restriction
  max cardinality: 1
  on property: name (slot)
subclass of: Restriction
  max cardinality: 1
  on property: software
subclass of: Restriction
  all values from: boolean
  on property: bothside
subclass of: Restriction
  all values from: integer
  on property: detect_bifurcation (slot)
subclass of: Restriction
  all values from: boolean
  on property: detect_fold (slot)
subclass of: Restriction
  all values from: float
  on property: ds (slot)
subclass of: Restriction
  all values from: float
  on property: ds_max (slot)
subclass of: Restriction
  all values from: float
  on property: ds_min (slot)
subclass of: Restriction
  all values from: integer
  on property: max_bisection_steps (slot)
subclass of: Restriction
  all values from: integer
  on property: max_steps (slot)
subclass of: Restriction
  all values from: integer
  on property: n_inversion (slot)
subclass of: Restriction
  all values from: integer
  on property: nev (slot)
subclass of: Restriction
  all values from: integer
  on property: newton_max_iterations (slot)
subclass of: Restriction
  all values from: float
  on property: newton_tol (slot)
subclass of: Restriction
  all values from: float
  on property: tol_stability (slot)
subclass of: Restriction
  min cardinality: 0
  on property: bothside
subclass of: Restriction
  min cardinality: 0
  on property: detect_bifurcation (slot)
subclass of: Restriction
  min cardinality: 0
  on property: detect_fold (slot)
subclass of: Restriction
  min cardinality: 0
  on property: ds (slot)
subclass of: Restriction
  min cardinality: 0
  on property: ds_max (slot)
subclass of: Restriction
  min cardinality: 0
  on property: ds_min (slot)
subclass of: Restriction
  min cardinality: 0
  on property: max_bisection_steps (slot)
subclass of: Restriction
  min cardinality: 0
  on property: max_steps (slot)
subclass of: Restriction
  min cardinality: 0
  on property: n_inversion (slot)
subclass of: Restriction
  min cardinality: 0
  on property: nev (slot)
subclass of: Restriction
  min cardinality: 0
  on property: newton_max_iterations (slot)
subclass of: Restriction
  min cardinality: 0
  on property: newton_tol (slot)
subclass of: Restriction
  min cardinality: 0
  on property: tol_stability (slot)
subclass of: Restriction
  max cardinality: 1
  on property: bothside
subclass of: Restriction
  max cardinality: 1
  on property: detect_bifurcation (slot)
subclass of: Restriction
  max cardinality: 1
  on property: detect_fold (slot)
subclass of: Restriction
  max cardinality: 1
  on property: ds (slot)
subclass of: Restriction
  max cardinality: 1
  on property: ds_max (slot)
subclass of: Restriction
  max cardinality: 1
  on property: ds_min (slot)
subclass of: Restriction
  max cardinality: 1
  on property: max_bisection_steps (slot)
subclass of: Restriction
  max cardinality: 1
  on property: max_steps (slot)
subclass of: Restriction
  max cardinality: 1
  on property: n_inversion (slot)
subclass of: Restriction
  max cardinality: 1
  on property: nev (slot)
definition: 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.
in scheme: tvbo

ContinuationAlgorithm
type: Class
equivalent class: Class
  union of: MoorePenrose (ContinuationAlgorithm)
  union of: Natural (ContinuationAlgorithm)
  union of: PALC (ContinuationAlgorithm)
subclass of: Thing
definition: Predictor-corrector algorithm for numerical continuation.
in scheme: tvbo
permissible values: MoorePenrose (ContinuationAlgorithm)
permissible values: Natural (ContinuationAlgorithm)
permissible values: PALC (ContinuationAlgorithm)

Coupling
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: Class
    union of: string
    union of: Function
  on property: aggregation
subclass of: Restriction
  all values from: Equation
  on property: coupling_function (slot)
subclass of: Restriction
  all values from: string
  on property: description (slot)
subclass of: Restriction
  all values from: Class
    union of: string
    union of: Function
  on property: distribution
subclass of: Restriction
  all values from: StateVariable
  on property: incoming_states (slot)
subclass of: Restriction
  all values from: Coupling
  on property: inner_coupling (slot)
subclass of: Restriction
  all values from: string
  on property: label (slot)
subclass of: Restriction
  all values from: StateVariable
  on property: local_states (slot)
subclass of: Restriction
  all values from: string
  on property: name (slot)
subclass of: Restriction
  all values from: DerivedVariable
  on property: observed
subclass of: Restriction
  all values from: string
  on property: outsym (slot)
subclass of: Restriction
  all values from: Parameter
  on property: parameters (slot)
subclass of: Restriction
  all values from: Equation
  on property: post_expression (slot)
subclass of: Restriction
  all values from: Equation
  on property: pre_expression (slot)
subclass of: Restriction
  all values from: RegionMapping
  on property: region_mapping (slot)
subclass of: Restriction
  all values from: Network
  on property: regional_connectivity (slot)
subclass of: Restriction
  all values from: string
  on property: symmetry (slot)
subclass of: Restriction
  min cardinality: 0
  on property: aggregation
subclass of: Restriction
  min cardinality: 0
  on property: coupling_function (slot)
subclass of: Restriction
  min cardinality: 0
  on property: description (slot)
subclass of: Restriction
  min cardinality: 0
  on property: distribution
subclass of: Restriction
  min cardinality: 0
  on property: incoming_states (slot)
subclass of: Restriction
  min cardinality: 0
  on property: inner_coupling (slot)
subclass of: Restriction
  min cardinality: 0
  on property: label (slot)
subclass of: Restriction
  min cardinality: 0
  on property: local_states (slot)
subclass of: Restriction
  min cardinality: 1
  on property: name (slot)
subclass of: Restriction
  min cardinality: 0
  on property: observed
subclass of: Restriction
  min cardinality: 0
  on property: outsym (slot)
subclass of: Restriction
  min cardinality: 0
  on property: parameters (slot)
subclass of: Restriction
  min cardinality: 0
  on property: post_expression (slot)
subclass of: Restriction
  min cardinality: 0
  on property: pre_expression (slot)
subclass of: Restriction
  min cardinality: 0
  on property: region_mapping (slot)
subclass of: Restriction
  min cardinality: 0
  on property: regional_connectivity (slot)
subclass of: Restriction
  min cardinality: 0
  on property: symmetry (slot)
subclass of: Restriction
  max cardinality: 1
  on property: aggregation
subclass of: Restriction
  max cardinality: 1
  on property: coupling_function (slot)
subclass of: Restriction
  max cardinality: 1
  on property: description (slot)
subclass of: Restriction
  max cardinality: 1
  on property: distribution
subclass of: Restriction
  max cardinality: 1
  on property: inner_coupling (slot)
subclass of: Restriction
  max cardinality: 1
  on property: label (slot)
subclass of: Restriction
  max cardinality: 1
  on property: name (slot)
subclass of: Restriction
  max cardinality: 1
  on property: post_expression (slot)
subclass of: Restriction
  max cardinality: 1
  on property: pre_expression (slot)
subclass of: Restriction
  max cardinality: 1
  on property: region_mapping (slot)
subclass of: Restriction
  max cardinality: 1
  on property: regional_connectivity (slot)
subclass of: Restriction
  max cardinality: 1
  on property: symmetry (slot)
subclass of: Restriction
  all values from: boolean
  on property: delayed
subclass of: Restriction
  all values from: anyURI
  on property: iri (slot)
subclass of: Restriction
  all values from: boolean
  on property: sparse (slot)
subclass of: Restriction
  min cardinality: 0
  on property: delayed
subclass of: Restriction
  min cardinality: 0
  on property: iri (slot)
subclass of: Restriction
  min cardinality: 0
  on property: sparse (slot)
subclass of: Restriction
  max cardinality: 1
  on property: delayed
subclass of: Restriction
  max cardinality: 1
  on property: iri (slot)
subclass of: Restriction
  max cardinality: 1
  on property: sparse (slot)
in scheme: tvbo

CouplingInput
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: description (slot)
subclass of: Restriction
  all values from: string
  on property: keys (slot)
subclass of: Restriction
  all values from: string
  on property: name (slot)
subclass of: Restriction
  all values from: string
  on property: source (slot)
subclass of: Restriction
  min cardinality: 0
  on property: description (slot)
subclass of: Restriction
  min cardinality: 1
  on property: name (slot)
subclass of: Restriction
  min cardinality: 0
  on property: source (slot)
subclass of: Restriction
  max cardinality: 1
  on property: description (slot)
subclass of: Restriction
  max cardinality: 1
  on property: name (slot)
subclass of: Restriction
  max cardinality: 1
  on property: source (slot)
subclass of: Restriction
  all values from: integer
  on property: dimension (slot)
subclass of: Restriction
  min cardinality: 0
  on property: dimension (slot)
subclass of: Restriction
  min cardinality: 0
  on property: keys (slot)
subclass of: Restriction
  max cardinality: 1
  on property: dimension (slot)
type: NamedIndividual
type: SKOS Concept
comment: Aggregate input arriving at a node from connected nodes; modelled as the postsynaptic potential induced by long-range projections.
definition: Specification of a coupling input channel for multi-coupling dynamics
in scheme: tvbo

DataSource
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: description (slot)
subclass of: Restriction
  all values from: string
  on property: format
subclass of: Restriction
  all values from: string
  on property: key
subclass of: Restriction
  all values from: string
  on property: label (slot)
subclass of: Restriction
  all values from: Callable
  on property: loader (slot)
subclass of: Restriction
  all values from: string
  on property: name (slot)
subclass of: Restriction
  all values from: string
  on property: path
subclass of: Restriction
  all values from: Function
  on property: preprocessing (slot)
subclass of: Restriction
  min cardinality: 0
  on property: description (slot)
subclass of: Restriction
  min cardinality: 0
  on property: format
subclass of: Restriction
  min cardinality: 0
  on property: label (slot)
subclass of: Restriction
  min cardinality: 0
  on property: loader (slot)
subclass of: Restriction
  min cardinality: 1
  on property: name (slot)
subclass of: Restriction
  min cardinality: 0
  on property: preprocessing (slot)
subclass of: Restriction
  max cardinality: 1
  on property: description (slot)
subclass of: Restriction
  max cardinality: 1
  on property: format
subclass of: Restriction
  max cardinality: 1
  on property: label (slot)
subclass of: Restriction
  max cardinality: 1
  on property: loader (slot)
subclass of: Restriction
  max cardinality: 1
  on property: name (slot)
subclass of: Restriction
  max cardinality: 1
  on property: preprocessing (slot)
subclass of: Restriction
  min cardinality: 0
  on property: key
subclass of: Restriction
  min cardinality: 0
  on property: path
subclass of: Restriction
  max cardinality: 1
  on property: key
subclass of: Restriction
  max cardinality: 1
  on property: path
definition: Specification for loading external/empirical data.
in scheme: tvbo

DerivedObservation
type: Class
subclass of: Observation
subclass of: Restriction
  all values from: Observation
  on property: source_observations (slot)
subclass of: Restriction
  min cardinality: 1
  on property: source_observations (slot)
definition: 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.
in scheme: tvbo

DerivedParameter
type: Class
subclass of: Parameter
subclass of: Restriction
  all values from: string
  on property: description (slot)
subclass of: Restriction
  all values from: Equation
  on property: equation (slot)
subclass of: Restriction
  all values from: string
  on property: name (slot)
subclass of: Restriction
  all values from: string
  on property: symbol (slot)
subclass of: Restriction
  min cardinality: 0
  on property: description (slot)
subclass of: Restriction
  min cardinality: 0
  on property: equation (slot)
subclass of: Restriction
  min cardinality: 1
  on property: name (slot)
subclass of: Restriction
  max cardinality: 1
  on property: description (slot)
subclass of: Restriction
  max cardinality: 1
  on property: equation (slot)
subclass of: Restriction
  max cardinality: 1
  on property: name (slot)
subclass of: Restriction
  min cardinality: 0
  on property: symbol (slot)
subclass of: Restriction
  max cardinality: 1
  on property: symbol (slot)
in scheme: tvbo

DerivedVariable
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: Case
  on property: cases (slot)
subclass of: Restriction
  all values from: string
  on property: description (slot)
subclass of: Restriction
  all values from: Equation
  on property: equation (slot)
subclass of: Restriction
  all values from: string
  on property: label (slot)
subclass of: Restriction
  all values from: string
  on property: name (slot)
subclass of: Restriction
  all values from: string
  on property: symbol (slot)
subclass of: Restriction
  min cardinality: 0
  on property: cases (slot)
subclass of: Restriction
  min cardinality: 0
  on property: description (slot)
subclass of: Restriction
  min cardinality: 0
  on property: equation (slot)
subclass of: Restriction
  min cardinality: 0
  on property: label (slot)
subclass of: Restriction
  min cardinality: 1
  on property: name (slot)
subclass of: Restriction
  max cardinality: 1
  on property: description (slot)
subclass of: Restriction
  max cardinality: 1
  on property: equation (slot)
subclass of: Restriction
  max cardinality: 1
  on property: label (slot)
subclass of: Restriction
  max cardinality: 1
  on property: name (slot)
subclass of: Restriction
  all values from: boolean
  on property: conditional (slot)
subclass of: Restriction
  all values from: anyURI
  on property: grounding (slot)
subclass of: Restriction
  all values from: boolean
  on property: record (slot)
subclass of: Restriction
  min cardinality: 0
  on property: conditional (slot)
subclass of: Restriction
  min cardinality: 0
  on property: grounding (slot)
subclass of: Restriction
  min cardinality: 0
  on property: record (slot)
subclass of: Restriction
  min cardinality: 0
  on property: symbol (slot)
subclass of: Restriction
  max cardinality: 1
  on property: conditional (slot)
subclass of: Restriction
  max cardinality: 1
  on property: record (slot)
subclass of: Restriction
  max cardinality: 1
  on property: symbol (slot)
in scheme: tvbo

Deterministic
type: Class
subclass of: Stochasticity character
type: NamedIndividual

DevelopmentStatus
type: Class
equivalent class: Class
  union of: active (DevelopmentStatus)
  union of: concept (DevelopmentStatus)
  union of: inactive (DevelopmentStatus)
  union of: moved (DevelopmentStatus)
  union of: suspended (DevelopmentStatus)
  union of: unsupported (DevelopmentStatus)
  union of: wip (DevelopmentStatus)
subclass of: Thing
definition: Development status of the software. Based on repostatus.org categories.
in scheme: software
permissible values: active (DevelopmentStatus)
permissible values: concept (DevelopmentStatus)
permissible values: inactive (DevelopmentStatus)
permissible values: moved (DevelopmentStatus)
permissible values: suspended (DevelopmentStatus)
permissible values: unsupported (DevelopmentStatus)
permissible values: wip (DevelopmentStatus)

DifferentialOperator
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: Parameter
  on property: coefficient (slot)
subclass of: Restriction
  all values from: string
  on property: definition (slot)
subclass of: Restriction
  all values from: Equation
  on property: equation (slot)
subclass of: Restriction
  all values from: Equation
  on property: expression
subclass of: Restriction
  all values from: string
  on property: label (slot)
subclass of: Restriction
  all values from: OperatorType
  on property: operator_type (slot)
subclass of: Restriction
  all values from: Parameter
  on property: tensor_coefficient (slot)
subclass of: Restriction
  min cardinality: 0
  on property: coefficient (slot)
subclass of: Restriction
  min cardinality: 0
  on property: equation (slot)
subclass of: Restriction
  min cardinality: 0
  on property: expression
subclass of: Restriction
  min cardinality: 0
  on property: label (slot)
subclass of: Restriction
  min cardinality: 0
  on property: operator_type (slot)
subclass of: Restriction
  min cardinality: 0
  on property: tensor_coefficient (slot)
subclass of: Restriction
  max cardinality: 1
  on property: coefficient (slot)
subclass of: Restriction
  max cardinality: 1
  on property: equation (slot)
subclass of: Restriction
  max cardinality: 1
  on property: expression
subclass of: Restriction
  max cardinality: 1
  on property: label (slot)
subclass of: Restriction
  max cardinality: 1
  on property: operator_type (slot)
subclass of: Restriction
  max cardinality: 1
  on property: tensor_coefficient (slot)
subclass of: Restriction
  min cardinality: 0
  on property: definition (slot)
subclass of: Restriction
  max cardinality: 1
  on property: definition (slot)
in scheme: tvbo

DimensionType
type: Class
equivalent class: Class
  union of: batch (DimensionType)
  union of: frequency (DimensionType)
  union of: mode (DimensionType)
  union of: node (DimensionType)
  union of: region (DimensionType)
  union of: sample (DimensionType)
  union of: state (DimensionType)
  union of: time (DimensionType)
subclass of: Thing
definition: Dimensions along which operations can be applied
in scheme: tvbo
permissible values: batch (DimensionType)
permissible values: frequency (DimensionType)
permissible values: mode (DimensionType)
permissible values: node (DimensionType)
permissible values: region (DimensionType)
permissible values: sample (DimensionType)
permissible values: state (DimensionType)
permissible values: time (DimensionType)

Discretization
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: Solver
  on property: linear_solver (slot)
subclass of: Restriction
  all values from: NumericalDiscretizationMethod
  on property: method
subclass of: Restriction
  all values from: Solver
  on property: ode_solver (slot)
subclass of: Restriction
  all values from: Option
  on property: options
subclass of: Restriction
  all values from: Parameter
  on property: parameters (slot)
subclass of: Restriction
  min cardinality: 0
  on property: linear_solver (slot)
subclass of: Restriction
  min cardinality: 0
  on property: method
subclass of: Restriction
  min cardinality: 0
  on property: ode_solver (slot)
subclass of: Restriction
  min cardinality: 0
  on property: options
subclass of: Restriction
  min cardinality: 0
  on property: parameters (slot)
subclass of: Restriction
  max cardinality: 1
  on property: linear_solver (slot)
subclass of: Restriction
  max cardinality: 1
  on property: method
subclass of: Restriction
  max cardinality: 1
  on property: ode_solver (slot)
subclass of: Restriction
  all values from: integer
  on property: degree (slot)
subclass of: Restriction
  all values from: integer
  on property: mesh_intervals (slot)
subclass of: Restriction
  all values from: integer
  on property: n_sections (slot)
subclass of: Restriction
  min cardinality: 0
  on property: degree (slot)
subclass of: Restriction
  min cardinality: 0
  on property: mesh_intervals (slot)
subclass of: Restriction
  min cardinality: 0
  on property: n_sections (slot)
subclass of: Restriction
  max cardinality: 1
  on property: degree (slot)
subclass of: Restriction
  max cardinality: 1
  on property: mesh_intervals (slot)
subclass of: Restriction
  max cardinality: 1
  on property: n_sections (slot)
definition: Discretization method for boundary value problems in continuation (periodic orbits, connecting orbits, quasi-periodic tori). Specifies the method; method-specific numerics go in parameters.
in scheme: tvbo

DiscretizationMethod
type: Class
equivalent class: Class
  union of: FDM (DiscretizationMethod)
  union of: FEM (DiscretizationMethod)
  union of: FVM (DiscretizationMethod)
  union of: Spectral (DiscretizationMethod)
subclass of: Thing
in scheme: tvbo
permissible values: FDM (DiscretizationMethod)
permissible values: FEM (DiscretizationMethod)
permissible values: FVM (DiscretizationMethod)
permissible values: Spectral (DiscretizationMethod)

Distribution
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: SamplingAxis
  on property: axis (slot)
subclass of: Restriction
  all values from: Matrix
  on property: correlation (slot)
subclass of: Restriction
  all values from: Range
  on property: domain (slot)
subclass of: Restriction
  all values from: Function
  on property: function
subclass of: Restriction
  all values from: string
  on property: name (slot)
subclass of: Restriction
  all values from: Parameter
  on property: parameters (slot)
subclass of: Restriction
  min cardinality: 0
  on property: axis (slot)
subclass of: Restriction
  min cardinality: 0
  on property: correlation (slot)
subclass of: Restriction
  min cardinality: 0
  on property: domain (slot)
subclass of: Restriction
  min cardinality: 0
  on property: function
subclass of: Restriction
  min cardinality: 1
  on property: name (slot)
subclass of: Restriction
  min cardinality: 0
  on property: parameters (slot)
subclass of: Restriction
  max cardinality: 1
  on property: axis (slot)
subclass of: Restriction
  max cardinality: 1
  on property: correlation (slot)
subclass of: Restriction
  max cardinality: 1
  on property: domain (slot)
subclass of: Restriction
  max cardinality: 1
  on property: function
subclass of: Restriction
  max cardinality: 1
  on property: name (slot)
subclass of: Restriction
  all values from: integer
  on property: seed
subclass of: Restriction
  min cardinality: 0
  on property: seed
subclass of: Restriction
  max cardinality: 1
  on property: seed
definition: 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.
in scheme: tvbo

Dynamical property
type: Class
subclass of: Thing
comment: Top-level grouping for qualitative phase-space properties.

Dynamical regime
type: Class
subclass of: Dynamical property

Dynamics
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: dataLocation
subclass of: Restriction
  all values from: CouplingInput
  on property: coupling_inputs (slot)
subclass of: Restriction
  all values from: Parameter
  on property: coupling_terms (slot)
subclass of: Restriction
  all values from: Dynamics
  on property: derived_from_model (slot)
subclass of: Restriction
  all values from: DerivedParameter
  on property: derived parameters
subclass of: Restriction
  all values from: DerivedVariable
  on property: derived variables
subclass of: Restriction
  all values from: string
  on property: description (slot)
subclass of: Restriction
  all values from: Event
  on property: events
subclass of: Restriction
  all values from: Function
  on property: functions
subclass of: Restriction
  all values from: string
  on property: has_reference (slot)
subclass of: Restriction
  all values from: string
  on property: label (slot)
subclass of: Restriction
  all values from: Parameter
  on property: local_coupling_term (slot)
subclass of: Restriction
  all values from: Dynamics
  on property: modes (slot)
subclass of: Restriction
  all values from: string
  on property: name (slot)
subclass of: Restriction
  all values from: DerivedVariable
  on property: observed
subclass of: Restriction
  all values from: string
  on property: output
subclass of: Restriction
  all values from: Parameter
  on property: parameters (slot)
subclass of: Restriction
  all values from: string
  on property: references (slot)
subclass of: Restriction
  all values from: string
  on property: source (slot)
subclass of: Restriction
  all values from: StateVariable
  on property: state variables
subclass of: Restriction
  all values from: Stimulus
  on property: stimulus (slot)
subclass of: Restriction
  all values from: SystemType
  on property: system_type (slot)
subclass of: Restriction
  min cardinality: 0
  on property: coupling_inputs (slot)
subclass of: Restriction
  min cardinality: 0
  on property: coupling_terms (slot)
subclass of: Restriction
  min cardinality: 0
  on property: derived_from_model (slot)
subclass of: Restriction
  min cardinality: 0
  on property: derived parameters
subclass of: Restriction
  min cardinality: 0
  on property: derived variables
subclass of: Restriction
  min cardinality: 0
  on property: description (slot)
subclass of: Restriction
  min cardinality: 0
  on property: events
subclass of: Restriction
  min cardinality: 0
  on property: functions
subclass of: Restriction
  min cardinality: 0
  on property: label (slot)
subclass of: Restriction
  min cardinality: 0
  on property: local_coupling_term (slot)
subclass of: Restriction
  min cardinality: 0
  on property: modes (slot)
subclass of: Restriction
  min cardinality: 1
  on property: name (slot)
subclass of: Restriction
  min cardinality: 0
  on property: observed
subclass of: Restriction
  min cardinality: 0
  on property: parameters (slot)
subclass of: Restriction
  min cardinality: 0
  on property: source (slot)
subclass of: Restriction
  min cardinality: 0
  on property: state variables
subclass of: Restriction
  min cardinality: 0
  on property: stimulus (slot)
subclass of: Restriction
  min cardinality: 0
  on property: system_type (slot)
subclass of: Restriction
  max cardinality: 1
  on property: derived_from_model (slot)
subclass of: Restriction
  max cardinality: 1
  on property: description (slot)
subclass of: Restriction
  max cardinality: 1
  on property: label (slot)
subclass of: Restriction
  max cardinality: 1
  on property: local_coupling_term (slot)
subclass of: Restriction
  max cardinality: 1
  on property: name (slot)
subclass of: Restriction
  max cardinality: 1
  on property: source (slot)
subclass of: Restriction
  max cardinality: 1
  on property: stimulus (slot)
subclass of: Restriction
  max cardinality: 1
  on property: system_type (slot)
subclass of: Restriction
  all values from: boolean
  on property: autonomous (slot)
subclass of: Restriction
  all values from: anyURI
  on property: iri (slot)
subclass of: Restriction
  all values from: boolean
  on property: modified (slot)
subclass of: Restriction
  all values from: integer
  on property: number_of_modes (slot)
subclass of: Restriction
  min cardinality: 0
  on property: dataLocation
subclass of: Restriction
  min cardinality: 0
  on property: autonomous (slot)
subclass of: Restriction
  min cardinality: 0
  on property: has_reference (slot)
subclass of: Restriction
  min cardinality: 0
  on property: iri (slot)
subclass of: Restriction
  min cardinality: 0
  on property: modified (slot)
subclass of: Restriction
  min cardinality: 0
  on property: number_of_modes (slot)
subclass of: Restriction
  min cardinality: 0
  on property: output
subclass of: Restriction
  min cardinality: 0
  on property: references (slot)
subclass of: Restriction
  max cardinality: 1
  on property: dataLocation
subclass of: Restriction
  max cardinality: 1
  on property: autonomous (slot)
subclass of: Restriction
  max cardinality: 1
  on property: has_reference (slot)
subclass of: Restriction
  max cardinality: 1
  on property: iri (slot)
subclass of: Restriction
  max cardinality: 1
  on property: modified (slot)
subclass of: Restriction
  max cardinality: 1
  on property: number_of_modes (slot)
alternative label: NeuralMassModel
in scheme: tvbo
note: Successor class replacing deprecated NeuralMassModel.

EcosystemEnum
type: Class
equivalent class: Class
  union of: conda_forge
  union of: pypi
  union of: maven
  union of: npm
  union of: cran
  union of: bioconda (EcosystemEnum)
  union of: github (EcosystemEnum)
  union of: julia_registry (EcosystemEnum)
subclass of: Thing
definition: Package ecosystem or registry the software is distributed through.
in scheme: software
permissible values: conda_forge
permissible values: pypi
permissible values: maven
permissible values: npm
permissible values: cran
permissible values: bioconda (EcosystemEnum)
permissible values: github (EcosystemEnum)
permissible values: julia_registry (EcosystemEnum)

Edge
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: Coupling
  on property: coupling
subclass of: Restriction
  all values from: string
  on property: description (slot)
subclass of: Restriction
  all values from: string
  on property: dimension_labels (slot)
subclass of: Restriction
  all values from: Dynamics
  on property: dynamics
subclass of: Restriction
  all values from: Event
  on property: events
subclass of: Restriction
  all values from: SparseFormat
  on property: format
subclass of: Restriction
  all values from: string
  on property: label (slot)
subclass of: Restriction
  all values from: Parameter
  on property: parameters (slot)
subclass of: Restriction
  all values from: string
  on property: source_var (slot)
subclass of: Restriction
  all values from: string
  on property: target_network (slot)
subclass of: Restriction
  all values from: string
  on property: target_var (slot)
subclass of: Restriction
  min cardinality: 0
  on property: coupling
subclass of: Restriction
  min cardinality: 0
  on property: description (slot)
subclass of: Restriction
  min cardinality: 0
  on property: dynamics
subclass of: Restriction
  min cardinality: 0
  on property: events
subclass of: Restriction
  min cardinality: 0
  on property: format
subclass of: Restriction
  min cardinality: 0
  on property: label (slot)
subclass of: Restriction
  min cardinality: 0
  on property: parameters (slot)
subclass of: Restriction
  min cardinality: 0
  on property: source (slot)
subclass of: Restriction
  max cardinality: 1
  on property: coupling
subclass of: Restriction
  max cardinality: 1
  on property: description (slot)
subclass of: Restriction
  max cardinality: 1
  on property: dynamics
subclass of: Restriction
  max cardinality: 1
  on property: format
subclass of: Restriction
  max cardinality: 1
  on property: label (slot)
subclass of: Restriction
  max cardinality: 1
  on property: source (slot)
subclass of: Restriction
  all values from: float
  on property: delay (slot)
subclass of: Restriction
  all values from: boolean
  on property: directed
subclass of: Restriction
  all values from: float
  on property: distance (slot)
subclass of: Restriction
  all values from: boolean
  on property: non_negative (slot)
subclass of: Restriction
  all values from: integer
  on property: source (slot)
subclass of: Restriction
  all values from: integer
  on property: target (slot)
subclass of: Restriction
  all values from: boolean
  on property: valid_diagonal (slot)
subclass of: Restriction
  all values from: float
  on property: weight (slot)
subclass of: Restriction
  all values from: boolean
  on property: weighted (slot)
subclass of: Restriction
  min cardinality: 0
  on property: delay (slot)
subclass of: Restriction
  min cardinality: 0
  on property: dimension_labels (slot)
subclass of: Restriction
  min cardinality: 0
  on property: directed
subclass of: Restriction
  min cardinality: 0
  on property: distance (slot)
subclass of: Restriction
  min cardinality: 0
  on property: non_negative (slot)
subclass of: Restriction
  min cardinality: 0
  on property: source_var (slot)
subclass of: Restriction
  min cardinality: 0
  on property: target (slot)
subclass of: Restriction
  min cardinality: 0
  on property: target_network (slot)
subclass of: Restriction
  min cardinality: 0
  on property: target_var (slot)
subclass of: Restriction
  min cardinality: 0
  on property: valid_diagonal (slot)
subclass of: Restriction
  min cardinality: 0
  on property: weight (slot)
subclass of: Restriction
  min cardinality: 0
  on property: weighted (slot)
subclass of: Restriction
  max cardinality: 1
  on property: delay (slot)
subclass of: Restriction
  max cardinality: 1
  on property: directed
subclass of: Restriction
  max cardinality: 1
  on property: distance (slot)
subclass of: Restriction
  max cardinality: 1
  on property: non_negative (slot)
subclass of: Restriction
  max cardinality: 1
  on property: source_var (slot)
subclass of: Restriction
  max cardinality: 1
  on property: target (slot)
subclass of: Restriction
  max cardinality: 1
  on property: target_network (slot)
subclass of: Restriction
  max cardinality: 1
  on property: target_var (slot)
subclass of: Restriction
  max cardinality: 1
  on property: valid_diagonal (slot)
subclass of: Restriction
  max cardinality: 1
  on property: weight (slot)
subclass of: Restriction
  max cardinality: 1
  on property: weighted (slot)
definition: 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.
in scheme: tvbo

ElementType
type: Class
equivalent class: Class
  union of: hexahedron (ElementType)
  union of: quad (ElementType)
  union of: tetrahedron (ElementType)
  union of: triangle (ElementType)
subclass of: Thing
in scheme: tvbo
permissible values: hexahedron (ElementType)
permissible values: quad (ElementType)
permissible values: tetrahedron (ElementType)
permissible values: triangle (ElementType)

EnvironmentType
type: Class
equivalent class: Class
  union of: conda (EnvironmentType)
  union of: docker (EnvironmentType)
  union of: singularity (EnvironmentType)
  union of: venv (EnvironmentType)
subclass of: Thing
in scheme: software
permissible values: conda (EnvironmentType)
permissible values: docker (EnvironmentType)
permissible values: singularity (EnvironmentType)
permissible values: venv (EnvironmentType)

Equation
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: ConditionalBlock
  on property: conditionals (slot)
subclass of: Restriction
  all values from: string
  on property: definition (slot)
subclass of: Restriction
  all values from: string
  on property: description (slot)
subclass of: Restriction
  all values from: SoftwareRequirement (software)
  on property: engine (slot)
subclass of: Restriction
  all values from: string
  on property: label (slot)
subclass of: Restriction
  all values from: string
  on property: lefthandside (slot)
subclass of: Restriction
  all values from: Parameter
  on property: parameters (slot)
subclass of: Restriction
  all values from: string
  on property: pycode
subclass of: Restriction
  all values from: string
  on property: righthandside (slot)
subclass of: Restriction
  min cardinality: 0
  on property: conditionals (slot)
subclass of: Restriction
  min cardinality: 0
  on property: description (slot)
subclass of: Restriction
  min cardinality: 0
  on property: engine (slot)
subclass of: Restriction
  min cardinality: 0
  on property: label (slot)
subclass of: Restriction
  min cardinality: 0
  on property: parameters (slot)
subclass of: Restriction
  max cardinality: 1
  on property: description (slot)
subclass of: Restriction
  max cardinality: 1
  on property: engine (slot)
subclass of: Restriction
  max cardinality: 1
  on property: label (slot)
subclass of: Restriction
  all values from: boolean
  on property: latex (slot)
subclass of: Restriction
  min cardinality: 0
  on property: definition (slot)
subclass of: Restriction
  min cardinality: 0
  on property: latex (slot)
subclass of: Restriction
  min cardinality: 0
  on property: lefthandside (slot)
subclass of: Restriction
  min cardinality: 0
  on property: pycode
subclass of: Restriction
  min cardinality: 0
  on property: righthandside (slot)
subclass of: Restriction
  max cardinality: 1
  on property: definition (slot)
subclass of: Restriction
  max cardinality: 1
  on property: latex (slot)
subclass of: Restriction
  max cardinality: 1
  on property: lefthandside (slot)
subclass of: Restriction
  max cardinality: 1
  on property: pycode
subclass of: Restriction
  max cardinality: 1
  on property: righthandside (slot)
in scheme: tvbo

Event
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: Equation
  on property: affect (slot)
subclass of: Restriction
  all values from: Equation
  on property: affect_negative (slot)
subclass of: Restriction
  all values from: string
  on property: affect_parameters (slot)
subclass of: Restriction
  all values from: string
  on property: affect_states (slot)
subclass of: Restriction
  all values from: Equation
  on property: condition
subclass of: Restriction
  all values from: string
  on property: condition_parameters (slot)
subclass of: Restriction
  all values from: string
  on property: condition_states (slot)
subclass of: Restriction
  all values from: string
  on property: description (slot)
subclass of: Restriction
  all values from: Equation
  on property: equation (slot)
subclass of: Restriction
  all values from: EventType
  on property: event_type (slot)
subclass of: Restriction
  all values from: string
  on property: label (slot)
subclass of: Restriction
  all values from: string
  on property: name (slot)
subclass of: Restriction
  all values from: Parameter
  on property: parameters (slot)
subclass of: Restriction
  all values from: string
  on property: target_component (slot)
subclass of: Restriction
  min cardinality: 0
  on property: affect (slot)
subclass of: Restriction
  min cardinality: 0
  on property: affect_negative (slot)
subclass of: Restriction
  min cardinality: 0
  on property: affect_parameters (slot)
subclass of: Restriction
  min cardinality: 0
  on property: affect_states (slot)
subclass of: Restriction
  min cardinality: 0
  on property: condition
subclass of: Restriction
  min cardinality: 0
  on property: condition_parameters (slot)
subclass of: Restriction
  min cardinality: 0
  on property: condition_states (slot)
subclass of: Restriction
  min cardinality: 0
  on property: description (slot)
subclass of: Restriction
  min cardinality: 0
  on property: equation (slot)
subclass of: Restriction
  min cardinality: 0
  on property: event_type (slot)
subclass of: Restriction
  min cardinality: 0
  on property: label (slot)
subclass of: Restriction
  min cardinality: 1
  on property: name (slot)
subclass of: Restriction
  min cardinality: 0
  on property: parameters (slot)
subclass of: Restriction
  min cardinality: 0
  on property: target_component (slot)
subclass of: Restriction
  max cardinality: 1
  on property: affect (slot)
subclass of: Restriction
  max cardinality: 1
  on property: affect_negative (slot)
subclass of: Restriction
  max cardinality: 1
  on property: condition
subclass of: Restriction
  max cardinality: 1
  on property: description (slot)
subclass of: Restriction
  max cardinality: 1
  on property: equation (slot)
subclass of: Restriction
  max cardinality: 1
  on property: event_type (slot)
subclass of: Restriction
  max cardinality: 1
  on property: label (slot)
subclass of: Restriction
  max cardinality: 1
  on property: name (slot)
subclass of: Restriction
  max cardinality: 1
  on property: target_component (slot)
subclass of: Restriction
  all values from: float
  on property: duration (slot)
subclass of: Restriction
  all values from: integer
  on property: regions
subclass of: Restriction
  all values from: float
  on property: trigger_times (slot)
subclass of: Restriction
  all values from: float
  on property: weighting
subclass of: Restriction
  min cardinality: 0
  on property: duration (slot)
subclass of: Restriction
  min cardinality: 0
  on property: regions
subclass of: Restriction
  min cardinality: 0
  on property: trigger_times (slot)
subclass of: Restriction
  min cardinality: 0
  on property: weighting
subclass of: Restriction
  max cardinality: 1
  on property: duration (slot)
definition: 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.
in scheme: tvbo

EventType
type: Class
equivalent class: Class
  union of: continuous (EventType)
  union of: discrete (EventType)
  union of: preset_time (EventType)
  union of: stimulus (EventType)
subclass of: Thing
definition: Type of event triggering mechanism.
in scheme: tvbo
permissible values: continuous (EventType)
permissible values: discrete (EventType)
permissible values: preset_time (EventType)
permissible values: stimulus (EventType)

Excitable
type: Class
subclass of: Dynamical regime
type: NamedIndividual

ExecutionConfig
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: accelerator (slot)
subclass of: Restriction
  all values from: string
  on property: precision (slot)
subclass of: Restriction
  all values from: integer
  on property: batch_size (slot)
subclass of: Restriction
  all values from: boolean
  on property: find_fixpoint (slot)
subclass of: Restriction
  all values from: integer
  on property: n_threads (slot)
subclass of: Restriction
  all values from: integer
  on property: n_workers (slot)
subclass of: Restriction
  all values from: integer
  on property: random_seed (slot)
subclass of: Restriction
  min cardinality: 0
  on property: accelerator (slot)
subclass of: Restriction
  min cardinality: 0
  on property: batch_size (slot)
subclass of: Restriction
  min cardinality: 0
  on property: find_fixpoint (slot)
subclass of: Restriction
  min cardinality: 0
  on property: n_threads (slot)
subclass of: Restriction
  min cardinality: 0
  on property: n_workers (slot)
subclass of: Restriction
  min cardinality: 0
  on property: precision (slot)
subclass of: Restriction
  min cardinality: 0
  on property: random_seed (slot)
subclass of: Restriction
  max cardinality: 1
  on property: accelerator (slot)
subclass of: Restriction
  max cardinality: 1
  on property: batch_size (slot)
subclass of: Restriction
  max cardinality: 1
  on property: find_fixpoint (slot)
subclass of: Restriction
  max cardinality: 1
  on property: n_threads (slot)
subclass of: Restriction
  max cardinality: 1
  on property: n_workers (slot)
subclass of: Restriction
  max cardinality: 1
  on property: precision (slot)
subclass of: Restriction
  max cardinality: 1
  on property: random_seed (slot)
definition: Configuration for computational execution (parallelization, precision, hardware).
in scheme: tvbo

Exploration
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: average (slot)
subclass of: Restriction
  all values from: string
  on property: description (slot)
subclass of: Restriction
  all values from: ExecutionConfig
  on property: execution
subclass of: Restriction
  all values from: string
  on property: label (slot)
subclass of: Restriction
  all values from: string
  on property: mode (slot)
subclass of: Restriction
  all values from: string
  on property: name (slot)
subclass of: Restriction
  all values from: FunctionCall
  on property: observable (slot)
subclass of: Restriction
  all values from: Parameter
  on property: parameters (slot)
subclass of: Restriction
  all values from: ExplorationAxis
  on property: space (slot)
subclass of: Restriction
  min cardinality: 0
  on property: description (slot)
subclass of: Restriction
  min cardinality: 0
  on property: execution
subclass of: Restriction
  min cardinality: 0
  on property: label (slot)
subclass of: Restriction
  min cardinality: 1
  on property: name (slot)
subclass of: Restriction
  min cardinality: 0
  on property: observable (slot)
subclass of: Restriction
  min cardinality: 0
  on property: parameters (slot)
subclass of: Restriction
  min cardinality: 0
  on property: space (slot)
subclass of: Restriction
  max cardinality: 1
  on property: description (slot)
subclass of: Restriction
  max cardinality: 1
  on property: execution
subclass of: Restriction
  max cardinality: 1
  on property: label (slot)
subclass of: Restriction
  max cardinality: 1
  on property: name (slot)
subclass of: Restriction
  max cardinality: 1
  on property: observable (slot)
subclass of: Restriction
  all values from: integer
  on property: n_parallel (slot)
subclass of: Restriction
  all values from: integer
  on property: n_trials (slot)
subclass of: Restriction
  min cardinality: 0
  on property: average (slot)
subclass of: Restriction
  min cardinality: 0
  on property: mode (slot)
subclass of: Restriction
  min cardinality: 0
  on property: n_parallel (slot)
subclass of: Restriction
  min cardinality: 0
  on property: n_trials (slot)
subclass of: Restriction
  max cardinality: 1
  on property: average (slot)
subclass of: Restriction
  max cardinality: 1
  on property: mode (slot)
subclass of: Restriction
  max cardinality: 1
  on property: n_parallel (slot)
subclass of: Restriction
  max cardinality: 1
  on property: n_trials (slot)
definition: Parameter space exploration (grid search, sweep).
in scheme: tvbo

ExplorationAxis
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: description (slot)
subclass of: Restriction
  all values from: Range
  on property: domain (slot)
subclass of: Restriction
  all values from: Range
  on property: element domains
subclass of: Restriction
  all values from: string
  on property: label (slot)
subclass of: Restriction
  all values from: Parameter
  on property: parameter
subclass of: Restriction
  min cardinality: 0
  on property: description (slot)
subclass of: Restriction
  min cardinality: 0
  on property: domain (slot)
subclass of: Restriction
  min cardinality: 0
  on property: element domains
subclass of: Restriction
  min cardinality: 0
  on property: label (slot)
subclass of: Restriction
  min cardinality: 1
  on property: parameter
subclass of: Restriction
  max cardinality: 1
  on property: description (slot)
subclass of: Restriction
  max cardinality: 1
  on property: domain (slot)
subclass of: Restriction
  max cardinality: 1
  on property: label (slot)
subclass of: Restriction
  max cardinality: 1
  on property: parameter
subclass of: Restriction
  all values from: float
  on property: explored values
subclass of: Restriction
  min cardinality: 0
  on property: explored values
definition: 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.
in scheme: tvbo

FieldStateVariable
type: Class
subclass of: StateVariable
subclass of: Restriction
  all values from: BoundaryCondition
  on property: boundary conditions
subclass of: Restriction
  all values from: string
  on property: description (slot)
subclass of: Restriction
  all values from: string
  on property: label (slot)
subclass of: Restriction
  all values from: Mesh
  on property: mesh
subclass of: Restriction
  min cardinality: 0
  on property: boundary conditions
subclass of: Restriction
  min cardinality: 0
  on property: description (slot)
subclass of: Restriction
  min cardinality: 0
  on property: label (slot)
subclass of: Restriction
  min cardinality: 0
  on property: mesh
subclass of: Restriction
  max cardinality: 1
  on property: description (slot)
subclass of: Restriction
  max cardinality: 1
  on property: label (slot)
subclass of: Restriction
  max cardinality: 1
  on property: mesh
in scheme: tvbo

File
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: description (slot)
subclass of: Restriction
  all values from: string
  on property: extension (slot)
subclass of: Restriction
  all values from: string
  on property: name (slot)
subclass of: Restriction
  all values from: string
  on property: path
subclass of: Restriction
  all values from: string
  on property: type
subclass of: Restriction
  min cardinality: 0
  on property: description (slot)
subclass of: Restriction
  min cardinality: 1
  on property: name (slot)
subclass of: Restriction
  min cardinality: 0
  on property: type
subclass of: Restriction
  max cardinality: 1
  on property: description (slot)
subclass of: Restriction
  max cardinality: 1
  on property: name (slot)
subclass of: Restriction
  max cardinality: 1
  on property: type
subclass of: Restriction
  min cardinality: 0
  on property: extension (slot)
subclass of: Restriction
  min cardinality: 0
  on property: path
subclass of: Restriction
  max cardinality: 1
  on property: extension (slot)
subclass of: Restriction
  max cardinality: 1
  on property: path
in scheme: tvbo

Fixed point
type: Class
subclass of: Attractor
type: NamedIndividual

Fold of limit cycles
type: Class
subclass of: Bifurcation

FreeParameter
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: description (slot)
subclass of: Restriction
  all values from: Range
  on property: domain (slot)
subclass of: Restriction
  all values from: ScalarValue
  on property: initial value
subclass of: Restriction
  all values from: string
  on property: label (slot)
subclass of: Restriction
  all values from: Parameter
  on property: parameter
subclass of: Restriction
  all values from: string
  on property: shape
subclass of: Restriction
  min cardinality: 0
  on property: description (slot)
subclass of: Restriction
  min cardinality: 0
  on property: domain (slot)
subclass of: Restriction
  min cardinality: 0
  on property: initial value
subclass of: Restriction
  min cardinality: 0
  on property: label (slot)
subclass of: Restriction
  min cardinality: 1
  on property: parameter
subclass of: Restriction
  max cardinality: 1
  on property: description (slot)
subclass of: Restriction
  max cardinality: 1
  on property: domain (slot)
subclass of: Restriction
  max cardinality: 1
  on property: initial value
subclass of: Restriction
  max cardinality: 1
  on property: label (slot)
subclass of: Restriction
  max cardinality: 1
  on property: parameter
subclass of: Restriction
  all values from: boolean
  on property: heterogeneous
subclass of: Restriction
  min cardinality: 0
  on property: heterogeneous
subclass of: Restriction
  min cardinality: 0
  on property: shape
subclass of: Restriction
  max cardinality: 1
  on property: heterogeneous
subclass of: Restriction
  max cardinality: 1
  on property: shape
definition: 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.
in scheme: tvbo

Function
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: acronym (slot)
subclass of: Restriction
  all values from: Aggregation
  on property: aggregate
subclass of: Restriction
  all values from: DimensionType
  on property: apply on dimension
subclass of: Restriction
  all values from: Argument
  on property: arguments
subclass of: Restriction
  all values from: Callable
  on property: callable
subclass of: Restriction
  all values from: string
  on property: definition (slot)
subclass of: Restriction
  all values from: string
  on property: description (slot)
subclass of: Restriction
  all values from: Equation
  on property: equation (slot)
subclass of: Restriction
  all values from: Function
  on property: input
subclass of: Restriction
  all values from: string
  on property: label (slot)
subclass of: Restriction
  all values from: string
  on property: name (slot)
subclass of: Restriction
  all values from: string
  on property: output
subclass of: Restriction
  all values from: Equation
  on property: output_equation (slot)
subclass of: Restriction
  all values from: SoftwareRequirement (software)
  on property: requirements (slot)
subclass of: Restriction
  all values from: string
  on property: source code
subclass of: Restriction
  all values from: Range
  on property: time range
subclass of: Restriction
  min cardinality: 0
  on property: aggregate
subclass of: Restriction
  min cardinality: 0
  on property: apply on dimension
subclass of: Restriction
  min cardinality: 0
  on property: arguments
subclass of: Restriction
  min cardinality: 0
  on property: callable
subclass of: Restriction
  min cardinality: 0
  on property: description (slot)
subclass of: Restriction
  min cardinality: 0
  on property: equation (slot)
subclass of: Restriction
  min cardinality: 0
  on property: input
subclass of: Restriction
  min cardinality: 0
  on property: label (slot)
subclass of: Restriction
  min cardinality: 1
  on property: name (slot)
subclass of: Restriction
  min cardinality: 0
  on property: output_equation (slot)
subclass of: Restriction
  min cardinality: 0
  on property: requirements (slot)
subclass of: Restriction
  min cardinality: 0
  on property: time range
subclass of: Restriction
  max cardinality: 1
  on property: aggregate
subclass of: Restriction
  max cardinality: 1
  on property: apply on dimension
subclass of: Restriction
  max cardinality: 1
  on property: callable
subclass of: Restriction
  max cardinality: 1
  on property: description (slot)
subclass of: Restriction
  max cardinality: 1
  on property: equation (slot)
subclass of: Restriction
  max cardinality: 1
  on property: input
subclass of: Restriction
  max cardinality: 1
  on property: label (slot)
subclass of: Restriction
  max cardinality: 1
  on property: name (slot)
subclass of: Restriction
  max cardinality: 1
  on property: output_equation (slot)
subclass of: Restriction
  max cardinality: 1
  on property: time range
subclass of: Restriction
  all values from: anyURI
  on property: iri (slot)
subclass of: Restriction
  min cardinality: 0
  on property: acronym (slot)
subclass of: Restriction
  min cardinality: 0
  on property: definition (slot)
subclass of: Restriction
  min cardinality: 0
  on property: iri (slot)
subclass of: Restriction
  min cardinality: 0
  on property: output
subclass of: Restriction
  min cardinality: 0
  on property: source code
subclass of: Restriction
  max cardinality: 1
  on property: acronym (slot)
subclass of: Restriction
  max cardinality: 1
  on property: definition (slot)
subclass of: Restriction
  max cardinality: 1
  on property: iri (slot)
subclass of: Restriction
  max cardinality: 1
  on property: output
subclass of: Restriction
  max cardinality: 1
  on property: source code
definition: 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.
in scheme: tvbo

FunctionCall
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: acronym (slot)
subclass of: Restriction
  all values from: Aggregation
  on property: aggregate
subclass of: Restriction
  all values from: DimensionType
  on property: apply on dimension
subclass of: Restriction
  all values from: Argument
  on property: arguments
subclass of: Restriction
  all values from: Callable
  on property: callable
subclass of: Restriction
  all values from: ClassReference
  on property: class_call (slot)
subclass of: Restriction
  all values from: string
  on property: description (slot)
subclass of: Restriction
  all values from: Equation
  on property: equation (slot)
subclass of: Restriction
  all values from: Function
  on property: function
subclass of: Restriction
  all values from: string
  on property: input
subclass of: Restriction
  all values from: string
  on property: label (slot)
subclass of: Restriction
  all values from: string
  on property: name (slot)
subclass of: Restriction
  all values from: string
  on property: output
subclass of: Restriction
  all values from: string
  on property: source code
subclass of: Restriction
  all values from: Range
  on property: time range
subclass of: Restriction
  min cardinality: 0
  on property: aggregate
subclass of: Restriction
  min cardinality: 0
  on property: apply on dimension
subclass of: Restriction
  min cardinality: 0
  on property: arguments
subclass of: Restriction
  min cardinality: 0
  on property: callable
subclass of: Restriction
  min cardinality: 0
  on property: class_call (slot)
subclass of: Restriction
  min cardinality: 0
  on property: description (slot)
subclass of: Restriction
  min cardinality: 0
  on property: equation (slot)
subclass of: Restriction
  min cardinality: 0
  on property: function
subclass of: Restriction
  min cardinality: 0
  on property: input
subclass of: Restriction
  min cardinality: 0
  on property: label (slot)
subclass of: Restriction
  min cardinality: 1
  on property: name (slot)
subclass of: Restriction
  min cardinality: 0
  on property: time range
subclass of: Restriction
  max cardinality: 1
  on property: aggregate
subclass of: Restriction
  max cardinality: 1
  on property: apply on dimension
subclass of: Restriction
  max cardinality: 1
  on property: callable
subclass of: Restriction
  max cardinality: 1
  on property: class_call (slot)
subclass of: Restriction
  max cardinality: 1
  on property: description (slot)
subclass of: Restriction
  max cardinality: 1
  on property: equation (slot)
subclass of: Restriction
  max cardinality: 1
  on property: function
subclass of: Restriction
  max cardinality: 1
  on property: input
subclass of: Restriction
  max cardinality: 1
  on property: label (slot)
subclass of: Restriction
  max cardinality: 1
  on property: name (slot)
subclass of: Restriction
  max cardinality: 1
  on property: time range
subclass of: Restriction
  min cardinality: 0
  on property: acronym (slot)
subclass of: Restriction
  min cardinality: 0
  on property: output
subclass of: Restriction
  min cardinality: 0
  on property: source code
subclass of: Restriction
  max cardinality: 1
  on property: acronym (slot)
subclass of: Restriction
  max cardinality: 1
  on property: output
subclass of: Restriction
  max cardinality: 1
  on property: source code
definition: 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).
in scheme: tvbo

GraphGenerator
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: description (slot)
subclass of: Restriction
  all values from: string
  on property: name (slot)
subclass of: Restriction
  all values from: Parameter
  on property: parameters (slot)
subclass of: Restriction
  all values from: string
  on property: type
subclass of: Restriction
  min cardinality: 0
  on property: description (slot)
subclass of: Restriction
  min cardinality: 1
  on property: name (slot)
subclass of: Restriction
  min cardinality: 0
  on property: parameters (slot)
subclass of: Restriction
  min cardinality: 1
  on property: type
subclass of: Restriction
  max cardinality: 1
  on property: description (slot)
subclass of: Restriction
  max cardinality: 1
  on property: name (slot)
subclass of: Restriction
  max cardinality: 1
  on property: type
subclass of: Restriction
  all values from: boolean
  on property: directed
subclass of: Restriction
  all values from: integer
  on property: seed
subclass of: Restriction
  min cardinality: 0
  on property: directed
subclass of: Restriction
  min cardinality: 0
  on property: seed
subclass of: Restriction
  max cardinality: 1
  on property: directed
subclass of: Restriction
  max cardinality: 1
  on property: seed
definition: 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.
in scheme: tvbo

Hemisphere
type: Class
equivalent class: Class
  union of: both (Hemisphere)
  union of: left (Hemisphere)
  union of: right (Hemisphere)
subclass of: Thing
in scheme: BrainAtlas
permissible values: both (Hemisphere)
permissible values: left (Hemisphere)
permissible values: right (Hemisphere)

Homoclinic
type: Class
subclass of: Bifurcation
type: NamedIndividual

Hopf
type: Class
subclass of: Bifurcation
type: NamedIndividual

ImagingModality
type: Class
equivalent class: Class
  union of: BOLD (ImagingModality)
  union of: EEG (ImagingModality)
  union of: IEEG (ImagingModality)
  union of: MEG (ImagingModality)
  union of: SEEG (ImagingModality)
subclass of: Thing
in scheme: tvbo
permissible values: BOLD (ImagingModality)
permissible values: EEG (ImagingModality)
permissible values: IEEG (ImagingModality)
permissible values: MEG (ImagingModality)
permissible values: SEEG (ImagingModality)

InitialState
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: InitialStateMethod
  on property: method
subclass of: Restriction
  all values from: Solver
  on property: solver
subclass of: Restriction
  all values from: string
  on property: source_branch (slot)
subclass of: Restriction
  all values from: string
  on property: source point
subclass of: Restriction
  min cardinality: 0
  on property: method
subclass of: Restriction
  min cardinality: 0
  on property: solver
subclass of: Restriction
  max cardinality: 1
  on property: method
subclass of: Restriction
  max cardinality: 1
  on property: solver
subclass of: Restriction
  all values from: float
  on property: abs tol
subclass of: Restriction
  all values from: float
  on property: duration (slot)
subclass of: Restriction
  all values from: float
  on property: rel tol
subclass of: Restriction
  min cardinality: 0
  on property: abs tol
subclass of: Restriction
  min cardinality: 0
  on property: duration (slot)
subclass of: Restriction
  min cardinality: 0
  on property: rel tol
subclass of: Restriction
  min cardinality: 0
  on property: source_branch (slot)
subclass of: Restriction
  min cardinality: 0
  on property: source point
subclass of: Restriction
  max cardinality: 1
  on property: abs tol
subclass of: Restriction
  max cardinality: 1
  on property: duration (slot)
subclass of: Restriction
  max cardinality: 1
  on property: rel tol
subclass of: Restriction
  max cardinality: 1
  on property: source_branch (slot)
subclass of: Restriction
  max cardinality: 1
  on property: source point
definition: How to obtain the starting equilibrium or periodic orbit for continuation. Most robust: time-integrate to steady state.
in scheme: tvbo

InitialStateMethod
type: Class
equivalent class: Class
  union of: from_branch (InitialStateMethod)
  union of: given (InitialStateMethod)
  union of: newton (InitialStateMethod)
  union of: time_integration (InitialStateMethod)
subclass of: Thing
definition: Strategy for obtaining the starting equilibrium or periodic orbit.
in scheme: tvbo
permissible values: from_branch (InitialStateMethod)
permissible values: given (InitialStateMethod)
permissible values: newton (InitialStateMethod)
permissible values: time_integration (InitialStateMethod)

Integrator
type: Class
subclass of: Solver
subclass of: Restriction
  all values from: string
  on property: description (slot)
subclass of: Restriction
  all values from: DerivedVariable
  on property: intermediate_expressions (slot)
subclass of: Restriction
  all values from: string
  on property: method
subclass of: Restriction
  all values from: Noise
  on property: noise
subclass of: Restriction
  all values from: Parameter
  on property: parameters (slot)
subclass of: Restriction
  all values from: UnitEnum
  on property: time_scale (slot)
subclass of: Restriction
  all values from: DerivedVariable
  on property: update_expression (slot)
subclass of: Restriction
  min cardinality: 0
  on property: description (slot)
subclass of: Restriction
  min cardinality: 0
  on property: intermediate_expressions (slot)
subclass of: Restriction
  min cardinality: 0
  on property: method
subclass of: Restriction
  min cardinality: 0
  on property: noise
subclass of: Restriction
  min cardinality: 0
  on property: parameters (slot)
subclass of: Restriction
  min cardinality: 0
  on property: time_scale (slot)
subclass of: Restriction
  min cardinality: 0
  on property: update_expression (slot)
subclass of: Restriction
  max cardinality: 1
  on property: description (slot)
subclass of: Restriction
  max cardinality: 1
  on property: method
subclass of: Restriction
  max cardinality: 1
  on property: noise
subclass of: Restriction
  max cardinality: 1
  on property: time_scale (slot)
subclass of: Restriction
  max cardinality: 1
  on property: update_expression (slot)
subclass of: Restriction
  all values from: boolean
  on property: delayed
subclass of: Restriction
  all values from: float
  on property: duration (slot)
subclass of: Restriction
  all values from: integer
  on property: number_of_stages (slot)
subclass of: Restriction
  all values from: boolean
  on property: scipy_ode_base (slot)
subclass of: Restriction
  all values from: float
  on property: state_wise_sigma (slot)
subclass of: Restriction
  all values from: float
  on property: step_size (slot)
subclass of: Restriction
  all values from: integer
  on property: steps (slot)
subclass of: Restriction
  all values from: float
  on property: transient_time (slot)
subclass of: Restriction
  min cardinality: 0
  on property: delayed
subclass of: Restriction
  min cardinality: 0
  on property: duration (slot)
subclass of: Restriction
  min cardinality: 0
  on property: number_of_stages (slot)
subclass of: Restriction
  min cardinality: 0
  on property: scipy_ode_base (slot)
subclass of: Restriction
  min cardinality: 0
  on property: state_wise_sigma (slot)
subclass of: Restriction
  min cardinality: 0
  on property: step_size (slot)
subclass of: Restriction
  min cardinality: 0
  on property: steps (slot)
subclass of: Restriction
  min cardinality: 0
  on property: transient_time (slot)
subclass of: Restriction
  max cardinality: 1
  on property: delayed
subclass of: Restriction
  max cardinality: 1
  on property: duration (slot)
subclass of: Restriction
  max cardinality: 1
  on property: number_of_stages (slot)
subclass of: Restriction
  max cardinality: 1
  on property: scipy_ode_base (slot)
subclass of: Restriction
  max cardinality: 1
  on property: step_size (slot)
subclass of: Restriction
  max cardinality: 1
  on property: steps (slot)
subclass of: Restriction
  max cardinality: 1
  on property: transient_time (slot)
definition: 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'.
in scheme: tvbo

Limit cycle
type: Class
subclass of: Attractor
type: NamedIndividual

LossFunction
type: Class
subclass of: Function
subclass of: Restriction
  all values from: Aggregation
  on property: aggregate
subclass of: Restriction
  min cardinality: 0
  on property: aggregate
subclass of: Restriction
  max cardinality: 1
  on property: aggregate
definition: A loss function for optimization with optional aggregation. Extends Function with aggregation specification for per-element losses.
in scheme: tvbo

Matrix
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: dataLocation
subclass of: Restriction
  all values from: string
  on property: description (slot)
subclass of: Restriction
  all values from: string
  on property: dtype
subclass of: Restriction
  all values from: SparseFormat
  on property: format
subclass of: Restriction
  all values from: string
  on property: label (slot)
subclass of: Restriction
  all values from: BrainRegionSeries
  on property: x (slot)
subclass of: Restriction
  all values from: BrainRegionSeries
  on property: y (slot)
subclass of: Restriction
  min cardinality: 0
  on property: description (slot)
subclass of: Restriction
  min cardinality: 0
  on property: format
subclass of: Restriction
  min cardinality: 0
  on property: label (slot)
subclass of: Restriction
  min cardinality: 0
  on property: values
subclass of: Restriction
  min cardinality: 0
  on property: x (slot)
subclass of: Restriction
  min cardinality: 0
  on property: y (slot)
subclass of: Restriction
  max cardinality: 1
  on property: description (slot)
subclass of: Restriction
  max cardinality: 1
  on property: format
subclass of: Restriction
  max cardinality: 1
  on property: label (slot)
subclass of: Restriction
  max cardinality: 1
  on property: x (slot)
subclass of: Restriction
  max cardinality: 1
  on property: y (slot)
subclass of: Restriction
  all values from: integer
  on property: shape
subclass of: Restriction
  all values from: float
  on property: values
subclass of: Restriction
  min cardinality: 0
  on property: dataLocation
subclass of: Restriction
  min cardinality: 0
  on property: dtype
subclass of: Restriction
  min cardinality: 0
  on property: shape
subclass of: Restriction
  max cardinality: 1
  on property: dataLocation
subclass of: Restriction
  max cardinality: 1
  on property: dtype
definition: Adjacency matrix of a network.
in scheme: tvbo

Mesh
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: dataLocation
subclass of: Restriction
  all values from: CommonCoordinateSpace
  on property: coordinate space
subclass of: Restriction
  all values from: Coordinate
  on property: coordinates (slot)
subclass of: Restriction
  all values from: string
  on property: description (slot)
subclass of: Restriction
  all values from: ElementType
  on property: element_type (slot)
subclass of: Restriction
  all values from: string
  on property: elements (slot)
subclass of: Restriction
  all values from: string
  on property: label (slot)
subclass of: Restriction
  all values from: string
  on property: mesh_file (slot)
subclass of: Restriction
  all values from: string
  on property: mesh_format (slot)
subclass of: Restriction
  min cardinality: 0
  on property: coordinate space
subclass of: Restriction
  min cardinality: 0
  on property: coordinates (slot)
subclass of: Restriction
  min cardinality: 0
  on property: description (slot)
subclass of: Restriction
  min cardinality: 0
  on property: element_type (slot)
subclass of: Restriction
  min cardinality: 0
  on property: label (slot)
subclass of: Restriction
  max cardinality: 1
  on property: coordinate space
subclass of: Restriction
  max cardinality: 1
  on property: description (slot)
subclass of: Restriction
  max cardinality: 1
  on property: element_type (slot)
subclass of: Restriction
  max cardinality: 1
  on property: label (slot)
subclass of: Restriction
  all values from: integer
  on property: number_of_elements (slot)
subclass of: Restriction
  all values from: integer
  on property: number_of_vertices (slot)
subclass of: Restriction
  min cardinality: 0
  on property: dataLocation
subclass of: Restriction
  min cardinality: 0
  on property: elements (slot)
subclass of: Restriction
  min cardinality: 0
  on property: mesh_file (slot)
subclass of: Restriction
  min cardinality: 0
  on property: mesh_format (slot)
subclass of: Restriction
  min cardinality: 0
  on property: number_of_elements (slot)
subclass of: Restriction
  min cardinality: 0
  on property: number_of_vertices (slot)
subclass of: Restriction
  max cardinality: 1
  on property: dataLocation
subclass of: Restriction
  max cardinality: 1
  on property: elements (slot)
subclass of: Restriction
  max cardinality: 1
  on property: mesh_file (slot)
subclass of: Restriction
  max cardinality: 1
  on property: mesh_format (slot)
subclass of: Restriction
  max cardinality: 1
  on property: number_of_elements (slot)
subclass of: Restriction
  max cardinality: 1
  on property: number_of_vertices (slot)
in scheme: tvbo

Model feature
type: Class
subclass of: Thing
comment: 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.

ModelParadigm
type: Class
equivalent class: Class
  union of: mean_field
  union of: multiscale
  union of: data_standard
  union of: rate_based
  union of: compartmental
  union of: phase_oscillator
  union of: neural_mass
  union of: conductance_based
  union of: plasticity
  union of: spiking
  union of: reaction_diffusion
  union of: bifurcation_analysis
  union of: dynamic_mean_field (ModelParadigm)
  union of: generic (ModelParadigm)
  union of: model_description (ModelParadigm)
subclass of: Thing
definition: Computational paradigm or modeling approach supported by the tool.
in scheme: software
permissible values: mean_field
permissible values: multiscale
permissible values: data_standard
permissible values: rate_based
permissible values: compartmental
permissible values: phase_oscillator
permissible values: neural_mass
permissible values: conductance_based
permissible values: plasticity
permissible values: spiking
permissible values: reaction_diffusion
permissible values: bifurcation_analysis
permissible values: dynamic_mean_field (ModelParadigm)
permissible values: generic (ModelParadigm)
permissible values: model_description (ModelParadigm)

ModelType
type: Class
equivalent class: Class
  union of: field (ModelType)
  union of: generic (ModelType)
  union of: mean_field (ModelType)
  union of: neural_mass (ModelType)
  union of: phase_oscillator (ModelType)
  union of: phenomenological (ModelType)
  union of: spiking (ModelType)
subclass of: Thing
definition: Coarse classification of a Dynamics model by its mathematical/biological origin. Used for filtering and display in list_db().
in scheme: tvbo
permissible values: field (ModelType)
permissible values: generic (ModelType)
permissible values: mean_field (ModelType)
permissible values: neural_mass (ModelType)
permissible values: phase_oscillator (ModelType)
permissible values: phenomenological (ModelType)
permissible values: spiking (ModelType)

Multiplicative noise
type: Class
subclass of: Stochasticity character

Multistable
type: Class
subclass of: Dynamical regime
type: NamedIndividual

NDArray
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: dataLocation (slot)
subclass of: Restriction
  all values from: string
  on property: description (slot)
subclass of: Restriction
  all values from: string
  on property: dtype
subclass of: Restriction
  all values from: string
  on property: label (slot)
subclass of: Restriction
  min cardinality: 0
  on property: description (slot)
subclass of: Restriction
  min cardinality: 0
  on property: label (slot)
subclass of: Restriction
  max cardinality: 1
  on property: description (slot)
subclass of: Restriction
  max cardinality: 1
  on property: label (slot)
subclass of: Restriction
  all values from: integer
  on property: shape
subclass of: Restriction
  min cardinality: 0
  on property: dataLocation (slot)
subclass of: Restriction
  min cardinality: 0
  on property: dtype
subclass of: Restriction
  min cardinality: 0
  on property: shape
subclass of: Restriction
  max cardinality: 1
  on property: dataLocation (slot)
subclass of: Restriction
  max cardinality: 1
  on property: dtype
in scheme: tvbo

Network
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: BidsEntities
  on property: bids (slot)
subclass of: Restriction
  all values from: string
  on property: bids_dir (slot)
subclass of: Restriction
  all values from: CommonCoordinateSpace
  on property: coordinate space
subclass of: Restriction
  all values from: Coupling
  on property: coupling
subclass of: Restriction
  all values from: string
  on property: data_file (slot)
subclass of: Restriction
  all values from: string
  on property: description (slot)
subclass of: Restriction
  all values from: string
  on property: descriptor (slot)
subclass of: Restriction
  all values from: UnitEnum
  on property: distance_unit (slot)
subclass of: Restriction
  all values from: Dynamics
  on property: dynamics
subclass of: Restriction
  all values from: File
  on property: edge_matrix_files (slot)
subclass of: Restriction
  all values from: Edge
  on property: edges (slot)
subclass of: Restriction
  all values from: GraphGenerator
  on property: graph_generator (slot)
subclass of: Restriction
  all values from: string
  on property: label (slot)
subclass of: Restriction
  all values from: string
  on property: node_mapping (slot)
subclass of: Restriction
  all values from: Node
  on property: nodes (slot)
subclass of: Restriction
  all values from: string
  on property: observational_measures (slot)
subclass of: Restriction
  all values from: Parameter
  on property: parameters (slot)
subclass of: Restriction
  all values from: Parcellation
  on property: parcellation (slot)
subclass of: Restriction
  all values from: string
  on property: parent_network (slot)
subclass of: Restriction
  all values from: Provenance
  on property: provenance (slot)
subclass of: Restriction
  all values from: string
  on property: structural_measures (slot)
subclass of: Restriction
  all values from: UnitEnum
  on property: time_unit (slot)
subclass of: Restriction
  all values from: Tractogram
  on property: tractogram (slot)
subclass of: Restriction
  all values from: Function
  on property: transforms (slot)
subclass of: Restriction
  min cardinality: 0
  on property: bids (slot)
subclass of: Restriction
  min cardinality: 0
  on property: coordinate space
subclass of: Restriction
  min cardinality: 0
  on property: coupling
subclass of: Restriction
  min cardinality: 0
  on property: description (slot)
subclass of: Restriction
  min cardinality: 0
  on property: distance_unit (slot)
subclass of: Restriction
  min cardinality: 0
  on property: dynamics
subclass of: Restriction
  min cardinality: 0
  on property: edge_matrix_files (slot)
subclass of: Restriction
  min cardinality: 0
  on property: edges (slot)
subclass of: Restriction
  min cardinality: 0
  on property: graph_generator (slot)
subclass of: Restriction
  min cardinality: 0
  on property: label (slot)
subclass of: Restriction
  min cardinality: 0
  on property: nodes (slot)
subclass of: Restriction
  min cardinality: 0
  on property: parameters (slot)
subclass of: Restriction
  min cardinality: 0
  on property: parcellation (slot)
subclass of: Restriction
  min cardinality: 0
  on property: provenance (slot)
subclass of: Restriction
  min cardinality: 0
  on property: time_unit (slot)
subclass of: Restriction
  min cardinality: 0
  on property: tractogram (slot)
subclass of: Restriction
  min cardinality: 0
  on property: transforms (slot)
subclass of: Restriction
  max cardinality: 1
  on property: bids (slot)
subclass of: Restriction
  max cardinality: 1
  on property: coordinate space
subclass of: Restriction
  max cardinality: 1
  on property: description (slot)
subclass of: Restriction
  max cardinality: 1
  on property: distance_unit (slot)
subclass of: Restriction
  max cardinality: 1
  on property: graph_generator (slot)
subclass of: Restriction
  max cardinality: 1
  on property: label (slot)
subclass of: Restriction
  max cardinality: 1
  on property: parcellation (slot)
subclass of: Restriction
  max cardinality: 1
  on property: provenance (slot)
subclass of: Restriction
  max cardinality: 1
  on property: time_unit (slot)
subclass of: Restriction
  max cardinality: 1
  on property: tractogram (slot)
subclass of: Restriction
  all values from: integer
  on property: number_of_nodes (slot)
subclass of: Restriction
  min cardinality: 0
  on property: bids_dir (slot)
subclass of: Restriction
  min cardinality: 0
  on property: data_file (slot)
subclass of: Restriction
  min cardinality: 0
  on property: descriptor (slot)
subclass of: Restriction
  min cardinality: 0
  on property: node_mapping (slot)
subclass of: Restriction
  min cardinality: 0
  on property: number_of_nodes (slot)
subclass of: Restriction
  min cardinality: 0
  on property: observational_measures (slot)
subclass of: Restriction
  min cardinality: 0
  on property: parent_network (slot)
subclass of: Restriction
  min cardinality: 0
  on property: structural_measures (slot)
subclass of: Restriction
  max cardinality: 1
  on property: bids_dir (slot)
subclass of: Restriction
  max cardinality: 1
  on property: data_file (slot)
subclass of: Restriction
  max cardinality: 1
  on property: descriptor (slot)
subclass of: Restriction
  max cardinality: 1
  on property: node_mapping (slot)
subclass of: Restriction
  max cardinality: 1
  on property: number_of_nodes (slot)
subclass of: Restriction
  max cardinality: 1
  on property: parent_network (slot)
alternative label: Connectivity
alternative label: Connectome
alternative label: Graph
definition: Network specification with nodes, edges, and reusable coupling configurations. Supports both explicit node/edge representation and matrix-based connectivity (Connectome compatibility).
in scheme: tvbo

Node
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: description (slot)
subclass of: Restriction
  all values from: Dynamics
  on property: dynamics
subclass of: Restriction
  all values from: Event
  on property: events
subclass of: Restriction
  all values from: string
  on property: label (slot)
subclass of: Restriction
  all values from: Parameter
  on property: parameters (slot)
subclass of: Restriction
  all values from: Coordinate
  on property: position (slot)
subclass of: Restriction
  all values from: string
  on property: region
subclass of: Restriction
  all values from: StateValue
  on property: state (slot)
subclass of: Restriction
  min cardinality: 0
  on property: description (slot)
subclass of: Restriction
  min cardinality: 0
  on property: dynamics
subclass of: Restriction
  min cardinality: 0
  on property: events
subclass of: Restriction
  min cardinality: 0
  on property: label (slot)
subclass of: Restriction
  min cardinality: 0
  on property: parameters (slot)
subclass of: Restriction
  min cardinality: 0
  on property: position (slot)
subclass of: Restriction
  min cardinality: 0
  on property: state (slot)
subclass of: Restriction
  max cardinality: 1
  on property: description (slot)
subclass of: Restriction
  max cardinality: 1
  on property: dynamics
subclass of: Restriction
  max cardinality: 1
  on property: label (slot)
subclass of: Restriction
  max cardinality: 1
  on property: position (slot)
subclass of: Restriction
  all values from: integer
  on property: id (slot)
subclass of: Restriction
  all values from: boolean
  on property: record (slot)
subclass of: Restriction
  min cardinality: 1
  on property: id (slot)
subclass of: Restriction
  min cardinality: 0
  on property: record (slot)
subclass of: Restriction
  min cardinality: 0
  on property: region
subclass of: Restriction
  max cardinality: 1
  on property: id (slot)
subclass of: Restriction
  max cardinality: 1
  on property: record (slot)
subclass of: Restriction
  max cardinality: 1
  on property: region
definition: A node in a network with its own dynamics and properties
in scheme: tvbo

Noise
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: Equation
  on property: equation (slot)
subclass of: Restriction
  all values from: Function
  on property: function
subclass of: Restriction
  all values from: Parameter
  on property: intensity (slot)
subclass of: Restriction
  all values from: string
  on property: noise_type (slot)
subclass of: Restriction
  all values from: Parameter
  on property: parameters (slot)
subclass of: Restriction
  all values from: string
  on property: pycode
subclass of: Restriction
  all values from: RandomStream
  on property: random_state (slot)
subclass of: Restriction
  all values from: StateVariable
  on property: targets (slot)
subclass of: Restriction
  min cardinality: 0
  on property: equation (slot)
subclass of: Restriction
  min cardinality: 0
  on property: function
subclass of: Restriction
  min cardinality: 0
  on property: intensity (slot)
subclass of: Restriction
  min cardinality: 0
  on property: parameters (slot)
subclass of: Restriction
  min cardinality: 0
  on property: random_state (slot)
subclass of: Restriction
  min cardinality: 0
  on property: targets (slot)
subclass of: Restriction
  max cardinality: 1
  on property: equation (slot)
subclass of: Restriction
  max cardinality: 1
  on property: function
subclass of: Restriction
  max cardinality: 1
  on property: intensity (slot)
subclass of: Restriction
  max cardinality: 1
  on property: random_state (slot)
subclass of: Restriction
  all values from: boolean
  on property: additive (slot)
subclass of: Restriction
  all values from: boolean
  on property: correlated (slot)
subclass of: Restriction
  all values from: boolean
  on property: gaussian (slot)
subclass of: Restriction
  all values from: integer
  on property: seed
subclass of: Restriction
  min cardinality: 0
  on property: additive (slot)
subclass of: Restriction
  min cardinality: 0
  on property: correlated (slot)
subclass of: Restriction
  min cardinality: 0
  on property: gaussian (slot)
subclass of: Restriction
  min cardinality: 0
  on property: noise_type (slot)
subclass of: Restriction
  min cardinality: 0
  on property: pycode
subclass of: Restriction
  min cardinality: 0
  on property: seed
subclass of: Restriction
  max cardinality: 1
  on property: additive (slot)
subclass of: Restriction
  max cardinality: 1
  on property: correlated (slot)
subclass of: Restriction
  max cardinality: 1
  on property: gaussian (slot)
subclass of: Restriction
  max cardinality: 1
  on property: noise_type (slot)
subclass of: Restriction
  max cardinality: 1
  on property: pycode
subclass of: Restriction
  max cardinality: 1
  on property: seed
in scheme: tvbo

NoiseType
type: Class
equivalent class: Class
  union of: brown (NoiseType)
  union of: gaussian (NoiseType)
  union of: pink (NoiseType)
  union of: white (NoiseType)
subclass of: Thing
in scheme: tvbo
permissible values: brown (NoiseType)
permissible values: gaussian (NoiseType)
permissible values: pink (NoiseType)
permissible values: white (NoiseType)

NumericalDiscretizationMethod
type: Class
equivalent class: Class
  union of: collocation (NumericalDiscretizationMethod)
  union of: poincare (NumericalDiscretizationMethod)
  union of: shooting (NumericalDiscretizationMethod)
  union of: trapezoid (NumericalDiscretizationMethod)
subclass of: Thing
definition: Numerical discretization method for boundary value problems (periodic orbits, connecting orbits, quasi-periodic tori).
in scheme: tvbo
permissible values: collocation (NumericalDiscretizationMethod)
permissible values: poincare (NumericalDiscretizationMethod)
permissible values: shooting (NumericalDiscretizationMethod)
permissible values: trapezoid (NumericalDiscretizationMethod)

Observation
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: acronym (slot)
subclass of: Restriction
  all values from: AggregationType
  on property: aggregation
subclass of: Restriction
  all values from: ClassReference
  on property: class_reference (slot)
subclass of: Restriction
  all values from: DataSource
  on property: data source
subclass of: Restriction
  all values from: string
  on property: description (slot)
subclass of: Restriction
  all values from: SoftwareEnvironment (software)
  on property: environment (slot)
subclass of: Restriction
  all values from: Equation
  on property: equation (slot)
subclass of: Restriction
  all values from: ImagingModality
  on property: imaging_modality (slot)
subclass of: Restriction
  all values from: string
  on property: label (slot)
subclass of: Restriction
  all values from: string
  on property: name (slot)
subclass of: Restriction
  all values from: Parameter
  on property: parameters (slot)
subclass of: Restriction
  all values from: FunctionCall
  on property: pipeline (slot)
subclass of: Restriction
  all values from: StateVariable
  on property: source (slot)
subclass of: Restriction
  all values from: UnitEnum
  on property: time_scale (slot)
subclass of: Restriction
  all values from: string
  on property: warmup source
subclass of: Restriction
  min cardinality: 0
  on property: aggregation
subclass of: Restriction
  min cardinality: 0
  on property: class_reference (slot)
subclass of: Restriction
  min cardinality: 0
  on property: data source
subclass of: Restriction
  min cardinality: 0
  on property: description (slot)
subclass of: Restriction
  min cardinality: 0
  on property: environment (slot)
subclass of: Restriction
  min cardinality: 0
  on property: equation (slot)
subclass of: Restriction
  min cardinality: 0
  on property: imaging_modality (slot)
subclass of: Restriction
  min cardinality: 0
  on property: label (slot)
subclass of: Restriction
  min cardinality: 1
  on property: name (slot)
subclass of: Restriction
  min cardinality: 0
  on property: parameters (slot)
subclass of: Restriction
  min cardinality: 0
  on property: pipeline (slot)
subclass of: Restriction
  min cardinality: 0
  on property: source (slot)
subclass of: Restriction
  min cardinality: 0
  on property: time_scale (slot)
subclass of: Restriction
  max cardinality: 1
  on property: aggregation
subclass of: Restriction
  max cardinality: 1
  on property: class_reference (slot)
subclass of: Restriction
  max cardinality: 1
  on property: data source
subclass of: Restriction
  max cardinality: 1
  on property: description (slot)
subclass of: Restriction
  max cardinality: 1
  on property: environment (slot)
subclass of: Restriction
  max cardinality: 1
  on property: equation (slot)
subclass of: Restriction
  max cardinality: 1
  on property: imaging_modality (slot)
subclass of: Restriction
  max cardinality: 1
  on property: label (slot)
subclass of: Restriction
  max cardinality: 1
  on property: name (slot)
subclass of: Restriction
  max cardinality: 1
  on property: source (slot)
subclass of: Restriction
  max cardinality: 1
  on property: time_scale (slot)
subclass of: Restriction
  all values from: float
  on property: downsample_period (slot)
subclass of: Restriction
  all values from: float
  on property: period (slot)
subclass of: Restriction
  all values from: integer
  on property: skip_t (slot)
subclass of: Restriction
  all values from: integer
  on property: tail_samples (slot)
subclass of: Restriction
  all values from: integer
  on property: voi (slot)
subclass of: Restriction
  all values from: integer
  on property: window_size (slot)
subclass of: Restriction
  min cardinality: 0
  on property: acronym (slot)
subclass of: Restriction
  min cardinality: 0
  on property: downsample_period (slot)
subclass of: Restriction
  min cardinality: 0
  on property: period (slot)
subclass of: Restriction
  min cardinality: 0
  on property: skip_t (slot)
subclass of: Restriction
  min cardinality: 0
  on property: tail_samples (slot)
subclass of: Restriction
  min cardinality: 0
  on property: voi (slot)
subclass of: Restriction
  min cardinality: 0
  on property: warmup source
subclass of: Restriction
  min cardinality: 0
  on property: window_size (slot)
subclass of: Restriction
  max cardinality: 1
  on property: acronym (slot)
subclass of: Restriction
  max cardinality: 1
  on property: downsample_period (slot)
subclass of: Restriction
  max cardinality: 1
  on property: period (slot)
subclass of: Restriction
  max cardinality: 1
  on property: skip_t (slot)
subclass of: Restriction
  max cardinality: 1
  on property: tail_samples (slot)
subclass of: Restriction
  max cardinality: 1
  on property: voi (slot)
subclass of: Restriction
  max cardinality: 1
  on property: warmup source
subclass of: Restriction
  max cardinality: 1
  on property: window_size (slot)
definition: 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.
in scheme: tvbo

OperatorType
type: Class
equivalent class: Class
  union of: curl (OperatorType)
  union of: divergence (OperatorType)
  union of: gradient (OperatorType)
  union of: laplacian (OperatorType)
subclass of: Thing
in scheme: tvbo
permissible values: curl (OperatorType)
permissible values: divergence (OperatorType)
permissible values: gradient (OperatorType)
permissible values: laplacian (OperatorType)

Optimization
type: Class
subclass of: OptimizationStage
subclass of: Restriction
  all values from: Algorithm
  on property: depends on
subclass of: Restriction
  all values from: ExecutionConfig
  on property: execution
subclass of: Restriction
  all values from: Integrator
  on property: integration
subclass of: Restriction
  all values from: FunctionCall
  on property: loss (slot)
subclass of: Restriction
  all values from: OptimizationStage
  on property: stages (slot)
subclass of: Restriction
  min cardinality: 0
  on property: depends on
subclass of: Restriction
  min cardinality: 0
  on property: execution
subclass of: Restriction
  min cardinality: 0
  on property: integration
subclass of: Restriction
  min cardinality: 0
  on property: loss (slot)
subclass of: Restriction
  min cardinality: 0
  on property: stages (slot)
subclass of: Restriction
  max cardinality: 1
  on property: depends on
subclass of: Restriction
  max cardinality: 1
  on property: execution
subclass of: Restriction
  max cardinality: 1
  on property: integration
subclass of: Restriction
  max cardinality: 1
  on property: loss (slot)
definition: 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.
in scheme: tvbo

OptimizationStage
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: algorithm
subclass of: Restriction
  all values from: string
  on property: description (slot)
subclass of: Restriction
  all values from: FreeParameter
  on property: free parameters
subclass of: Restriction
  all values from: Parameter
  on property: freeze_parameters (slot)
subclass of: Restriction
  all values from: Parameter
  on property: hyperparameters
subclass of: Restriction
  all values from: string
  on property: label (slot)
subclass of: Restriction
  all values from: string
  on property: name (slot)
subclass of: Restriction
  all values from: OptimizationStage
  on property: warmup_from (slot)
subclass of: Restriction
  min cardinality: 0
  on property: algorithm
subclass of: Restriction
  min cardinality: 0
  on property: description (slot)
subclass of: Restriction
  min cardinality: 0
  on property: free parameters
subclass of: Restriction
  min cardinality: 0
  on property: freeze_parameters (slot)
subclass of: Restriction
  min cardinality: 0
  on property: hyperparameters
subclass of: Restriction
  min cardinality: 0
  on property: label (slot)
subclass of: Restriction
  min cardinality: 1
  on property: name (slot)
subclass of: Restriction
  min cardinality: 0
  on property: warmup_from (slot)
subclass of: Restriction
  max cardinality: 1
  on property: algorithm
subclass of: Restriction
  max cardinality: 1
  on property: description (slot)
subclass of: Restriction
  max cardinality: 1
  on property: label (slot)
subclass of: Restriction
  max cardinality: 1
  on property: name (slot)
subclass of: Restriction
  max cardinality: 1
  on property: warmup_from (slot)
subclass of: Restriction
  all values from: float
  on property: learning rate
subclass of: Restriction
  all values from: integer
  on property: max_iterations (slot)
subclass of: Restriction
  min cardinality: 0
  on property: learning rate
subclass of: Restriction
  min cardinality: 0
  on property: max_iterations (slot)
subclass of: Restriction
  max cardinality: 1
  on property: learning rate
subclass of: Restriction
  max cardinality: 1
  on property: max_iterations (slot)
definition: A single stage in a multi-stage optimization workflow. Stages run sequentially, with each stage potentially using different parameters, shapes, learning rates, and algorithms.
in scheme: tvbo

Option
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: name (slot)
subclass of: Restriction
  all values from: string
  on property: value (slot)
subclass of: Restriction
  min cardinality: 1
  on property: name (slot)
subclass of: Restriction
  min cardinality: 1
  on property: value (slot)
subclass of: Restriction
  max cardinality: 1
  on property: name (slot)
subclass of: Restriction
  max cardinality: 1
  on property: value (slot)
definition: 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).
in scheme: tvbo

Oscillatory
type: Class
subclass of: Dynamical regime
type: NamedIndividual

PDE
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: BoundaryCondition
  on property: boundary conditions
subclass of: Restriction
  all values from: DerivedParameter
  on property: derived parameters
subclass of: Restriction
  all values from: DerivedVariable
  on property: derived variables
subclass of: Restriction
  all values from: string
  on property: description (slot)
subclass of: Restriction
  all values from: SpatialDomain
  on property: domain (slot)
subclass of: Restriction
  all values from: SpatialField
  on property: field (slot)
subclass of: Restriction
  all values from: Function
  on property: functions
subclass of: Restriction
  all values from: string
  on property: label (slot)
subclass of: Restriction
  all values from: Mesh
  on property: mesh
subclass of: Restriction
  all values from: DifferentialOperator
  on property: operators (slot)
subclass of: Restriction
  all values from: Parameter
  on property: parameters (slot)
subclass of: Restriction
  all values from: PDESolver
  on property: solver
subclass of: Restriction
  all values from: Equation
  on property: sources (slot)
subclass of: Restriction
  all values from: FieldStateVariable
  on property: state variables
subclass of: Restriction
  min cardinality: 0
  on property: boundary conditions
subclass of: Restriction
  min cardinality: 0
  on property: derived parameters
subclass of: Restriction
  min cardinality: 0
  on property: derived variables
subclass of: Restriction
  min cardinality: 0
  on property: description (slot)
subclass of: Restriction
  min cardinality: 0
  on property: domain (slot)
subclass of: Restriction
  min cardinality: 0
  on property: field (slot)
subclass of: Restriction
  min cardinality: 0
  on property: functions
subclass of: Restriction
  min cardinality: 0
  on property: label (slot)
subclass of: Restriction
  min cardinality: 0
  on property: mesh
subclass of: Restriction
  min cardinality: 0
  on property: operators (slot)
subclass of: Restriction
  min cardinality: 0
  on property: parameters (slot)
subclass of: Restriction
  min cardinality: 0
  on property: solver
subclass of: Restriction
  min cardinality: 0
  on property: sources (slot)
subclass of: Restriction
  min cardinality: 0
  on property: state variables
subclass of: Restriction
  max cardinality: 1
  on property: description (slot)
subclass of: Restriction
  max cardinality: 1
  on property: domain (slot)
subclass of: Restriction
  max cardinality: 1
  on property: field (slot)
subclass of: Restriction
  max cardinality: 1
  on property: label (slot)
subclass of: Restriction
  max cardinality: 1
  on property: mesh
subclass of: Restriction
  max cardinality: 1
  on property: solver
definition: Partial differential equation problem definition.
in scheme: tvbo

PDESolver
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: description (slot)
subclass of: Restriction
  all values from: DiscretizationMethod
  on property: discretization
subclass of: Restriction
  all values from: SoftwareEnvironment (software)
  on property: environment (slot)
subclass of: Restriction
  all values from: string
  on property: label (slot)
subclass of: Restriction
  all values from: string
  on property: preconditioner (slot)
subclass of: Restriction
  all values from: SoftwareRequirement (software)
  on property: requirements (slot)
subclass of: Restriction
  all values from: string
  on property: time_integrator (slot)
subclass of: Restriction
  all values from: string
  on property: tolerances (slot)
subclass of: Restriction
  min cardinality: 0
  on property: description (slot)
subclass of: Restriction
  min cardinality: 0
  on property: discretization
subclass of: Restriction
  min cardinality: 0
  on property: environment (slot)
subclass of: Restriction
  min cardinality: 0
  on property: label (slot)
subclass of: Restriction
  min cardinality: 0
  on property: requirements (slot)
subclass of: Restriction
  max cardinality: 1
  on property: description (slot)
subclass of: Restriction
  max cardinality: 1
  on property: discretization
subclass of: Restriction
  max cardinality: 1
  on property: environment (slot)
subclass of: Restriction
  max cardinality: 1
  on property: label (slot)
subclass of: Restriction
  all values from: float
  on property: dt (slot)
subclass of: Restriction
  min cardinality: 0
  on property: dt (slot)
subclass of: Restriction
  min cardinality: 0
  on property: preconditioner (slot)
subclass of: Restriction
  min cardinality: 0
  on property: time_integrator (slot)
subclass of: Restriction
  min cardinality: 0
  on property: tolerances (slot)
subclass of: Restriction
  max cardinality: 1
  on property: dt (slot)
subclass of: Restriction
  max cardinality: 1
  on property: preconditioner (slot)
subclass of: Restriction
  max cardinality: 1
  on property: time_integrator (slot)
subclass of: Restriction
  max cardinality: 1
  on property: tolerances (slot)
in scheme: tvbo

Parameter
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: comment (slot)
subclass of: Restriction
  all values from: string
  on property: dataset_path (slot)
subclass of: Restriction
  all values from: string
  on property: default (slot)
subclass of: Restriction
  all values from: string
  on property: definition (slot)
subclass of: Restriction
  all values from: string
  on property: description (slot)
subclass of: Restriction
  all values from: Distribution
  on property: distribution
subclass of: Restriction
  all values from: Range
  on property: domain (slot)
subclass of: Restriction
  all values from: Range
  on property: element domains
subclass of: Restriction
  all values from: Equation
  on property: equation (slot)
subclass of: Restriction
  all values from: string
  on property: label (slot)
subclass of: Restriction
  all values from: string
  on property: name (slot)
subclass of: Restriction
  all values from: string
  on property: shape
subclass of: Restriction
  all values from: string
  on property: symbol (slot)
subclass of: Restriction
  all values from: ScalarValue
  on property: value (slot)
subclass of: Restriction
  min cardinality: 0
  on property: description (slot)
subclass of: Restriction
  min cardinality: 0
  on property: distribution
subclass of: Restriction
  min cardinality: 0
  on property: domain (slot)
subclass of: Restriction
  min cardinality: 0
  on property: element domains
subclass of: Restriction
  min cardinality: 0
  on property: equation (slot)
subclass of: Restriction
  min cardinality: 0
  on property: label (slot)
subclass of: Restriction
  min cardinality: 1
  on property: name (slot)
subclass of: Restriction
  min cardinality: 0
  on property: value (slot)
subclass of: Restriction
  max cardinality: 1
  on property: description (slot)
subclass of: Restriction
  max cardinality: 1
  on property: distribution
subclass of: Restriction
  max cardinality: 1
  on property: domain (slot)
subclass of: Restriction
  max cardinality: 1
  on property: equation (slot)
subclass of: Restriction
  max cardinality: 1
  on property: label (slot)
subclass of: Restriction
  max cardinality: 1
  on property: name (slot)
subclass of: Restriction
  max cardinality: 1
  on property: value (slot)
subclass of: Restriction
  all values from: float
  on property: explored values
subclass of: Restriction
  all values from: boolean
  on property: free (slot)
subclass of: Restriction
  all values from: anyURI
  on property: grounding (slot)
subclass of: Restriction
  all values from: boolean
  on property: heterogeneous
subclass of: Restriction
  all values from: float
  on property: reported_optimum (slot)
subclass of: Restriction
  min cardinality: 0
  on property: comment (slot)
subclass of: Restriction
  min cardinality: 0
  on property: dataset_path (slot)
subclass of: Restriction
  min cardinality: 0
  on property: default (slot)
subclass of: Restriction
  min cardinality: 0
  on property: definition (slot)
subclass of: Restriction
  min cardinality: 0
  on property: explored values
subclass of: Restriction
  min cardinality: 0
  on property: free (slot)
subclass of: Restriction
  min cardinality: 0
  on property: grounding (slot)
subclass of: Restriction
  min cardinality: 0
  on property: heterogeneous
subclass of: Restriction
  min cardinality: 0
  on property: reported_optimum (slot)
subclass of: Restriction
  min cardinality: 0
  on property: shape
subclass of: Restriction
  min cardinality: 0
  on property: symbol (slot)
subclass of: Restriction
  max cardinality: 1
  on property: comment (slot)
subclass of: Restriction
  max cardinality: 1
  on property: dataset_path (slot)
subclass of: Restriction
  max cardinality: 1
  on property: default (slot)
subclass of: Restriction
  max cardinality: 1
  on property: definition (slot)
subclass of: Restriction
  max cardinality: 1
  on property: free (slot)
subclass of: Restriction
  max cardinality: 1
  on property: heterogeneous
subclass of: Restriction
  max cardinality: 1
  on property: reported_optimum (slot)
subclass of: Restriction
  max cardinality: 1
  on property: shape
subclass of: Restriction
  max cardinality: 1
  on property: symbol (slot)
in scheme: tvbo

Parcellation
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: BrainAtlas
  on property: atlas
subclass of: Restriction
  all values from: string
  on property: data source
subclass of: Restriction
  all values from: string
  on property: label (slot)
subclass of: Restriction
  min cardinality: 1
  on property: atlas
subclass of: Restriction
  min cardinality: 0
  on property: data source
subclass of: Restriction
  min cardinality: 0
  on property: label (slot)
subclass of: Restriction
  max cardinality: 1
  on property: atlas
subclass of: Restriction
  max cardinality: 1
  on property: data source
subclass of: Restriction
  max cardinality: 1
  on property: label (slot)
in scheme: tvbo

Period doubling
type: Class
subclass of: Bifurcation

PhysicalDimension
type: Class
equivalent class: Class
  union of: capacitance (PhysicalDimension)
  union of: charge (PhysicalDimension)
  union of: concentration (PhysicalDimension)
  union of: conductance (PhysicalDimension)
  union of: current (PhysicalDimension)
  union of: length (PhysicalDimension)
  union of: none (PhysicalDimension)
  union of: per_time (PhysicalDimension)
  union of: resistance (PhysicalDimension)
  union of: substance (PhysicalDimension)
  union of: temperature (PhysicalDimension)
  union of: time (PhysicalDimension)
  union of: voltage (PhysicalDimension)
  union of: volume (PhysicalDimension)
subclass of: Thing
definition: Physical dimension categories for LEMS and dimensional analysis. Each dimension decomposes into SI base dimensions (M, L, T, I, K, N).
in scheme: units
permissible values: capacitance (PhysicalDimension)
permissible values: charge (PhysicalDimension)
permissible values: concentration (PhysicalDimension)
permissible values: conductance (PhysicalDimension)
permissible values: current (PhysicalDimension)
permissible values: length (PhysicalDimension)
permissible values: none (PhysicalDimension)
permissible values: per_time (PhysicalDimension)
permissible values: resistance (PhysicalDimension)
permissible values: substance (PhysicalDimension)
permissible values: temperature (PhysicalDimension)
permissible values: time (PhysicalDimension)
permissible values: voltage (PhysicalDimension)
permissible values: volume (PhysicalDimension)

Pitchfork
type: Class
subclass of: Bifurcation

ProgrammingLanguageEnum
type: Class
equivalent class: Class
  union of: C
  union of: MATLAB
  union of: JavaScript
  union of: R
  union of: XML
  union of: C#
  union of: C++
  union of: Java
  union of: Python
  union of: Haskell
  union of: Julia
  union of: Rust
  union of: HOC
  union of: Fortran
subclass of: Thing
definition: Programming languages relevant to computational neuroscience tools. Mapped to Wikidata identifiers.
in scheme: software
permissible values: C
permissible values: MATLAB
permissible values: JavaScript
permissible values: R
permissible values: XML
permissible values: C#
permissible values: C++
permissible values: Java
permissible values: Python
permissible values: Haskell
permissible values: Julia
permissible values: Rust
permissible values: HOC
permissible values: Fortran

Provenance
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: date_created (slot)
subclass of: Restriction
  all values from: string
  on property: derived_from (slot)
subclass of: Restriction
  all values from: string
  on property: generated_by (slot)
subclass of: Restriction
  all values from: string
  on property: license (slot)
subclass of: Restriction
  all values from: string
  on property: references (slot)
subclass of: Restriction
  min cardinality: 0
  on property: date_created (slot)
subclass of: Restriction
  min cardinality: 0
  on property: derived_from (slot)
subclass of: Restriction
  min cardinality: 0
  on property: generated_by (slot)
subclass of: Restriction
  min cardinality: 0
  on property: license (slot)
subclass of: Restriction
  min cardinality: 0
  on property: references (slot)
subclass of: Restriction
  max cardinality: 1
  on property: date_created (slot)
subclass of: Restriction
  max cardinality: 1
  on property: derived_from (slot)
subclass of: Restriction
  max cardinality: 1
  on property: generated_by (slot)
subclass of: Restriction
  max cardinality: 1
  on property: license (slot)
definition: W3C PROV-O aligned provenance. Reusable on any entity (Network, TimeSeries, Dynamics, etc.).
in scheme: tvbo

Quiescent
type: Class
subclass of: Dynamical regime
type: NamedIndividual

RandomStream
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: dataLocation
subclass of: Restriction
  all values from: string
  on property: description (slot)
subclass of: Restriction
  all values from: string
  on property: label (slot)
subclass of: Restriction
  min cardinality: 0
  on property: description (slot)
subclass of: Restriction
  min cardinality: 0
  on property: label (slot)
subclass of: Restriction
  max cardinality: 1
  on property: description (slot)
subclass of: Restriction
  max cardinality: 1
  on property: label (slot)
subclass of: Restriction
  min cardinality: 0
  on property: dataLocation
subclass of: Restriction
  max cardinality: 1
  on property: dataLocation
in scheme: tvbo

Range
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: ScalarValue
  on property: hi (slot)
subclass of: Restriction
  all values from: ScalarValue
  on property: lo (slot)
subclass of: Restriction
  all values from: ScalarValue
  on property: step (slot)
subclass of: Restriction
  min cardinality: 0
  on property: hi (slot)
subclass of: Restriction
  min cardinality: 0
  on property: lo (slot)
subclass of: Restriction
  min cardinality: 0
  on property: step (slot)
subclass of: Restriction
  max cardinality: 1
  on property: hi (slot)
subclass of: Restriction
  max cardinality: 1
  on property: lo (slot)
subclass of: Restriction
  max cardinality: 1
  on property: step (slot)
subclass of: Restriction
  all values from: integer
  on property: element (slot)
subclass of: Restriction
  all values from: float
  on property: explored values
subclass of: Restriction
  all values from: boolean
  on property: log_scale (slot)
subclass of: Restriction
  all values from: integer
  on property: n (slot)
subclass of: Restriction
  min cardinality: 0
  on property: element (slot)
subclass of: Restriction
  min cardinality: 0
  on property: explored values
subclass of: Restriction
  min cardinality: 0
  on property: log_scale (slot)
subclass of: Restriction
  min cardinality: 0
  on property: n (slot)
subclass of: Restriction
  max cardinality: 1
  on property: element (slot)
subclass of: Restriction
  max cardinality: 1
  on property: log_scale (slot)
subclass of: Restriction
  max cardinality: 1
  on property: n (slot)
definition: Specifies a range for array generation, parameter bounds, or grid exploration.
in scheme: tvbo

ReductionType
type: Class
equivalent class: Class
  union of: max (ReductionType)
  union of: mean (ReductionType)
  union of: min (ReductionType)
  union of: none (ReductionType)
  union of: sum (ReductionType)
subclass of: Thing
definition: Operations for reducing/aggregating values across dimensions
in scheme: tvbo
permissible values: max (ReductionType)
permissible values: mean (ReductionType)
permissible values: min (ReductionType)
permissible values: none (ReductionType)
permissible values: sum (ReductionType)

RegionMapping
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: dataLocation
subclass of: Restriction
  all values from: string
  on property: description (slot)
subclass of: Restriction
  all values from: string
  on property: label (slot)
subclass of: Restriction
  min cardinality: 0
  on property: description (slot)
subclass of: Restriction
  min cardinality: 0
  on property: label (slot)
subclass of: Restriction
  max cardinality: 1
  on property: description (slot)
subclass of: Restriction
  max cardinality: 1
  on property: label (slot)
subclass of: Restriction
  all values from: integer
  on property: n_regions (slot)
subclass of: Restriction
  all values from: integer
  on property: n_vertices (slot)
subclass of: Restriction
  all values from: integer
  on property: vertex_to_region (slot)
subclass of: Restriction
  min cardinality: 0
  on property: dataLocation
subclass of: Restriction
  min cardinality: 0
  on property: n_regions (slot)
subclass of: Restriction
  min cardinality: 0
  on property: n_vertices (slot)
subclass of: Restriction
  min cardinality: 0
  on property: vertex_to_region (slot)
subclass of: Restriction
  max cardinality: 1
  on property: dataLocation
subclass of: Restriction
  max cardinality: 1
  on property: n_regions (slot)
subclass of: Restriction
  max cardinality: 1
  on property: n_vertices (slot)
definition: Maps vertices to parent regions for hierarchical/aggregated coupling
in scheme: tvbo

RequirementRole
type: Class
equivalent class: Class
  union of: analysis (RequirementRole)
  union of: dev (RequirementRole)
  union of: engine (RequirementRole)
  union of: optional (RequirementRole)
  union of: runtime (RequirementRole)
subclass of: Thing
in scheme: software
permissible values: analysis (RequirementRole)
permissible values: dev (RequirementRole)
permissible values: engine (RequirementRole)
permissible values: optional (RequirementRole)
permissible values: runtime (RequirementRole)

Saddle-node
type: Class
subclass of: Bifurcation
type: NamedIndividual

Sample
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: groups (slot)
subclass of: Restriction
  all values from: integer
  on property: size (slot)
subclass of: Restriction
  min cardinality: 0
  on property: groups (slot)
subclass of: Restriction
  min cardinality: 0
  on property: size (slot)
subclass of: Restriction
  max cardinality: 1
  on property: size (slot)
in scheme: tvbo

SamplingAxis
type: Class
equivalent class: Class
  union of: space (SamplingAxis)
  union of: time (SamplingAxis)
subclass of: Thing
definition: Dimension along which a distribution is sampled.
in scheme: tvbo
permissible values: space (SamplingAxis)
permissible values: time (SamplingAxis)

ScalarValue
type: Class
subclass of: Thing
definition: 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.
in scheme: tvbo

SexEnum
type: Class
equivalent class: Class
  union of: female (SexEnum)
  union of: male (SexEnum)
  union of: other (SexEnum)
subclass of: Thing
in scheme: study
permissible values: female (SexEnum)
permissible values: male (SexEnum)
permissible values: other (SexEnum)

SimulationExperiment
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: Equation
  on property: additional_equations (slot)
subclass of: Restriction
  all values from: Algorithm
  on property: algorithms (slot)
subclass of: Restriction
  all values from: Network
  on property: connectivity (slot)
subclass of: Restriction
  all values from: Continuation
  on property: continuations (slot)
subclass of: Restriction
  all values from: Coupling
  on property: coupling
subclass of: Restriction
  all values from: Dataset (study)
  on property: dataset (slot)
subclass of: Restriction
  all values from: DerivedObservation
  on property: derived_observations (slot)
subclass of: Restriction
  all values from: string
  on property: description (slot)
subclass of: Restriction
  all values from: Dynamics
  on property: dynamics
subclass of: Restriction
  all values from: SoftwareEnvironment (software)
  on property: environment (slot)
subclass of: Restriction
  all values from: Event
  on property: events
subclass of: Restriction
  all values from: ExecutionConfig
  on property: execution
subclass of: Restriction
  all values from: Exploration
  on property: explorations (slot)
subclass of: Restriction
  all values from: PDE
  on property: field_dynamics (slot)
subclass of: Restriction
  all values from: Function
  on property: functions
subclass of: Restriction
  all values from: Integrator
  on property: integration
subclass of: Restriction
  all values from: string
  on property: label (slot)
subclass of: Restriction
  all values from: Dynamics
  on property: model (slot)
subclass of: Restriction
  all values from: Network
  on property: network (slot)
subclass of: Restriction
  all values from: Observation
  on property: observations
subclass of: Restriction
  all values from: Optimization
  on property: optimizations (slot)
subclass of: Restriction
  all values from: string
  on property: references (slot)
subclass of: Restriction
  all values from: SoftwareRequirement (software)
  on property: software
subclass of: Restriction
  all values from: Stimulus
  on property: stimulation (slot)
subclass of: Restriction
  min cardinality: 0
  on property: additional_equations (slot)
subclass of: Restriction
  min cardinality: 0
  on property: algorithms (slot)
subclass of: Restriction
  min cardinality: 0
  on property: connectivity (slot)
subclass of: Restriction
  min cardinality: 0
  on property: continuations (slot)
subclass of: Restriction
  min cardinality: 0
  on property: coupling
subclass of: Restriction
  min cardinality: 0
  on property: dataset (slot)
subclass of: Restriction
  min cardinality: 0
  on property: derived_observations (slot)
subclass of: Restriction
  min cardinality: 0
  on property: description (slot)
subclass of: Restriction
  min cardinality: 0
  on property: dynamics
subclass of: Restriction
  min cardinality: 0
  on property: environment (slot)
subclass of: Restriction
  min cardinality: 0
  on property: events
subclass of: Restriction
  min cardinality: 0
  on property: execution
subclass of: Restriction
  min cardinality: 0
  on property: explorations (slot)
subclass of: Restriction
  min cardinality: 0
  on property: field_dynamics (slot)
subclass of: Restriction
  min cardinality: 0
  on property: functions
subclass of: Restriction
  min cardinality: 0
  on property: integration
subclass of: Restriction
  min cardinality: 0
  on property: label (slot)
subclass of: Restriction
  min cardinality: 0
  on property: model (slot)
subclass of: Restriction
  min cardinality: 0
  on property: network (slot)
subclass of: Restriction
  min cardinality: 0
  on property: observations
subclass of: Restriction
  min cardinality: 0
  on property: optimizations (slot)
subclass of: Restriction
  min cardinality: 0
  on property: software
subclass of: Restriction
  min cardinality: 0
  on property: stimulation (slot)
subclass of: Restriction
  max cardinality: 1
  on property: connectivity (slot)
subclass of: Restriction
  max cardinality: 1
  on property: coupling
subclass of: Restriction
  max cardinality: 1
  on property: dataset (slot)
subclass of: Restriction
  max cardinality: 1
  on property: description (slot)
subclass of: Restriction
  max cardinality: 1
  on property: dynamics
subclass of: Restriction
  max cardinality: 1
  on property: environment (slot)
subclass of: Restriction
  max cardinality: 1
  on property: execution
subclass of: Restriction
  max cardinality: 1
  on property: field_dynamics (slot)
subclass of: Restriction
  max cardinality: 1
  on property: integration
subclass of: Restriction
  max cardinality: 1
  on property: label (slot)
subclass of: Restriction
  max cardinality: 1
  on property: model (slot)
subclass of: Restriction
  max cardinality: 1
  on property: network (slot)
subclass of: Restriction
  max cardinality: 1
  on property: software
subclass of: Restriction
  max cardinality: 1
  on property: stimulation (slot)
subclass of: Restriction
  all values from: integer
  on property: id (slot)
subclass of: Restriction
  min cardinality: 1
  on property: id (slot)
subclass of: Restriction
  min cardinality: 0
  on property: references (slot)
subclass of: Restriction
  max cardinality: 1
  on property: id (slot)
in scheme: tvbo

SimulationScale
type: Class
equivalent class: Class
  union of: network_system
  union of: neuron
  union of: neural_network
  union of: neural_mass
  union of: channel
subclass of: Thing
definition: Spatial / organizational scale at which a tool operates. Multi-valued: a tool can span multiple scales. Mapped to SIO and Wikidata where possible.
in scheme: software
permissible values: network_system
permissible values: neuron
permissible values: neural_network
permissible values: neural_mass
permissible values: channel

SimulationStudy
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: derived_from (slot)
subclass of: Restriction
  all values from: string
  on property: description (slot)
subclass of: Restriction
  all values from: string
  on property: doi (slot)
subclass of: Restriction
  all values from: string
  on property: key
subclass of: Restriction
  all values from: string
  on property: label (slot)
subclass of: Restriction
  all values from: Dynamics
  on property: model (slot)
subclass of: Restriction
  all values from: Sample
  on property: sample (slot)
subclass of: Restriction
  all values from: SimulationExperiment
  on property: simulation_experiments (slot)
subclass of: Restriction
  all values from: string
  on property: title (slot)
subclass of: Restriction
  min cardinality: 0
  on property: description (slot)
subclass of: Restriction
  min cardinality: 0
  on property: label (slot)
subclass of: Restriction
  min cardinality: 0
  on property: model (slot)
subclass of: Restriction
  min cardinality: 0
  on property: sample (slot)
subclass of: Restriction
  min cardinality: 0
  on property: simulation_experiments (slot)
subclass of: Restriction
  max cardinality: 1
  on property: description (slot)
subclass of: Restriction
  max cardinality: 1
  on property: label (slot)
subclass of: Restriction
  max cardinality: 1
  on property: model (slot)
subclass of: Restriction
  max cardinality: 1
  on property: sample (slot)
subclass of: Restriction
  all values from: integer
  on property: year (slot)
subclass of: Restriction
  min cardinality: 0
  on property: derived_from (slot)
subclass of: Restriction
  min cardinality: 0
  on property: doi (slot)
subclass of: Restriction
  min cardinality: 0
  on property: key
subclass of: Restriction
  min cardinality: 0
  on property: title (slot)
subclass of: Restriction
  min cardinality: 0
  on property: year (slot)
subclass of: Restriction
  max cardinality: 1
  on property: derived_from (slot)
subclass of: Restriction
  max cardinality: 1
  on property: doi (slot)
subclass of: Restriction
  max cardinality: 1
  on property: key
subclass of: Restriction
  max cardinality: 1
  on property: title (slot)
subclass of: Restriction
  max cardinality: 1
  on property: year (slot)
in scheme: tvbo

Simulation task
type: Class
subclass of: Thing
comment: A computational task: forward integration in some formalism, parameter exploration, gradient-based optimisation, numerical continuation, or bifurcation analysis.

Software package
type: Class
subclass of: Thing

Solver
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: method
subclass of: Restriction
  min cardinality: 0
  on property: method
subclass of: Restriction
  max cardinality: 1
  on property: method
subclass of: Restriction
  all values from: float
  on property: abs tol
subclass of: Restriction
  all values from: float
  on property: rel tol
subclass of: Restriction
  min cardinality: 0
  on property: abs tol
subclass of: Restriction
  min cardinality: 0
  on property: rel tol
subclass of: Restriction
  max cardinality: 1
  on property: abs tol
subclass of: Restriction
  max cardinality: 1
  on property: rel tol
definition: 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.
in scheme: tvbo

SparseFormat
type: Class
equivalent class: Class
  union of: coo (SparseFormat)
  union of: csr (SparseFormat)
  union of: dense (SparseFormat)
subclass of: Thing
in scheme: tvbo
permissible values: coo (SparseFormat)
permissible values: csr (SparseFormat)
permissible values: dense (SparseFormat)

SpatialDomain
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: CommonCoordinateSpace
  on property: coordinate space
subclass of: Restriction
  all values from: string
  on property: description (slot)
subclass of: Restriction
  all values from: string
  on property: geometry (slot)
subclass of: Restriction
  all values from: string
  on property: label (slot)
subclass of: Restriction
  all values from: string
  on property: region
subclass of: Restriction
  min cardinality: 0
  on property: coordinate space
subclass of: Restriction
  min cardinality: 0
  on property: description (slot)
subclass of: Restriction
  min cardinality: 0
  on property: label (slot)
subclass of: Restriction
  max cardinality: 1
  on property: coordinate space
subclass of: Restriction
  max cardinality: 1
  on property: description (slot)
subclass of: Restriction
  max cardinality: 1
  on property: label (slot)
subclass of: Restriction
  min cardinality: 0
  on property: geometry (slot)
subclass of: Restriction
  min cardinality: 0
  on property: region
subclass of: Restriction
  max cardinality: 1
  on property: geometry (slot)
subclass of: Restriction
  max cardinality: 1
  on property: region
in scheme: tvbo

SpatialField
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: description (slot)
subclass of: Restriction
  all values from: Equation
  on property: initial_expression (slot)
subclass of: Restriction
  all values from: string
  on property: label (slot)
subclass of: Restriction
  all values from: Mesh
  on property: mesh
subclass of: Restriction
  all values from: string
  on property: quantity_kind (slot)
subclass of: Restriction
  all values from: NDArray
  on property: values
subclass of: Restriction
  min cardinality: 0
  on property: description (slot)
subclass of: Restriction
  min cardinality: 0
  on property: initial_expression (slot)
subclass of: Restriction
  min cardinality: 0
  on property: initial value
subclass of: Restriction
  min cardinality: 0
  on property: label (slot)
subclass of: Restriction
  min cardinality: 0
  on property: mesh
subclass of: Restriction
  min cardinality: 0
  on property: values
subclass of: Restriction
  max cardinality: 1
  on property: description (slot)
subclass of: Restriction
  max cardinality: 1
  on property: initial_expression (slot)
subclass of: Restriction
  max cardinality: 1
  on property: initial value
subclass of: Restriction
  max cardinality: 1
  on property: label (slot)
subclass of: Restriction
  max cardinality: 1
  on property: mesh
subclass of: Restriction
  max cardinality: 1
  on property: values
subclass of: Restriction
  all values from: float
  on property: initial value
subclass of: Restriction
  all values from: boolean
  on property: time dependent
subclass of: Restriction
  min cardinality: 0
  on property: quantity_kind (slot)
subclass of: Restriction
  min cardinality: 0
  on property: time dependent
subclass of: Restriction
  max cardinality: 1
  on property: quantity_kind (slot)
subclass of: Restriction
  max cardinality: 1
  on property: time dependent
in scheme: tvbo

SpecimenEnum
type: Class
equivalent class: Class
  union of: Subject (SpecimenEnum)
  union of: SubjectGroup (SpecimenEnum)
  union of: TissueSample (SpecimenEnum)
  union of: TissueSampleCollection (SpecimenEnum)
subclass of: Thing
definition: A set of permissible types for specimens used in brain atlas creation.
in scheme: BrainAtlas
permissible values: Subject (SpecimenEnum)
permissible values: SubjectGroup (SpecimenEnum)
permissible values: TissueSample (SpecimenEnum)
permissible values: TissueSampleCollection (SpecimenEnum)

StandardGraphType
type: Class
equivalent class: Class
  union of: BarabasiAlbert (StandardGraphType)
  union of: Complete (StandardGraphType)
  union of: Cycle (StandardGraphType)
  union of: ErdosRenyi (StandardGraphType)
  union of: Grid (StandardGraphType)
  union of: RandomRegular (StandardGraphType)
  union of: Star (StandardGraphType)
  union of: WattsStrogatz (StandardGraphType)
subclass of: Thing
definition: 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).
in scheme: tvbo
permissible values: BarabasiAlbert (StandardGraphType)
permissible values: Complete (StandardGraphType)
permissible values: Cycle (StandardGraphType)
permissible values: ErdosRenyi (StandardGraphType)
permissible values: Grid (StandardGraphType)
permissible values: RandomRegular (StandardGraphType)
permissible values: Star (StandardGraphType)
permissible values: WattsStrogatz (StandardGraphType)

StateValue
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: name (slot)
subclass of: Restriction
  all values from: ScalarValue
  on property: value (slot)
subclass of: Restriction
  min cardinality: 1
  on property: name (slot)
subclass of: Restriction
  min cardinality: 0
  on property: value (slot)
subclass of: Restriction
  max cardinality: 1
  on property: name (slot)
subclass of: Restriction
  max cardinality: 1
  on property: value (slot)
definition: A named state variable value for per-node initialization.
in scheme: tvbo

StateVariable
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: Range
  on property: boundaries (slot)
subclass of: Restriction
  all values from: string
  on property: definition (slot)
subclass of: Restriction
  all values from: string
  on property: description (slot)
subclass of: Restriction
  all values from: Distribution
  on property: distribution
subclass of: Restriction
  all values from: Range
  on property: domain (slot)
subclass of: Restriction
  all values from: Equation
  on property: equation (slot)
subclass of: Restriction
  all values from: string
  on property: equation_type (slot)
subclass of: Restriction
  all values from: TimeSeries
  on property: history (slot)
subclass of: Restriction
  all values from: string
  on property: label (slot)
subclass of: Restriction
  all values from: string
  on property: name (slot)
subclass of: Restriction
  all values from: Noise
  on property: noise
subclass of: Restriction
  all values from: string
  on property: symbol (slot)
subclass of: Restriction
  min cardinality: 0
  on property: boundaries (slot)
subclass of: Restriction
  min cardinality: 0
  on property: description (slot)
subclass of: Restriction
  min cardinality: 0
  on property: distribution
subclass of: Restriction
  min cardinality: 0
  on property: domain (slot)
subclass of: Restriction
  min cardinality: 0
  on property: equation (slot)
subclass of: Restriction
  min cardinality: 0
  on property: history (slot)
subclass of: Restriction
  min cardinality: 0
  on property: initial value
subclass of: Restriction
  min cardinality: 0
  on property: label (slot)
subclass of: Restriction
  min cardinality: 1
  on property: name (slot)
subclass of: Restriction
  min cardinality: 0
  on property: noise
subclass of: Restriction
  max cardinality: 1
  on property: boundaries (slot)
subclass of: Restriction
  max cardinality: 1
  on property: description (slot)
subclass of: Restriction
  max cardinality: 1
  on property: distribution
subclass of: Restriction
  max cardinality: 1
  on property: domain (slot)
subclass of: Restriction
  max cardinality: 1
  on property: equation (slot)
subclass of: Restriction
  max cardinality: 1
  on property: history (slot)
subclass of: Restriction
  max cardinality: 1
  on property: initial value
subclass of: Restriction
  max cardinality: 1
  on property: label (slot)
subclass of: Restriction
  max cardinality: 1
  on property: name (slot)
subclass of: Restriction
  max cardinality: 1
  on property: noise
subclass of: Restriction
  all values from: boolean
  on property: coupling_variable (slot)
subclass of: Restriction
  all values from: float
  on property: derivative_initial_value (slot)
subclass of: Restriction
  all values from: integer
  on property: equation_order (slot)
subclass of: Restriction
  all values from: anyURI
  on property: grounding (slot)
subclass of: Restriction
  all values from: float
  on property: initial value
subclass of: Restriction
  all values from: boolean
  on property: record (slot)
subclass of: Restriction
  all values from: boolean
  on property: stimulation_variable (slot)
subclass of: Restriction
  all values from: boolean
  on property: variable_of_interest (slot)
subclass of: Restriction
  min cardinality: 0
  on property: coupling_variable (slot)
subclass of: Restriction
  min cardinality: 0
  on property: definition (slot)
subclass of: Restriction
  min cardinality: 0
  on property: derivative_initial_value (slot)
subclass of: Restriction
  min cardinality: 0
  on property: equation_order (slot)
subclass of: Restriction
  min cardinality: 0
  on property: equation_type (slot)
subclass of: Restriction
  min cardinality: 0
  on property: grounding (slot)
subclass of: Restriction
  min cardinality: 0
  on property: record (slot)
subclass of: Restriction
  min cardinality: 0
  on property: stimulation_variable (slot)
subclass of: Restriction
  min cardinality: 0
  on property: symbol (slot)
subclass of: Restriction
  min cardinality: 0
  on property: variable_of_interest (slot)
subclass of: Restriction
  max cardinality: 1
  on property: coupling_variable (slot)
subclass of: Restriction
  max cardinality: 1
  on property: definition (slot)
subclass of: Restriction
  max cardinality: 1
  on property: derivative_initial_value (slot)
subclass of: Restriction
  max cardinality: 1
  on property: equation_order (slot)
subclass of: Restriction
  max cardinality: 1
  on property: equation_type (slot)
subclass of: Restriction
  max cardinality: 1
  on property: record (slot)
subclass of: Restriction
  max cardinality: 1
  on property: stimulation_variable (slot)
subclass of: Restriction
  max cardinality: 1
  on property: symbol (slot)
subclass of: Restriction
  max cardinality: 1
  on property: variable_of_interest (slot)
in scheme: tvbo

Stimulus
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: dataLocation
subclass of: Restriction
  all values from: string
  on property: description (slot)
subclass of: Restriction
  all values from: Equation
  on property: equation (slot)
subclass of: Restriction
  all values from: string
  on property: label (slot)
subclass of: Restriction
  all values from: Parameter
  on property: parameters (slot)
subclass of: Restriction
  min cardinality: 0
  on property: description (slot)
subclass of: Restriction
  min cardinality: 0
  on property: equation (slot)
subclass of: Restriction
  min cardinality: 0
  on property: label (slot)
subclass of: Restriction
  min cardinality: 0
  on property: parameters (slot)
subclass of: Restriction
  max cardinality: 1
  on property: description (slot)
subclass of: Restriction
  max cardinality: 1
  on property: equation (slot)
subclass of: Restriction
  max cardinality: 1
  on property: label (slot)
subclass of: Restriction
  all values from: float
  on property: duration (slot)
subclass of: Restriction
  all values from: integer
  on property: regions
subclass of: Restriction
  all values from: float
  on property: weighting
subclass of: Restriction
  min cardinality: 0
  on property: dataLocation
subclass of: Restriction
  min cardinality: 0
  on property: duration (slot)
subclass of: Restriction
  min cardinality: 0
  on property: regions
subclass of: Restriction
  min cardinality: 0
  on property: weighting
subclass of: Restriction
  max cardinality: 1
  on property: dataLocation
subclass of: Restriction
  max cardinality: 1
  on property: duration (slot)
in scheme: tvbo

Stochasticity character
type: Class
subclass of: Dynamical property
comment: Stochasticity character of the model definition itself, independent of any optional integrator-level noise injection.

Strange attractor
type: Class
subclass of: Attractor
type: NamedIndividual

Subcritical Hopf
type: Class
subclass of: Hopf

Supercritical Hopf
type: Class
subclass of: Hopf
type: NamedIndividual

SystemType
type: Class
equivalent class: Class
  union of: continuous (SystemType)
  union of: discrete (SystemType)
subclass of: Thing
in scheme: tvbo
permissible values: continuous (SystemType)
permissible values: discrete (SystemType)

TemporalApplicableEquation
type: Class
subclass of: Equation
subclass of: Restriction
  all values from: Parameter
  on property: parameters (slot)
subclass of: Restriction
  min cardinality: 0
  on property: parameters (slot)
subclass of: Restriction
  all values from: boolean
  on property: time dependent
subclass of: Restriction
  min cardinality: 0
  on property: time dependent
subclass of: Restriction
  max cardinality: 1
  on property: time dependent
in scheme: tvbo

TimeSeries
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: dataLocation
subclass of: Restriction
  all values from: string
  on property: connectivity_ref (slot)
subclass of: Restriction
  all values from: Matrix
  on property: data (slot)
subclass of: Restriction
  all values from: string
  on property: description (slot)
subclass of: Restriction
  all values from: string
  on property: label (slot)
subclass of: Restriction
  all values from: string
  on property: labels_dimensions (slot)
subclass of: Restriction
  all values from: string
  on property: labels_ordering (slot)
subclass of: Restriction
  all values from: ImagingModality
  on property: modality (slot)
subclass of: Restriction
  all values from: string
  on property: model_equation_ref (slot)
subclass of: Restriction
  all values from: string
  on property: model_param_ref (slot)
subclass of: Restriction
  all values from: string
  on property: sampling_period_unit (slot)
subclass of: Restriction
  all values from: string
  on property: session_id (slot)
subclass of: Restriction
  all values from: SoftwareEnvironment (software)
  on property: software_environment (slot)
subclass of: Restriction
  all values from: SimulationExperiment
  on property: source_experiment (slot)
subclass of: Restriction
  all values from: string
  on property: subject_id (slot)
subclass of: Restriction
  all values from: string
  on property: task_name (slot)
subclass of: Restriction
  all values from: Matrix
  on property: time (slot)
subclass of: Restriction
  min cardinality: 0
  on property: data (slot)
subclass of: Restriction
  min cardinality: 0
  on property: description (slot)
subclass of: Restriction
  min cardinality: 0
  on property: label (slot)
subclass of: Restriction
  min cardinality: 0
  on property: modality (slot)
subclass of: Restriction
  min cardinality: 0
  on property: software_environment (slot)
subclass of: Restriction
  min cardinality: 0
  on property: source_experiment (slot)
subclass of: Restriction
  min cardinality: 0
  on property: time (slot)
subclass of: Restriction
  max cardinality: 1
  on property: data (slot)
subclass of: Restriction
  max cardinality: 1
  on property: description (slot)
subclass of: Restriction
  max cardinality: 1
  on property: label (slot)
subclass of: Restriction
  max cardinality: 1
  on property: modality (slot)
subclass of: Restriction
  max cardinality: 1
  on property: software_environment (slot)
subclass of: Restriction
  max cardinality: 1
  on property: source_experiment (slot)
subclass of: Restriction
  max cardinality: 1
  on property: time (slot)
subclass of: Restriction
  all values from: dateTime
  on property: generated_at (slot)
subclass of: Restriction
  all values from: integer
  on property: run_id (slot)
subclass of: Restriction
  all values from: float
  on property: sampling_period (slot)
subclass of: Restriction
  all values from: float
  on property: sampling_rate (slot)
subclass of: Restriction
  min cardinality: 0
  on property: dataLocation
subclass of: Restriction
  min cardinality: 0
  on property: connectivity_ref (slot)
subclass of: Restriction
  min cardinality: 0
  on property: generated_at (slot)
subclass of: Restriction
  min cardinality: 0
  on property: labels_dimensions (slot)
subclass of: Restriction
  min cardinality: 0
  on property: labels_ordering (slot)
subclass of: Restriction
  min cardinality: 0
  on property: model_equation_ref (slot)
subclass of: Restriction
  min cardinality: 0
  on property: model_param_ref (slot)
subclass of: Restriction
  min cardinality: 0
  on property: run_id (slot)
subclass of: Restriction
  min cardinality: 0
  on property: sampling_period (slot)
subclass of: Restriction
  min cardinality: 0
  on property: sampling_period_unit (slot)
subclass of: Restriction
  min cardinality: 0
  on property: sampling_rate (slot)
subclass of: Restriction
  min cardinality: 1
  on property: session_id (slot)
subclass of: Restriction
  min cardinality: 1
  on property: subject_id (slot)
subclass of: Restriction
  min cardinality: 0
  on property: task_name (slot)
subclass of: Restriction
  max cardinality: 1
  on property: dataLocation
subclass of: Restriction
  max cardinality: 1
  on property: connectivity_ref (slot)
subclass of: Restriction
  max cardinality: 1
  on property: generated_at (slot)
subclass of: Restriction
  max cardinality: 1
  on property: labels_dimensions (slot)
subclass of: Restriction
  max cardinality: 1
  on property: model_equation_ref (slot)
subclass of: Restriction
  max cardinality: 1
  on property: model_param_ref (slot)
subclass of: Restriction
  max cardinality: 1
  on property: run_id (slot)
subclass of: Restriction
  max cardinality: 1
  on property: sampling_period (slot)
subclass of: Restriction
  max cardinality: 1
  on property: sampling_period_unit (slot)
subclass of: Restriction
  max cardinality: 1
  on property: sampling_rate (slot)
subclass of: Restriction
  max cardinality: 1
  on property: session_id (slot)
subclass of: Restriction
  max cardinality: 1
  on property: subject_id (slot)
subclass of: Restriction
  max cardinality: 1
  on property: task_name (slot)
definition: Time series data from simulations or measurements. Supports BIDS-compatible export for computational modeling (BEP034).
in scheme: tvbo
note: Supports BIDS BEP034 computational modeling extension.
note: Use to_bids() method in Python class to export as BIDS dataset.

ToolRole
type: Class
equivalent class: Class
  union of: simulator
  union of: specification_language
  union of: framework
  union of: model_repository
  union of: optimization_framework
  union of: bifurcation_analysis
  union of: visualization_tool
  union of: analysis_tool
  union of: backend_runtime (ToolRole)
  union of: workflow_framework (ToolRole)
subclass of: Thing
definition: Primary function of the tool in a simulation workflow.
in scheme: software
permissible values: simulator
permissible values: specification_language
permissible values: framework
permissible values: model_repository
permissible values: optimization_framework
permissible values: bifurcation_analysis
permissible values: visualization_tool
permissible values: analysis_tool
permissible values: backend_runtime (ToolRole)
permissible values: workflow_framework (ToolRole)

Torus
type: Class
subclass of: Attractor
type: NamedIndividual

Tractogram
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: acquisition
subclass of: Restriction
  all values from: string
  on property: data source
subclass of: Restriction
  all values from: string
  on property: description (slot)
subclass of: Restriction
  all values from: string
  on property: label (slot)
subclass of: Restriction
  all values from: string
  on property: name (slot)
subclass of: Restriction
  all values from: string
  on property: processing_pipeline (slot)
subclass of: Restriction
  all values from: string
  on property: reference (slot)
subclass of: Restriction
  min cardinality: 0
  on property: data source
subclass of: Restriction
  min cardinality: 0
  on property: description (slot)
subclass of: Restriction
  min cardinality: 0
  on property: label (slot)
subclass of: Restriction
  min cardinality: 1
  on property: name (slot)
subclass of: Restriction
  max cardinality: 1
  on property: data source
subclass of: Restriction
  max cardinality: 1
  on property: description (slot)
subclass of: Restriction
  max cardinality: 1
  on property: label (slot)
subclass of: Restriction
  max cardinality: 1
  on property: name (slot)
subclass of: Restriction
  all values from: integer
  on property: number_of_subjects (slot)
subclass of: Restriction
  min cardinality: 0
  on property: acquisition
subclass of: Restriction
  min cardinality: 0
  on property: number_of_subjects (slot)
subclass of: Restriction
  min cardinality: 0
  on property: processing_pipeline (slot)
subclass of: Restriction
  min cardinality: 0
  on property: reference (slot)
subclass of: Restriction
  max cardinality: 1
  on property: acquisition
subclass of: Restriction
  max cardinality: 1
  on property: number_of_subjects (slot)
subclass of: Restriction
  max cardinality: 1
  on property: processing_pipeline (slot)
subclass of: Restriction
  max cardinality: 1
  on property: reference (slot)
definition: Reference to tractography/diffusion MRI data used to derive structural connectivity
in scheme: tvbo

Transcritical
type: Class
subclass of: Bifurcation

TuningObjective
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: description (slot)
subclass of: Restriction
  all values from: string
  on property: label (slot)
subclass of: Restriction
  all values from: Equation
  on property: metric (slot)
subclass of: Restriction
  all values from: Observation
  on property: target_data (slot)
subclass of: Restriction
  all values from: StateVariable
  on property: target_variable (slot)
subclass of: Restriction
  all values from: string
  on property: type
subclass of: Restriction
  min cardinality: 0
  on property: description (slot)
subclass of: Restriction
  min cardinality: 0
  on property: label (slot)
subclass of: Restriction
  min cardinality: 0
  on property: metric (slot)
subclass of: Restriction
  min cardinality: 0
  on property: target_data (slot)
subclass of: Restriction
  min cardinality: 0
  on property: target_variable (slot)
subclass of: Restriction
  min cardinality: 0
  on property: type
subclass of: Restriction
  max cardinality: 1
  on property: description (slot)
subclass of: Restriction
  max cardinality: 1
  on property: label (slot)
subclass of: Restriction
  max cardinality: 1
  on property: metric (slot)
subclass of: Restriction
  max cardinality: 1
  on property: target_data (slot)
subclass of: Restriction
  max cardinality: 1
  on property: target_variable (slot)
subclass of: Restriction
  max cardinality: 1
  on property: type
subclass of: Restriction
  all values from: float
  on property: target_value (slot)
subclass of: Restriction
  min cardinality: 0
  on property: target_value (slot)
subclass of: Restriction
  max cardinality: 1
  on property: target_value (slot)
definition: Defines what the tuning algorithm optimizes for. Can be an activity target (FIC) or a connectivity target (EIB).
in scheme: tvbo

UnitEnum
type: Class
equivalent class: Class
  union of: A
  union of: cm
  union of: degC
  union of: H_per_m
  union of: Hz
  union of: kg
  union of: kHz
  union of: m
  union of: m_per_s
  union of: m_per_s2
  union of: mol_per_m3
  union of: um3
  union of: uS
  union of: us
  union of: mm
  union of: mm_per_ms
  union of: mmol_per_m3
  union of: ms
  union of: mV
  union of: mV_per_ms
  union of: mV_per_s
  union of: N_per_m
  union of: nA
  union of: nF
  union of: nS
  union of: ohm
  union of: per_ms
  union of: per_mV
  union of: per_nC
  union of: per_pC
  union of: per_s
  union of: percent
  union of: pA
  union of: pF
  union of: pS
  union of: rad
  union of: rad_per_s
  union of: S_per_m
  union of: s
  union of: s2
  union of: dimensionless
  union of: V
  union of: Hz_per_nA (UnitEnum)
  union of: Mohm (UnitEnum)
  union of: S_per_cm2 (UnitEnum)
  union of: S_per_m2 (UnitEnum)
  union of: arbitrary_unit (UnitEnum)
  union of: kg_per_s (UnitEnum)
  union of: kohm_cm (UnitEnum)
  union of: mS_per_cm2 (UnitEnum)
  union of: mol_per_cm3 (UnitEnum)
  union of: mol_per_m_per_A_per_s (UnitEnum)
  union of: nS_per_mV (UnitEnum)
  union of: per_unit (UnitEnum)
  union of: rad_per_ms (UnitEnum)
  union of: uA_per_cm2 (UnitEnum)
  union of: uF_per_cm2 (UnitEnum)
subclass of: Thing
definition: 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.
in scheme: units
permissible values: A
permissible values: cm
permissible values: degC
permissible values: H_per_m
permissible values: Hz
permissible values: kg
permissible values: kHz
permissible values: m
permissible values: m_per_s
permissible values: m_per_s2
permissible values: mol_per_m3
permissible values: um3
permissible values: uS
permissible values: us
permissible values: mm
permissible values: mm_per_ms
permissible values: mmol_per_m3
permissible values: ms
permissible values: mV
permissible values: mV_per_ms
permissible values: mV_per_s
permissible values: N_per_m
permissible values: nA
permissible values: nF
permissible values: nS
permissible values: ohm
permissible values: per_ms
permissible values: per_mV
permissible values: per_nC
permissible values: per_pC
permissible values: per_s
permissible values: percent
permissible values: pA
permissible values: pF
permissible values: pS
permissible values: rad
permissible values: rad_per_s
permissible values: S_per_m
permissible values: s
permissible values: s2
permissible values: dimensionless
permissible values: V
permissible values: Hz_per_nA (UnitEnum)
permissible values: Mohm (UnitEnum)
permissible values: S_per_cm2 (UnitEnum)
permissible values: S_per_m2 (UnitEnum)
permissible values: arbitrary_unit (UnitEnum)
permissible values: kg_per_s (UnitEnum)
permissible values: kohm_cm (UnitEnum)
permissible values: mS_per_cm2 (UnitEnum)
permissible values: mol_per_cm3 (UnitEnum)
permissible values: mol_per_m_per_A_per_s (UnitEnum)
permissible values: nS_per_mV (UnitEnum)
permissible values: per_unit (UnitEnum)
permissible values: rad_per_ms (UnitEnum)
permissible values: uA_per_cm2 (UnitEnum)
permissible values: uF_per_cm2 (UnitEnum)

UpdateRule
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: Range
  on property: bounds (slot)
subclass of: Restriction
  all values from: string
  on property: description (slot)
subclass of: Restriction
  all values from: Equation
  on property: equation (slot)
subclass of: Restriction
  all values from: string
  on property: name (slot)
subclass of: Restriction
  all values from: Observation
  on property: requires (slot)
subclass of: Restriction
  all values from: Parameter
  on property: target_parameter (slot)
subclass of: Restriction
  min cardinality: 0
  on property: bounds (slot)
subclass of: Restriction
  min cardinality: 0
  on property: description (slot)
subclass of: Restriction
  min cardinality: 1
  on property: equation (slot)
subclass of: Restriction
  min cardinality: 1
  on property: name (slot)
subclass of: Restriction
  min cardinality: 0
  on property: requires (slot)
subclass of: Restriction
  min cardinality: 1
  on property: target_parameter (slot)
subclass of: Restriction
  max cardinality: 1
  on property: bounds (slot)
subclass of: Restriction
  max cardinality: 1
  on property: description (slot)
subclass of: Restriction
  max cardinality: 1
  on property: equation (slot)
subclass of: Restriction
  max cardinality: 1
  on property: name (slot)
subclass of: Restriction
  max cardinality: 1
  on property: target_parameter (slot)
subclass of: Restriction
  all values from: boolean
  on property: warmup (slot)
subclass of: Restriction
  min cardinality: 0
  on property: warmup (slot)
subclass of: Restriction
  max cardinality: 1
  on property: warmup (slot)
definition: 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.
in scheme: tvbo

first (AggregationType)
type: Class
subclass of: AggregationType
definition: First value in window
notation: first

last (AggregationType)
type: Class
subclass of: AggregationType
definition: Last value in window
notation: last

mean (AggregationType)
type: Class
subclass of: AggregationType
definition: Average over time
notation: mean

none (AggregationType)
type: Class
subclass of: AggregationType
definition: No aggregation
notation: none

window (AggregationType)
type: Class
subclass of: AggregationType
definition: Sliding window aggregation
notation: window

Dirichlet (BoundaryConditionType)
type: Class
subclass of: BoundaryConditionType
notation: Dirichlet

Neumann (BoundaryConditionType)
type: Class
subclass of: BoundaryConditionType
notation: Neumann

Periodic (BoundaryConditionType)
type: Class
subclass of: BoundaryConditionType
notation: Periodic

Robin (BoundaryConditionType)
type: Class
subclass of: BoundaryConditionType
notation: Robin

MoorePenrose (ContinuationAlgorithm)
type: Class
subclass of: ContinuationAlgorithm
definition: Moore-Penrose continuation.
notation: MoorePenrose

Natural (ContinuationAlgorithm)
type: Class
subclass of: ContinuationAlgorithm
definition: Natural parameter continuation. Simple parameter stepping, no arc-length constraint.
notation: Natural

PALC (ContinuationAlgorithm)
type: Class
subclass of: ContinuationAlgorithm
definition: Pseudo-arclength continuation (default). Uses weighted dot product constraint.
notation: PALC

active (DevelopmentStatus)
type: Class
subclass of: DevelopmentStatus
definition: Actively developed with regular releases.
notation: active

concept (DevelopmentStatus)
type: Class
subclass of: DevelopmentStatus
definition: Minimal or no implementation; ideas / prototypes.
notation: concept

inactive (DevelopmentStatus)
type: Class
subclass of: DevelopmentStatus
definition: No longer actively developed; may still work.
notation: inactive

moved (DevelopmentStatus)
type: Class
subclass of: DevelopmentStatus
definition: Project has been moved to a different location.
notation: moved

suspended (DevelopmentStatus)
type: Class
subclass of: DevelopmentStatus
definition: Development paused; may resume in future.
notation: suspended

unsupported (DevelopmentStatus)
type: Class
subclass of: DevelopmentStatus
definition: Released but no longer supported.
notation: unsupported

wip (DevelopmentStatus)
type: Class
subclass of: DevelopmentStatus
definition: Work in progress; not yet feature-complete.
notation: wip

batch (DimensionType)
type: Class
subclass of: DimensionType
definition: Batch dimension (for parallel processing)
notation: batch

frequency (DimensionType)
type: Class
subclass of: DimensionType
definition: Frequency dimension (spectral analysis)
notation: frequency

mode (DimensionType)
type: Class
subclass of: DimensionType
definition: Mode dimension (e.g., coupling modes)
notation: mode

node (DimensionType)
type: Class
subclass of: DimensionType
definition: Network node dimension (general graph term)
notation: node

region (DimensionType)
type: Class
subclass of: DimensionType
definition: Spatial/regional dimension (alias for node in brain networks)
notation: region

sample (DimensionType)
type: Class
subclass of: DimensionType
definition: Sample/trial/realization dimension
notation: sample

state (DimensionType)
type: Class
subclass of: DimensionType
definition: State variable dimension
notation: state

time (DimensionType)
type: Class
subclass of: DimensionType
definition: Temporal dimension
notation: time

FDM (DiscretizationMethod)
type: Class
subclass of: DiscretizationMethod
definition: Finite Difference Method
notation: FDM

FEM (DiscretizationMethod)
type: Class
subclass of: DiscretizationMethod
definition: Finite Element Method
notation: FEM

FVM (DiscretizationMethod)
type: Class
subclass of: DiscretizationMethod
definition: Finite Volume Method
notation: FVM

Spectral (DiscretizationMethod)
type: Class
subclass of: DiscretizationMethod
notation: Spectral

bioconda (EcosystemEnum)
type: Class
subclass of: EcosystemEnum
definition: Bioinformatics Conda channel.
notation: bioconda

github (EcosystemEnum)
type: Class
subclass of: EcosystemEnum
definition: Distributed via GitHub releases.
notation: github

julia_registry (EcosystemEnum)
type: Class
subclass of: EcosystemEnum
definition: Julia General package registry.
notation: julia_registry

hexahedron (ElementType)
type: Class
subclass of: ElementType
notation: hexahedron

quad (ElementType)
type: Class
subclass of: ElementType
notation: quad

tetrahedron (ElementType)
type: Class
subclass of: ElementType
notation: tetrahedron

triangle (ElementType)
type: Class
subclass of: ElementType
notation: triangle

conda (EnvironmentType)
type: Class
subclass of: EnvironmentType
definition: Conda environment.
notation: conda

docker (EnvironmentType)
type: Class
subclass of: EnvironmentType
definition: Docker container.
notation: docker

singularity (EnvironmentType)
type: Class
subclass of: EnvironmentType
definition: Singularity/Apptainer container.
notation: singularity

venv (EnvironmentType)
type: Class
subclass of: EnvironmentType
definition: Python virtual environment.
notation: venv

continuous (EventType)
type: Class
subclass of: EventType
definition: Triggered when condition function crosses zero (root-finding). Maps to ContinuousCallback / ContinuousComponentCallback.
notation: continuous

discrete (EventType)
type: Class
subclass of: EventType
definition: Triggered when condition function returns true (checked at each step). Maps to DiscreteCallback / DiscreteComponentCallback.
notation: discrete

preset_time (EventType)
type: Class
subclass of: EventType
definition: Triggered at predetermined time points. Maps to PresetTimeCallback / PresetTimeComponentCallback.
notation: preset_time

stimulus (EventType)
type: Class
subclass of: EventType
definition: Continuous time-dependent input signal (e.g., external current). Legacy Stimulus behavior.
notation: stimulus

both (Hemisphere)
type: Class
subclass of: Hemisphere
alternative label: B
alternative label: LR
alternative label: bilateral
notation: both

left (Hemisphere)
type: Class
subclass of: Hemisphere
alternative label: L
alternative label: lh
notation: left

right (Hemisphere)
type: Class
subclass of: Hemisphere
alternative label: R
alternative label: rh
notation: right

BOLD (ImagingModality)
type: Class
subclass of: ImagingModality
definition: Blood Oxygen Level Dependent signal.
notation: BOLD

EEG (ImagingModality)
type: Class
subclass of: ImagingModality
definition: Electroencephalography.
notation: EEG

IEEG (ImagingModality)
type: Class
subclass of: ImagingModality
definition: Intracranial Electroencephalography.
notation: IEEG

MEG (ImagingModality)
type: Class
subclass of: ImagingModality
definition: Magnetoencephalography.
notation: MEG

SEEG (ImagingModality)
type: Class
subclass of: ImagingModality
definition: Stereoelectroencephalography.
notation: SEEG

from_branch (InitialStateMethod)
type: Class
subclass of: InitialStateMethod
definition: Start from a point on a previously computed branch.
notation: from_branch

given (InitialStateMethod)
type: Class
subclass of: InitialStateMethod
definition: Use the model's default initial values directly.
notation: given

newton (InitialStateMethod)
type: Class
subclass of: InitialStateMethod
definition: Use Newton's method to find the nearest fixed point.
notation: newton

time_integration (InitialStateMethod)
type: Class
subclass of: InitialStateMethod
definition: Integrate the ODE forward until convergence (robust, default).
notation: time_integration

dynamic_mean_field (ModelParadigm)
type: Class
subclass of: ModelParadigm
definition: Dynamic mean-field approximation (e.g., Deco et al.).
notation: dynamic_mean_field

generic (ModelParadigm)
type: Class
subclass of: ModelParadigm
definition: General-purpose, not specific to neuroscience.
notation: generic

model_description (ModelParadigm)
type: Class
subclass of: ModelParadigm
definition: Declarative model specification language.
notation: model_description

field (ModelType)
type: Class
subclass of: ModelType
definition: Spatially distributed neural-field models described by integro- differential or PDE formulations.
notation: field

generic (ModelType)
type: Class
subclass of: ModelType
definition: Generic / normal-form dynamical systems not specific to neural modelling (e.g. Generic2dOscillator, GenericLinear).
notation: generic

mean_field (ModelType)
type: Class
subclass of: ModelType
definition: Mathematically derived mean-field models obtained by exact reduction of spiking networks (Ott-Antonsen ansatz, Lorentzian heterogeneity, etc.). Examples: MontbrioPazoRoxin, CoombesByrne, ReducedWongWang, ZerlautAdaptationFirstOrder.
notation: mean_field

neural_mass (ModelType)
type: Class
subclass of: ModelType
definition: 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.
notation: neural_mass

phase_oscillator (ModelType)
type: Class
subclass of: ModelType
definition: Phase-reduced or Kuramoto-type oscillator models. Examples: Kuramoto, SupHopf.
notation: phase_oscillator

phenomenological (ModelType)
type: Class
subclass of: ModelType
definition: Empirical / phenomenological models that capture macroscopic dynamics without direct biophysical derivation. Examples: Epileptor2D, Epileptor5D.
notation: phenomenological

spiking (ModelType)
type: Class
subclass of: ModelType
definition: 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.
notation: spiking

brown (NoiseType)
type: Class
subclass of: NoiseType
notation: brown

gaussian (NoiseType)
type: Class
subclass of: NoiseType
notation: gaussian

pink (NoiseType)
type: Class
subclass of: NoiseType
notation: pink

white (NoiseType)
type: Class
subclass of: NoiseType
notation: white

collocation (NumericalDiscretizationMethod)
type: Class
subclass of: NumericalDiscretizationMethod
definition: Orthogonal collocation at Gauss points.
notation: collocation

poincare (NumericalDiscretizationMethod)
type: Class
subclass of: NumericalDiscretizationMethod
definition: Poincaré shooting.
notation: poincare

shooting (NumericalDiscretizationMethod)
type: Class
subclass of: NumericalDiscretizationMethod
definition: Standard multiple shooting.
notation: shooting

trapezoid (NumericalDiscretizationMethod)
type: Class
subclass of: NumericalDiscretizationMethod
definition: Trapezoidal rule discretization.
notation: trapezoid

curl (OperatorType)
type: Class
subclass of: OperatorType
notation: curl

divergence (OperatorType)
type: Class
subclass of: OperatorType
notation: divergence

gradient (OperatorType)
type: Class
subclass of: OperatorType
notation: gradient

laplacian (OperatorType)
type: Class
subclass of: OperatorType
notation: laplacian

capacitance (PhysicalDimension)
type: Class
subclass of: PhysicalDimension
definition: Capacitance [M⁻¹ L⁻² T⁴ I²]
notation: capacitance

charge (PhysicalDimension)
type: Class
subclass of: PhysicalDimension
definition: Electric charge [T I]
notation: charge

concentration (PhysicalDimension)
type: Class
subclass of: PhysicalDimension
definition: Concentration [L⁻³ N]
notation: concentration

conductance (PhysicalDimension)
type: Class
subclass of: PhysicalDimension
definition: Conductance [M⁻¹ L⁻² T³ I²]
notation: conductance

current (PhysicalDimension)
type: Class
subclass of: PhysicalDimension
definition: Electric current [I]
notation: current

length (PhysicalDimension)
type: Class
subclass of: PhysicalDimension
definition: Length [L]
notation: length

none (PhysicalDimension)
type: Class
subclass of: PhysicalDimension
definition: Dimensionless
notation: none

per_time (PhysicalDimension)
type: Class
subclass of: PhysicalDimension
definition: Inverse time [T⁻¹]
notation: per_time

resistance (PhysicalDimension)
type: Class
subclass of: PhysicalDimension
definition: Resistance [M L² T⁻³ I⁻²]
notation: resistance

substance (PhysicalDimension)
type: Class
subclass of: PhysicalDimension
definition: Amount of substance [N]
notation: substance

temperature (PhysicalDimension)
type: Class
subclass of: PhysicalDimension
definition: Temperature [K]
notation: temperature

time (PhysicalDimension)
type: Class
subclass of: PhysicalDimension
definition: Time [T]
notation: time

voltage (PhysicalDimension)
type: Class
subclass of: PhysicalDimension
definition: Voltage [M L² T⁻³ I⁻¹]
notation: voltage

volume (PhysicalDimension)
type: Class
subclass of: PhysicalDimension
definition: Volume [L³]
notation: volume

max (ReductionType)
type: Class
subclass of: ReductionType
definition: Maximum value
notation: max

mean (ReductionType)
type: Class
subclass of: ReductionType
definition: Arithmetic mean
notation: mean

min (ReductionType)
type: Class
subclass of: ReductionType
definition: Minimum value
notation: min

none (ReductionType)
type: Class
subclass of: ReductionType
definition: No reduction (return per-element values)
notation: none

sum (ReductionType)
type: Class
subclass of: ReductionType
definition: Sum of values
notation: sum

analysis (RequirementRole)
type: Class
subclass of: RequirementRole
definition: Post-processing / analysis tool.
notation: analysis

dev (RequirementRole)
type: Class
subclass of: RequirementRole
definition: Development / build dependency.
notation: dev

engine (RequirementRole)
type: Class
subclass of: RequirementRole
definition: Primary simulation/processing engine.
notation: engine

optional (RequirementRole)
type: Class
subclass of: RequirementRole
definition: Optional or extra feature dependency.
notation: optional

runtime (RequirementRole)
type: Class
subclass of: RequirementRole
definition: General runtime dependency.
notation: runtime

space (SamplingAxis)
type: Class
subclass of: SamplingAxis
definition: Sample once per node (heterogeneous parameter or spatially varying IC).
notation: space

time (SamplingAxis)
type: Class
subclass of: SamplingAxis
definition: Resample every integration timestep (stochastic time-varying input).
notation: time

female (SexEnum)
type: Class
subclass of: SexEnum
definition: Female
notation: female

male (SexEnum)
type: Class
subclass of: SexEnum
definition: Male
notation: male

other (SexEnum)
type: Class
subclass of: SexEnum
definition: Other or not reported
notation: other

coo (SparseFormat)
type: Class
subclass of: SparseFormat
definition: Coordinate list (data, row, col)
notation: coo

csr (SparseFormat)
type: Class
subclass of: SparseFormat
definition: Compressed Sparse Row (data, indices, indptr)
notation: csr

dense (SparseFormat)
type: Class
subclass of: SparseFormat
definition: Dense N×N array with gzip compression
notation: dense

Subject (SpecimenEnum)
type: Class
subclass of: SpecimenEnum
notation: Subject

SubjectGroup (SpecimenEnum)
type: Class
subclass of: SpecimenEnum
notation: SubjectGroup

TissueSample (SpecimenEnum)
type: Class
subclass of: SpecimenEnum
notation: TissueSample

TissueSampleCollection (SpecimenEnum)
type: Class
subclass of: SpecimenEnum
notation: TissueSampleCollection

BarabasiAlbert (StandardGraphType)
type: Class
subclass of: StandardGraphType
definition: Barabasi-Albert preferential attachment (params: k)
notation: BarabasiAlbert

Complete (StandardGraphType)
type: Class
subclass of: StandardGraphType
definition: Complete graph (all-to-all)
notation: Complete

Cycle (StandardGraphType)
type: Class
subclass of: StandardGraphType
definition: Cycle graph (ring)
notation: Cycle

ErdosRenyi (StandardGraphType)
type: Class
subclass of: StandardGraphType
definition: Erdos-Renyi random graph (params: p)
notation: ErdosRenyi

Grid (StandardGraphType)
type: Class
subclass of: StandardGraphType
definition: Grid/lattice graph (params: dims)
notation: Grid

RandomRegular (StandardGraphType)
type: Class
subclass of: StandardGraphType
definition: Random regular graph (params: k)
notation: RandomRegular

Star (StandardGraphType)
type: Class
subclass of: StandardGraphType
definition: Star graph
notation: Star

WattsStrogatz (StandardGraphType)
type: Class
subclass of: StandardGraphType
definition: Watts-Strogatz small-world (params: k, p)
notation: WattsStrogatz

continuous (SystemType)
type: Class
subclass of: SystemType
definition: Continuous-time dynamics (e.g., ODE/SDE).
notation: continuous

discrete (SystemType)
type: Class
subclass of: SystemType
definition: Discrete-time dynamics (e.g., maps, iterated updates).
notation: discrete

backend_runtime (ToolRole)
type: Class
subclass of: ToolRole
definition: Optimized execution backend for another simulator.
notation: backend_runtime

workflow_framework (ToolRole)
type: Class
subclass of: ToolRole
definition: Orchestration, model-building, or pipeline tool.
notation: workflow_framework

Hz_per_nA (UnitEnum)
type: Class
subclass of: UnitEnum
definition: Hertz per nanoampere (neural gain)
notation: Hz_per_nA

Mohm (UnitEnum)
type: Class
subclass of: UnitEnum
definition: Megaohm (MΩ)
notation: Mohm

S_per_cm2 (UnitEnum)
type: Class
subclass of: UnitEnum
definition: Siemens per square centimetre (conductance density)
notation: S_per_cm2

S_per_m2 (UnitEnum)
type: Class
subclass of: UnitEnum
definition: Siemens per square metre (conductance density, SI)
notation: S_per_m2

arbitrary_unit (UnitEnum)
type: Class
subclass of: UnitEnum
definition: Arbitrary units (a.u.)
notation: arbitrary_unit

kg_per_s (UnitEnum)
type: Class
subclass of: UnitEnum
definition: Kilogram per second
notation: kg_per_s

kohm_cm (UnitEnum)
type: Class
subclass of: UnitEnum
definition: Kilo-ohm centimetre (axial resistivity)
notation: kohm_cm

mS_per_cm2 (UnitEnum)
type: Class
subclass of: UnitEnum
definition: Millisiemens per square centimetre (conductance density)
notation: mS_per_cm2

mol_per_cm3 (UnitEnum)
type: Class
subclass of: UnitEnum
definition: Mole per cubic centimetre (mol/cm³)
notation: mol_per_cm3

mol_per_m_per_A_per_s (UnitEnum)
type: Class
subclass of: UnitEnum
definition: Mole per metre per ampere per second (concentration-current coupling)
notation: mol_per_m_per_A_per_s

nS_per_mV (UnitEnum)
type: Class
subclass of: UnitEnum
definition: Nanosiemens per millivolt
notation: nS_per_mV

per_unit (UnitEnum)
type: Class
subclass of: UnitEnum
definition: Per-unit (dimensionless power-systems convention)
notation: per_unit

rad_per_ms (UnitEnum)
type: Class
subclass of: UnitEnum
definition: Radian per millisecond
notation: rad_per_ms

uA_per_cm2 (UnitEnum)
type: Class
subclass of: UnitEnum
definition: Microampere per square centimetre (current density)
notation: uA_per_cm2

uF_per_cm2 (UnitEnum)
type: Class
subclass of: UnitEnum
definition: Microfarad per square centimetre (specific capacitance)
notation: uF_per_cm2

ClinicalImprovement (dbs)
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: evaluator (dbs)
subclass of: Restriction
  all values from: ClinicalScore (dbs)
  on property: score (dbs)
subclass of: Restriction
  all values from: string
  on property: timepoint (dbs)
subclass of: Restriction
  min cardinality: 0
  on property: score (dbs)
subclass of: Restriction
  max cardinality: 1
  on property: score (dbs)
subclass of: Restriction
  all values from: float
  on property: absolute_value (dbs)
subclass of: Restriction
  all values from: float
  on property: baseline_value (dbs)
subclass of: Restriction
  all values from: float
  on property: percent_change (dbs)
subclass of: Restriction
  all values from: float
  on property: time_post_surgery (dbs)
subclass of: Restriction
  min cardinality: 0
  on property: absolute_value (dbs)
subclass of: Restriction
  min cardinality: 0
  on property: baseline_value (dbs)
subclass of: Restriction
  min cardinality: 0
  on property: evaluator (dbs)
subclass of: Restriction
  min cardinality: 0
  on property: percent_change (dbs)
subclass of: Restriction
  min cardinality: 0
  on property: time_post_surgery (dbs)
subclass of: Restriction
  min cardinality: 0
  on property: timepoint (dbs)
subclass of: Restriction
  max cardinality: 1
  on property: absolute_value (dbs)
subclass of: Restriction
  max cardinality: 1
  on property: baseline_value (dbs)
subclass of: Restriction
  max cardinality: 1
  on property: evaluator (dbs)
subclass of: Restriction
  max cardinality: 1
  on property: percent_change (dbs)
subclass of: Restriction
  max cardinality: 1
  on property: time_post_surgery (dbs)
subclass of: Restriction
  max cardinality: 1
  on property: timepoint (dbs)
definition: Relative improvement on a defined clinical score.
in scheme: dbs
notation: ClinicalImprovement

ClinicalScale (dbs)
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: acronym (dbs)
subclass of: Restriction
  all values from: string
  on property: domain
subclass of: Restriction
  all values from: string
  on property: name (dbs)
subclass of: Restriction
  all values from: string
  on property: reference (dbs)
subclass of: Restriction
  all values from: string
  on property: version (dbs)
subclass of: Restriction
  min cardinality: 0
  on property: acronym (dbs)
subclass of: Restriction
  min cardinality: 0
  on property: domain
subclass of: Restriction
  min cardinality: 1
  on property: name (dbs)
subclass of: Restriction
  min cardinality: 0
  on property: reference (dbs)
subclass of: Restriction
  min cardinality: 0
  on property: version (dbs)
subclass of: Restriction
  max cardinality: 1
  on property: acronym (dbs)
subclass of: Restriction
  max cardinality: 1
  on property: domain
subclass of: Restriction
  max cardinality: 1
  on property: name (dbs)
subclass of: Restriction
  max cardinality: 1
  on property: reference (dbs)
subclass of: Restriction
  max cardinality: 1
  on property: version (dbs)
definition: A clinical assessment inventory or structured scale composed of multiple scores or items.
in scheme: dbs
notation: ClinicalScale

ClinicalScore (dbs)
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: acronym (dbs)
subclass of: Restriction
  all values from: string
  on property: description (dbs)
subclass of: Restriction
  all values from: string
  on property: domain
subclass of: Restriction
  all values from: string
  on property: name (dbs)
subclass of: Restriction
  all values from: ClinicalScore (dbs)
  on property: parent_score (dbs)
subclass of: Restriction
  all values from: string
  on property: reference (dbs)
subclass of: Restriction
  all values from: ClinicalScale (dbs)
  on property: scale (dbs)
subclass of: Restriction
  min cardinality: 0
  on property: parent_score (dbs)
subclass of: Restriction
  min cardinality: 0
  on property: scale (dbs)
subclass of: Restriction
  max cardinality: 1
  on property: parent_score (dbs)
subclass of: Restriction
  max cardinality: 1
  on property: scale (dbs)
subclass of: Restriction
  min cardinality: 0
  on property: acronym (dbs)
subclass of: Restriction
  min cardinality: 0
  on property: description (dbs)
subclass of: Restriction
  min cardinality: 0
  on property: domain
subclass of: Restriction
  min cardinality: 1
  on property: name (dbs)
subclass of: Restriction
  min cardinality: 0
  on property: reference (dbs)
subclass of: Restriction
  max cardinality: 1
  on property: acronym (dbs)
subclass of: Restriction
  max cardinality: 1
  on property: description (dbs)
subclass of: Restriction
  max cardinality: 1
  on property: domain
subclass of: Restriction
  max cardinality: 1
  on property: name (dbs)
subclass of: Restriction
  max cardinality: 1
  on property: reference (dbs)
definition: Metadata about a clinical score or scale.
in scheme: dbs
notation: ClinicalScore

Contact (dbs)
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: Coordinate
  on property: coordinate (dbs)
subclass of: Restriction
  all values from: string
  on property: label (dbs)
subclass of: Restriction
  min cardinality: 0
  on property: coordinate (dbs)
subclass of: Restriction
  max cardinality: 1
  on property: coordinate (dbs)
subclass of: Restriction
  all values from: integer
  on property: contact_id (dbs)
subclass of: Restriction
  min cardinality: 0
  on property: contact_id (dbs)
subclass of: Restriction
  min cardinality: 0
  on property: label (dbs)
subclass of: Restriction
  max cardinality: 1
  on property: contact_id (dbs)
subclass of: Restriction
  max cardinality: 1
  on property: label (dbs)
definition: Individual contact on a DBS electrode.
in scheme: dbs
notation: Contact

DBSDataset (dbs)
type: Class
subclass of: Dataset (study)
subclass of: Restriction
  all values from: ClinicalScore (dbs)
  on property: clinical_scores (dbs)
subclass of: Restriction
  all values from: CommonCoordinateSpace
  on property: coordinate space
subclass of: Restriction
  all values from: DBSSubject (dbs)
  on property: subjects (study)
subclass of: Restriction
  min cardinality: 0
  on property: clinical_scores (dbs)
subclass of: Restriction
  min cardinality: 0
  on property: coordinate space
subclass of: Restriction
  min cardinality: 0
  on property: subjects (study)
subclass of: Restriction
  max cardinality: 1
  on property: coordinate space
definition: Collection of data related to a specific DBS study.
in scheme: dbs
notation: DBSDataset

DBSProtocol (dbs)
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: name (slot)
subclass of: Restriction
  all values from: ClinicalImprovement (dbs)
  on property: clinical_improvement (dbs)
subclass of: Restriction
  all values from: Electrode (dbs)
  on property: electrodes (dbs)
subclass of: Restriction
  all values from: string
  on property: notes (dbs)
subclass of: Restriction
  all values from: StimulationSetting (dbs)
  on property: settings (dbs)
subclass of: Restriction
  all values from: string
  on property: timing_info (dbs)
subclass of: Restriction
  min cardinality: 1
  on property: name (slot)
subclass of: Restriction
  min cardinality: 0
  on property: clinical_improvement (dbs)
subclass of: Restriction
  min cardinality: 0
  on property: electrodes (dbs)
subclass of: Restriction
  min cardinality: 0
  on property: settings (dbs)
subclass of: Restriction
  max cardinality: 1
  on property: name (slot)
subclass of: Restriction
  min cardinality: 0
  on property: notes (dbs)
subclass of: Restriction
  min cardinality: 0
  on property: timing_info (dbs)
subclass of: Restriction
  max cardinality: 1
  on property: notes (dbs)
subclass of: Restriction
  max cardinality: 1
  on property: timing_info (dbs)
definition: A protocol describing DBS therapy, potentially bilateral or multi-lead.
in scheme: dbs
notation: DBSProtocol

DBSSubject (dbs)
type: Class
subclass of: Subject (study)
subclass of: Restriction
  all values from: CommonCoordinateSpace
  on property: coordinate space
subclass of: Restriction
  all values from: string
  on property: diagnosis (dbs)
subclass of: Restriction
  all values from: string
  on property: handedness (dbs)
subclass of: Restriction
  all values from: DBSProtocol (dbs)
  on property: protocols (dbs)
subclass of: Restriction
  min cardinality: 0
  on property: coordinate space
subclass of: Restriction
  min cardinality: 0
  on property: protocols (dbs)
subclass of: Restriction
  max cardinality: 1
  on property: coordinate space
subclass of: Restriction
  min cardinality: 0
  on property: diagnosis (dbs)
subclass of: Restriction
  min cardinality: 0
  on property: handedness (dbs)
subclass of: Restriction
  max cardinality: 1
  on property: diagnosis (dbs)
subclass of: Restriction
  max cardinality: 1
  on property: handedness (dbs)
definition: Human or animal subject receiving DBS.
in scheme: dbs
notation: DBSSubject

EField (dbs)
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: CommonCoordinateSpace
  on property: coordinate space
subclass of: Restriction
  all values from: string
  on property: volume_data (dbs)
subclass of: Restriction
  min cardinality: 0
  on property: coordinate space
subclass of: Restriction
  max cardinality: 1
  on property: coordinate space
subclass of: Restriction
  all values from: float
  on property: threshold_applied (dbs)
subclass of: Restriction
  min cardinality: 0
  on property: threshold_applied (dbs)
subclass of: Restriction
  min cardinality: 0
  on property: volume_data (dbs)
subclass of: Restriction
  max cardinality: 1
  on property: threshold_applied (dbs)
subclass of: Restriction
  max cardinality: 1
  on property: volume_data (dbs)
definition: Simulated electric field from DBS modeling.
in scheme: dbs
notation: EField

Electrode (dbs)
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: Contact (dbs)
  on property: contacts (dbs)
subclass of: Restriction
  all values from: CommonCoordinateSpace
  on property: coordinate space
subclass of: Restriction
  all values from: string
  on property: electrode_id (dbs)
subclass of: Restriction
  all values from: Coordinate
  on property: head (dbs)
subclass of: Restriction
  all values from: string
  on property: hemisphere (dbs)
subclass of: Restriction
  all values from: string
  on property: manufacturer (dbs)
subclass of: Restriction
  all values from: string
  on property: model (dbs)
subclass of: Restriction
  all values from: string
  on property: recon_path (dbs)
subclass of: Restriction
  all values from: Coordinate
  on property: tail (dbs)
subclass of: Restriction
  all values from: ParcellationEntity
  on property: target_structure (dbs)
subclass of: Restriction
  all values from: Coordinate
  on property: trajectory (dbs)
subclass of: Restriction
  min cardinality: 0
  on property: contacts (dbs)
subclass of: Restriction
  min cardinality: 0
  on property: coordinate space
subclass of: Restriction
  min cardinality: 0
  on property: head (dbs)
subclass of: Restriction
  min cardinality: 0
  on property: tail (dbs)
subclass of: Restriction
  min cardinality: 0
  on property: target_structure (dbs)
subclass of: Restriction
  min cardinality: 0
  on property: trajectory (dbs)
subclass of: Restriction
  max cardinality: 1
  on property: coordinate space
subclass of: Restriction
  max cardinality: 1
  on property: head (dbs)
subclass of: Restriction
  max cardinality: 1
  on property: tail (dbs)
subclass of: Restriction
  max cardinality: 1
  on property: target_structure (dbs)
subclass of: Restriction
  min cardinality: 0
  on property: electrode_id (dbs)
subclass of: Restriction
  min cardinality: 0
  on property: hemisphere (dbs)
subclass of: Restriction
  min cardinality: 0
  on property: manufacturer (dbs)
subclass of: Restriction
  min cardinality: 0
  on property: model (dbs)
subclass of: Restriction
  min cardinality: 0
  on property: recon_path (dbs)
subclass of: Restriction
  max cardinality: 1
  on property: electrode_id (dbs)
subclass of: Restriction
  max cardinality: 1
  on property: hemisphere (dbs)
subclass of: Restriction
  max cardinality: 1
  on property: manufacturer (dbs)
subclass of: Restriction
  max cardinality: 1
  on property: model (dbs)
subclass of: Restriction
  max cardinality: 1
  on property: recon_path (dbs)
definition: Implanted DBS electrode and contact geometry.
in scheme: dbs
notation: Electrode

StimulationSetting (dbs)
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: Parameter
  on property: amplitude (dbs)
subclass of: Restriction
  all values from: EField (dbs)
  on property: efield (dbs)
subclass of: Restriction
  all values from: Electrode (dbs)
  on property: electrode_reference (dbs)
subclass of: Restriction
  all values from: Parameter
  on property: frequency (dbs)
subclass of: Restriction
  all values from: string
  on property: mode (dbs)
subclass of: Restriction
  all values from: Parameter
  on property: pulse_width (dbs)
subclass of: Restriction
  min cardinality: 0
  on property: amplitude (dbs)
subclass of: Restriction
  min cardinality: 0
  on property: efield (dbs)
subclass of: Restriction
  min cardinality: 0
  on property: electrode_reference (dbs)
subclass of: Restriction
  min cardinality: 0
  on property: frequency (dbs)
subclass of: Restriction
  min cardinality: 0
  on property: mode (dbs)
subclass of: Restriction
  min cardinality: 0
  on property: pulse_width (dbs)
subclass of: Restriction
  max cardinality: 1
  on property: amplitude (dbs)
subclass of: Restriction
  max cardinality: 1
  on property: efield (dbs)
subclass of: Restriction
  max cardinality: 1
  on property: electrode_reference (dbs)
subclass of: Restriction
  max cardinality: 1
  on property: frequency (dbs)
subclass of: Restriction
  max cardinality: 1
  on property: mode (dbs)
subclass of: Restriction
  max cardinality: 1
  on property: pulse_width (dbs)
subclass of: Restriction
  all values from: integer
  on property: active_contacts (dbs)
subclass of: Restriction
  min cardinality: 0
  on property: active_contacts (dbs)
definition: DBS parameters for a specific session.
in scheme: dbs
notation: StimulationSetting

SimulationTool (software)
type: Class
subclass of: SoftwarePackage (software)
subclass of: Restriction
  all values from: string
  on property: application_category (software)
subclass of: Restriction
  all values from: string
  on property: author (software)
subclass of: Restriction
  all values from: string
  on property: citation (software)
subclass of: Restriction
  all values from: DevelopmentStatus
  on property: development_status (software)
subclass of: Restriction
  all values from: string
  on property: funder (software)
subclass of: Restriction
  all values from: SimulationTool (software)
  on property: interoperates_with (software)
subclass of: Restriction
  all values from: string
  on property: keywords (software)
subclass of: Restriction
  all values from: string
  on property: maintainer (software)
subclass of: Restriction
  all values from: ModelParadigm
  on property: model_paradigm (software)
subclass of: Restriction
  all values from: string
  on property: operating_system (software)
subclass of: Restriction
  all values from: ProgrammingLanguageEnum
  on property: programming_language (software)
subclass of: Restriction
  all values from: string
  on property: reference_publication (software)
subclass of: Restriction
  all values from: string
  on property: runtime_platform (software)
subclass of: Restriction
  all values from: SimulationScale
  on property: scale (software)
subclass of: Restriction
  all values from: ToolRole
  on property: tool_role (software)
subclass of: Restriction
  all values from: string
  on property: version
subclass of: Restriction
  min cardinality: 0
  on property: development_status (software)
subclass of: Restriction
  min cardinality: 0
  on property: interoperates_with (software)
subclass of: Restriction
  min cardinality: 0
  on property: model_paradigm (software)
subclass of: Restriction
  min cardinality: 0
  on property: programming_language (software)
subclass of: Restriction
  min cardinality: 0
  on property: scale (software)
subclass of: Restriction
  min cardinality: 0
  on property: tool_role (software)
subclass of: Restriction
  max cardinality: 1
  on property: development_status (software)
subclass of: Restriction
  all values from: date
  on property: date_created (software)
subclass of: Restriction
  all values from: date
  on property: date_modified (software)
subclass of: Restriction
  all values from: boolean
  on property: is_accessible_for_free (software)
subclass of: Restriction
  all values from: anyURI
  on property: issue_tracker (software)
subclass of: Restriction
  all values from: anyURI
  on property: same_as (software)
subclass of: Restriction
  min cardinality: 0
  on property: application_category (software)
subclass of: Restriction
  min cardinality: 0
  on property: author (software)
subclass of: Restriction
  min cardinality: 0
  on property: citation (software)
subclass of: Restriction
  min cardinality: 0
  on property: date_created (software)
subclass of: Restriction
  min cardinality: 0
  on property: date_modified (software)
subclass of: Restriction
  min cardinality: 0
  on property: funder (software)
subclass of: Restriction
  min cardinality: 0
  on property: is_accessible_for_free (software)
subclass of: Restriction
  min cardinality: 0
  on property: issue_tracker (software)
subclass of: Restriction
  min cardinality: 0
  on property: keywords (software)
subclass of: Restriction
  min cardinality: 0
  on property: maintainer (software)
subclass of: Restriction
  min cardinality: 0
  on property: operating_system (software)
subclass of: Restriction
  min cardinality: 0
  on property: reference_publication (software)
subclass of: Restriction
  min cardinality: 0
  on property: runtime_platform (software)
subclass of: Restriction
  min cardinality: 0
  on property: same_as (software)
subclass of: Restriction
  min cardinality: 0
  on property: version
subclass of: Restriction
  max cardinality: 1
  on property: application_category (software)
subclass of: Restriction
  max cardinality: 1
  on property: date_created (software)
subclass of: Restriction
  max cardinality: 1
  on property: date_modified (software)
subclass of: Restriction
  max cardinality: 1
  on property: is_accessible_for_free (software)
subclass of: Restriction
  max cardinality: 1
  on property: issue_tracker (software)
subclass of: Restriction
  max cardinality: 1
  on property: reference_publication (software)
subclass of: Restriction
  max cardinality: 1
  on property: version
definition: 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.
in scheme: software
notation: SimulationTool

SoftwareEnvironment (software)
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: name (slot)
subclass of: Restriction
  all values from: string
  on property: build_hash (software)
subclass of: Restriction
  all values from: string
  on property: container_image (software)
subclass of: Restriction
  all values from: string
  on property: dataLocation
subclass of: Restriction
  all values from: string
  on property: description (software)
subclass of: Restriction
  all values from: EnvironmentType
  on property: environment_type (software)
subclass of: Restriction
  all values from: string
  on property: label (software)
subclass of: Restriction
  all values from: string
  on property: platform (software)
subclass of: Restriction
  all values from: SoftwareRequirement (software)
  on property: requirements (software)
subclass of: Restriction
  all values from: string
  on property: version
subclass of: Restriction
  min cardinality: 1
  on property: name (slot)
subclass of: Restriction
  min cardinality: 0
  on property: environment_type (software)
subclass of: Restriction
  min cardinality: 0
  on property: requirements (software)
subclass of: Restriction
  max cardinality: 1
  on property: name (slot)
subclass of: Restriction
  max cardinality: 1
  on property: environment_type (software)
subclass of: Restriction
  min cardinality: 0
  on property: build_hash (software)
subclass of: Restriction
  min cardinality: 0
  on property: container_image (software)
subclass of: Restriction
  min cardinality: 0
  on property: dataLocation
subclass of: Restriction
  min cardinality: 0
  on property: description (software)
subclass of: Restriction
  min cardinality: 0
  on property: label (software)
subclass of: Restriction
  min cardinality: 0
  on property: platform (software)
subclass of: Restriction
  min cardinality: 0
  on property: version
subclass of: Restriction
  max cardinality: 1
  on property: build_hash (software)
subclass of: Restriction
  max cardinality: 1
  on property: container_image (software)
subclass of: Restriction
  max cardinality: 1
  on property: dataLocation
subclass of: Restriction
  max cardinality: 1
  on property: description (software)
subclass of: Restriction
  max cardinality: 1
  on property: label (software)
subclass of: Restriction
  max cardinality: 1
  on property: platform (software)
subclass of: Restriction
  max cardinality: 1
  on property: version
definition: A reproducible software environment aggregating one or more SoftwareRequirement entries. Used by SimulationExperiment to specify the execution context.
in scheme: software
notation: SoftwareEnvironment
note: An environment aggregates one or more SoftwareRequirement entries.
note: Use SimulationExperiment.environment to reference a reusable environment.

SoftwarePackage (software)
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: name (slot)
subclass of: Restriction
  all values from: string
  on property: description (software)
subclass of: Restriction
  all values from: string
  on property: doi (software)
subclass of: Restriction
  all values from: EcosystemEnum
  on property: ecosystem (software)
subclass of: Restriction
  all values from: string
  on property: license (software)
subclass of: Restriction
  min cardinality: 1
  on property: name (slot)
subclass of: Restriction
  min cardinality: 0
  on property: ecosystem (software)
subclass of: Restriction
  max cardinality: 1
  on property: name (slot)
subclass of: Restriction
  all values from: anyURI
  on property: homepage (software)
subclass of: Restriction
  all values from: anyURI
  on property: repository (software)
subclass of: Restriction
  min cardinality: 0
  on property: description (software)
subclass of: Restriction
  min cardinality: 0
  on property: doi (software)
subclass of: Restriction
  min cardinality: 0
  on property: homepage (software)
subclass of: Restriction
  min cardinality: 0
  on property: license (software)
subclass of: Restriction
  min cardinality: 0
  on property: repository (software)
subclass of: Restriction
  max cardinality: 1
  on property: description (software)
subclass of: Restriction
  max cardinality: 1
  on property: doi (software)
subclass of: Restriction
  max cardinality: 1
  on property: homepage (software)
subclass of: Restriction
  max cardinality: 1
  on property: license (software)
subclass of: Restriction
  max cardinality: 1
  on property: repository (software)
definition: Identity and metadata for a software package, aligned with schema.org/SoftwareApplication and CodeMeta v3.
in scheme: software
notation: SoftwarePackage

SoftwareRequirement (software)
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: name (slot)
subclass of: Restriction
  all values from: string
  on property: dataLocation
subclass of: Restriction
  all values from: string
  on property: description (software)
subclass of: Restriction
  all values from: string
  on property: hash (software)
subclass of: Restriction
  all values from: string
  on property: license (software)
subclass of: Restriction
  all values from: string
  on property: modules (software)
subclass of: Restriction
  all values from: SoftwarePackage (software)
  on property: package (software)
subclass of: Restriction
  all values from: RequirementRole
  on property: role (software)
subclass of: Restriction
  all values from: string
  on property: source_url (software)
subclass of: Restriction
  all values from: string
  on property: url (software)
subclass of: Restriction
  all values from: string
  on property: version
subclass of: Restriction
  all values from: string
  on property: version_spec (software)
subclass of: Restriction
  min cardinality: 1
  on property: name (slot)
subclass of: Restriction
  min cardinality: 0
  on property: package (software)
subclass of: Restriction
  min cardinality: 0
  on property: role (software)
subclass of: Restriction
  max cardinality: 1
  on property: name (slot)
subclass of: Restriction
  max cardinality: 1
  on property: package (software)
subclass of: Restriction
  max cardinality: 1
  on property: role (software)
subclass of: Restriction
  all values from: boolean
  on property: optional (software)
subclass of: Restriction
  min cardinality: 0
  on property: dataLocation
subclass of: Restriction
  min cardinality: 0
  on property: description (software)
subclass of: Restriction
  min cardinality: 0
  on property: hash (software)
subclass of: Restriction
  min cardinality: 0
  on property: license (software)
subclass of: Restriction
  min cardinality: 0
  on property: modules (software)
subclass of: Restriction
  min cardinality: 0
  on property: optional (software)
subclass of: Restriction
  min cardinality: 0
  on property: source_url (software)
subclass of: Restriction
  min cardinality: 0
  on property: url (software)
subclass of: Restriction
  min cardinality: 0
  on property: version
subclass of: Restriction
  min cardinality: 0
  on property: version_spec (software)
subclass of: Restriction
  max cardinality: 1
  on property: dataLocation
subclass of: Restriction
  max cardinality: 1
  on property: description (software)
subclass of: Restriction
  max cardinality: 1
  on property: hash (software)
subclass of: Restriction
  max cardinality: 1
  on property: license (software)
subclass of: Restriction
  max cardinality: 1
  on property: optional (software)
subclass of: Restriction
  max cardinality: 1
  on property: source_url (software)
subclass of: Restriction
  max cardinality: 1
  on property: url (software)
subclass of: Restriction
  max cardinality: 1
  on property: version
subclass of: Restriction
  max cardinality: 1
  on property: version_spec (software)
definition: An individual software requirement binding a package to a version constraint and a role within an environment.
in scheme: software
notation: SoftwareRequirement
note: Represents an individual requirement (package/module/library).
note: Use 'version_spec' instead of 'version' for semantic clarity.

Dataset (study)
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: bids_root (study)
subclass of: Restriction
  all values from: string
  on property: conditions (study)
subclass of: Restriction
  all values from: string
  on property: dataset_id (study)
subclass of: Restriction
  all values from: string
  on property: description (study)
subclass of: Restriction
  all values from: string
  on property: label (study)
subclass of: Restriction
  all values from: string
  on property: reference (study)
subclass of: Restriction
  all values from: Subject (study)
  on property: subjects (study)
subclass of: Restriction
  min cardinality: 0
  on property: subjects (study)
subclass of: Restriction
  min cardinality: 0
  on property: bids_root (study)
subclass of: Restriction
  min cardinality: 0
  on property: conditions (study)
subclass of: Restriction
  min cardinality: 1
  on property: dataset_id (study)
subclass of: Restriction
  min cardinality: 0
  on property: description (study)
subclass of: Restriction
  min cardinality: 0
  on property: label (study)
subclass of: Restriction
  min cardinality: 0
  on property: reference (study)
subclass of: Restriction
  max cardinality: 1
  on property: bids_root (study)
subclass of: Restriction
  max cardinality: 1
  on property: dataset_id (study)
subclass of: Restriction
  max cardinality: 1
  on property: description (study)
subclass of: Restriction
  max cardinality: 1
  on property: label (study)
subclass of: Restriction
  max cardinality: 1
  on property: reference (study)
definition: 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.
in scheme: study
notation: Dataset

Session (study)
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: condition (study)
subclass of: Restriction
  all values from: string
  on property: empirical_data (study)
subclass of: Restriction
  all values from: string
  on property: label (study)
subclass of: Restriction
  all values from: string
  on property: network
subclass of: Restriction
  all values from: string
  on property: session_id (study)
subclass of: Restriction
  min cardinality: 0
  on property: condition (study)
subclass of: Restriction
  min cardinality: 0
  on property: empirical_data (study)
subclass of: Restriction
  min cardinality: 0
  on property: label (study)
subclass of: Restriction
  min cardinality: 0
  on property: network
subclass of: Restriction
  min cardinality: 1
  on property: session_id (study)
subclass of: Restriction
  max cardinality: 1
  on property: condition (study)
subclass of: Restriction
  max cardinality: 1
  on property: label (study)
subclass of: Restriction
  max cardinality: 1
  on property: network
subclass of: Restriction
  max cardinality: 1
  on property: session_id (study)
definition: 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.
in scheme: study
notation: Session

Subject (study)
type: Class
subclass of: Thing
subclass of: Restriction
  all values from: string
  on property: group (study)
subclass of: Restriction
  all values from: string
  on property: label (study)
subclass of: Restriction
  all values from: string
  on property: metadata (study)
subclass of: Restriction
  all values from: string
  on property: network
subclass of: Restriction
  all values from: Session (study)
  on property: sessions (study)
subclass of: Restriction
  all values from: SexEnum
  on property: sex (study)
subclass of: Restriction
  all values from: string
  on property: subject_id (study)
subclass of: Restriction
  min cardinality: 0
  on property: sessions (study)
subclass of: Restriction
  min cardinality: 0
  on property: sex (study)
subclass of: Restriction
  max cardinality: 1
  on property: sex (study)
subclass of: Restriction
  all values from: float
  on property: age (study)
subclass of: Restriction
  min cardinality: 0
  on property: age (study)
subclass of: Restriction
  min cardinality: 0
  on property: group (study)
subclass of: Restriction
  min cardinality: 0
  on property: label (study)
subclass of: Restriction
  min cardinality: 0
  on property: metadata (study)
subclass of: Restriction
  min cardinality: 0
  on property: network
subclass of: Restriction
  min cardinality: 1
  on property: subject_id (study)
subclass of: Restriction
  max cardinality: 1
  on property: age (study)
subclass of: Restriction
  max cardinality: 1
  on property: group (study)
subclass of: Restriction
  max cardinality: 1
  on property: label (study)
subclass of: Restriction
  max cardinality: 1
  on property: metadata (study)
subclass of: Restriction
  max cardinality: 1
  on property: network
subclass of: Restriction
  max cardinality: 1
  on property: subject_id (study)
definition: A participant in a study. Each subject typically has their own brain network (connectome) and empirical recordings. Corresponds to a BIDS 'sub-' entity.
in scheme: study
notation: Subject

Automatic differentiation
type: NamedIndividual
type: Backend capability

Bifurcation analysis
type: NamedIndividual
type: Simulation task
comment: Detection and classification of bifurcations along a continuation branch.

BifurcationKit.jl
type: NamedIndividual
type: Backend
provides capability: Continuation solver
provides capability: Julia JIT
supports task: Bifurcation analysis
supports task: Numerical continuation

Built-in model library
type: NamedIndividual
type: Backend capability

CakanObermayer
type: NamedIndividual
type: Dynamics
exhibits bifurcation: BifurcationEvent
  bifurcation type: Hopf
  type: Bifurcation event
exhibits regime: Bistable
exhibits regime: Oscillatory
exhibits regime: Quiescent
has attractor: Fixed point
has attractor: Limit cycle
has model feature: Excitatory/inhibitory subpopulations
has stochasticity character: Deterministic
models anatomical region: UBERON_0000956
models cell type: CL_0000099
models cell type: CL_0000598
models neurotransmitter system: GO_0007214
models neurotransmitter system: GO_0035249
has timescale separation: true
phase-space dimension: 6
description: 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.
preferred label: Cakan-Obermayer ALN
has derived variable: r_E (CakanObermayer derived variable)
has derived variable: r_I (CakanObermayer derived variable)
has parameter: C (CakanObermayer parameter)
has parameter: E_A (CakanObermayer parameter)
has parameter: E_L (CakanObermayer parameter)
has parameter: I_A (CakanObermayer parameter)
has parameter: J_EE (CakanObermayer parameter)
has parameter: J_EI (CakanObermayer parameter)
has parameter: J_IE (CakanObermayer parameter)
has parameter: J_II (CakanObermayer parameter)
has parameter: k_phi (CakanObermayer parameter)
has parameter: mu_E (CakanObermayer parameter)
has parameter: mu_I (CakanObermayer parameter)
has parameter: mu_th (CakanObermayer parameter)
has parameter: r_max (CakanObermayer parameter)
has parameter: s_EE (CakanObermayer parameter)
has parameter: s_EI (CakanObermayer parameter)
has parameter: s_IE (CakanObermayer parameter)
has parameter: s_II (CakanObermayer parameter)
has parameter: tau_A (CakanObermayer parameter)
has parameter: tau_se (CakanObermayer parameter)
has parameter: tau_si (CakanObermayer parameter)
has state variable: I_A_var (CakanObermayer state variable)
has state variable: mu_se (CakanObermayer state variable)
has state variable: mu_si (CakanObermayer state variable)
model_type (slot): neural_mass

Symbolic code generation
type: NamedIndividual
type: Backend capability
comment: Backend emits standalone simulator source code from a model specification.

Continuation solver
type: NamedIndividual
type: Backend capability

CoombesByrne
type: NamedIndividual
type: Dynamics
exhibits bifurcation: BifurcationEvent
  bifurcation type: Hopf
  type: Bifurcation event
exhibits regime: Oscillatory
exhibits regime: Quiescent
has attractor: Fixed point
has attractor: Limit cycle
has stochasticity character: Deterministic
models anatomical region: UBERON_0000956
phase-space dimension: 4
description: 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: Next generation neural mass models
preferred label: Coombes-Byrne
has parameter: Delta (CoombesByrne parameter)
has parameter: alpha (CoombesByrne parameter)
has parameter: eta (CoombesByrne parameter)
has parameter: k (CoombesByrne parameter)
has parameter: v_syn (CoombesByrne parameter)
has state variable: V (CoombesByrne state variable)
has state variable: g (CoombesByrne state variable)
has state variable: q (CoombesByrne state variable)
has state variable: r (CoombesByrne state variable)
model_type (slot): mean_field

CoombesByrne2D
type: NamedIndividual
type: Dynamics
exhibits bifurcation: BifurcationEvent
  bifurcation type: Hopf
  type: Bifurcation event
exhibits regime: Oscillatory
exhibits regime: Quiescent
has attractor: Fixed point
has attractor: Limit cycle
has stochasticity character: Deterministic
models anatomical region: UBERON_0000956
phase-space dimension: 2
references: Next generation neural mass models
preferred label: Coombes-Byrne 2D
has parameter: Delta (CoombesByrne2D parameter)
has parameter: eta (CoombesByrne2D parameter)
has parameter: k (CoombesByrne2D parameter)
has parameter: v_syn (CoombesByrne2D parameter)
has state variable: V (CoombesByrne2D state variable)
has state variable: r (CoombesByrne2D state variable)
model_type (slot): mean_field

DDE integration
type: NamedIndividual
type: Simulation task
comment: Forward integration of a delay differential equation (e.g. long-range axonal delays).

Delay history buffer
type: NamedIndividual
type: Backend capability
comment: Storage and interpolation of past states required for DDE/SDDE integration.

DifferentialEquations.jl integrators
type: NamedIndividual
type: Backend capability

DumontGutkin
type: NamedIndividual
type: Dynamics
exhibits bifurcation: BifurcationEvent
  bifurcation type: Hopf
  type: Bifurcation event
exhibits regime: Bistable
exhibits regime: Oscillatory
has attractor: Fixed point
has attractor: Limit cycle
has model feature: Excitatory/inhibitory subpopulations
has stochasticity character: Deterministic
models anatomical region: UBERON_0000956
phase-space dimension: 8
references: A reduced model of coupled neural masses with complex dynamics
preferred label: Dumont-Gutkin
has parameter: Delta_e (DumontGutkin parameter)
has parameter: Delta_i (DumontGutkin parameter)
has parameter: Gamma (DumontGutkin parameter)
has parameter: I_e (DumontGutkin parameter)
has parameter: I_i (DumontGutkin parameter)
has parameter: J_ee (DumontGutkin parameter)
has parameter: J_ei (DumontGutkin parameter)
has parameter: J_ie (DumontGutkin parameter)
has parameter: J_ii (DumontGutkin parameter)
has parameter: eta_e (DumontGutkin parameter)
has parameter: eta_i (DumontGutkin parameter)
has parameter: tau_e (DumontGutkin parameter)
has parameter: tau_i (DumontGutkin parameter)
has parameter: tau_s (DumontGutkin parameter)
has state variable: V_e (DumontGutkin state variable)
has state variable: V_i (DumontGutkin state variable)
has state variable: r_e (DumontGutkin state variable)
has state variable: r_i (DumontGutkin state variable)
has state variable: s_ee (DumontGutkin state variable)
has state variable: s_ei (DumontGutkin state variable)
has state variable: s_ie (DumontGutkin state variable)
has state variable: s_ii (DumontGutkin state variable)
model_type (slot): mean_field

E/I balance
type: NamedIndividual
type: SKOS Concept
comment: Dynamic equilibrium between excitatory and inhibitory drive.
broad match: GO_0099177

Epileptor
type: NamedIndividual
exhibits bifurcation: BifurcationEvent
  bifurcation type: Saddle-node
  type: Bifurcation event
exhibits bifurcation: BifurcationEvent
  bifurcation type: Homoclinic
  type: Bifurcation event
exhibits regime: Bistable
exhibits regime: Bursting
exhibits regime: Oscillatory
has attractor: Fixed point
has attractor: Limit cycle
has model feature: Fast-slow decomposition
has stochasticity character: Deterministic
models anatomical region: UBERON_0002728
has timescale separation: true
phase-space dimension: 6
subject: D004827

Epileptor2D
type: NamedIndividual
type: Dynamics
exhibits bifurcation: BifurcationEvent
  bifurcation type: Saddle-node
  type: Bifurcation event
exhibits regime: Bistable
exhibits regime: Oscillatory
has attractor: Fixed point
has attractor: Limit cycle
has stochasticity character: Deterministic
models anatomical region: UBERON_0002728
phase-space dimension: 2
description: 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: A neural mass model of seizure initiation and propagation
references: Individual structural connectivity defines propagation networks in partial epilepsy
subject: D004827
preferred label: Epileptor 2D
has derived variable: h (Epileptor2D derived variable)
has derived variable: x1cond (Epileptor2D derived variable)
has derived variable: zcond (Epileptor2D derived variable)
has parameter: Iext (Epileptor2D parameter)
has parameter: Ks (Epileptor2D parameter)
has parameter: Kvf (Epileptor2D parameter)
has parameter: a (Epileptor2D parameter)
has parameter: b (Epileptor2D parameter)
has parameter: c (Epileptor2D parameter)
has parameter: d (Epileptor2D parameter)
has parameter: modification (Epileptor2D parameter)
has parameter: r (Epileptor2D parameter)
has parameter: slope (Epileptor2D parameter)
has parameter: tt (Epileptor2D parameter)
has parameter: x0 (Epileptor2D parameter)
has state variable: x1 (Epileptor2D state variable)
has state variable: z (Epileptor2D state variable)
model_type (slot): phenomenological

Epileptor3DStefanescuMcDonald
type: NamedIndividual
type: Dynamics
exhibits regime: Bistable
exhibits regime: Bursting
has attractor: Fixed point
has attractor: Limit cycle
has model feature: Fast-slow decomposition
has stochasticity character: Deterministic
models anatomical region: UBERON_0002728
has timescale separation: true
phase-space dimension: 3
description: 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: D004827
preferred label: Epileptor 3D (Stefanescu-McDonald)
has parameter: N (Epileptor3DStefanescuMcDonald parameter)
has parameter: tau_z (Epileptor3DStefanescuMcDonald parameter)
has parameter: x_0 (Epileptor3DStefanescuMcDonald parameter)
has state variable: x1 (Epileptor3DStefanescuMcDonald state variable)
has state variable: z (Epileptor3DStefanescuMcDonald state variable)
model_type (slot): neural_mass

Epileptor5D
type: NamedIndividual
type: Dynamics
exhibits bifurcation: BifurcationEvent
  bifurcation type: Saddle-node
  type: Bifurcation event
exhibits regime: Bistable
exhibits regime: Bursting
exhibits regime: Oscillatory
has attractor: Fixed point
has attractor: Limit cycle
has model feature: Fast-slow decomposition
has stochasticity character: Deterministic
models anatomical region: UBERON_0002728
has timescale separation: true
phase-space dimension: 5
description: 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: On the nature of seizure dynamics
references: A neural mass model of seizure initiation and propagation
subject: D004827
preferred label: Epileptor 5D
has derived variable: h (Epileptor5D derived variable)
has derived variable: x1cond (Epileptor5D derived variable)
has derived variable: y2cond (Epileptor5D derived variable)
has derived variable: zcond (Epileptor5D derived variable)
has parameter: Iext (Epileptor5D parameter)
has parameter: Iext2 (Epileptor5D parameter)
has parameter: Kf (Epileptor5D parameter)
has parameter: Ks (Epileptor5D parameter)
has parameter: Kvf (Epileptor5D parameter)
has parameter: a (Epileptor5D parameter)
has parameter: aa (Epileptor5D parameter)
has parameter: b (Epileptor5D parameter)
has parameter: bb (Epileptor5D parameter)
has parameter: c (Epileptor5D parameter)
has parameter: d (Epileptor5D parameter)
has parameter: modification (Epileptor5D parameter)
has parameter: r (Epileptor5D parameter)
has parameter: s (Epileptor5D parameter)
has parameter: slope (Epileptor5D parameter)
has parameter: tau (Epileptor5D parameter)
has parameter: tt (Epileptor5D parameter)
has parameter: x0 (Epileptor5D parameter)
has state variable: g (Epileptor5D state variable)
has state variable: x1 (Epileptor5D state variable)
has state variable: x2 (Epileptor5D state variable)
has state variable: y1 (Epileptor5D state variable)
has state variable: y2 (Epileptor5D state variable)
has state variable: z (Epileptor5D state variable)
model_type (slot): phenomenological

EpileptorRestingState
type: NamedIndividual
type: Dynamics
exhibits bifurcation: BifurcationEvent
  bifurcation type: Saddle-node
  type: Bifurcation event
exhibits regime: Bistable
exhibits regime: Bursting
exhibits regime: Oscillatory
has attractor: Fixed point
has attractor: Limit cycle
has model feature: Fast-slow decomposition
has stochasticity character: Deterministic
models anatomical region: UBERON_0000956
models anatomical region: UBERON_0002728
has timescale separation: true
phase-space dimension: 8
description: 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: The brain resting state: dynamics and models
references: On the nature of seizure dynamics
subject: D004827
preferred label: Epileptor (resting-state)
has derived variable: lc_1 (EpileptorRestingState derived variable)
has derived variable: output (EpileptorRestingState derived variable)
has derived variable: x1cond (EpileptorRestingState derived variable)
has derived variable: y2cond (EpileptorRestingState derived variable)
has derived variable: zcond (EpileptorRestingState derived variable)
has parameter: I_rs (EpileptorRestingState parameter)
has parameter: Iext (EpileptorRestingState parameter)
has parameter: Iext2 (EpileptorRestingState parameter)
has parameter: K_rs (EpileptorRestingState parameter)
has parameter: Kf (EpileptorRestingState parameter)
has parameter: Ks (EpileptorRestingState parameter)
has parameter: Kvf (EpileptorRestingState parameter)
has parameter: a (EpileptorRestingState parameter)
has parameter: a_rs (EpileptorRestingState parameter)
has parameter: aa (EpileptorRestingState parameter)
has parameter: alpha_rs (EpileptorRestingState parameter)
has parameter: b (EpileptorRestingState parameter)
has parameter: b_rs (EpileptorRestingState parameter)
has parameter: bb (EpileptorRestingState parameter)
has parameter: beta_rs (EpileptorRestingState parameter)
has parameter: c (EpileptorRestingState parameter)
has parameter: d (EpileptorRestingState parameter)
has parameter: d_rs (EpileptorRestingState parameter)
has parameter: e_rs (EpileptorRestingState parameter)
has parameter: f_rs (EpileptorRestingState parameter)
has parameter: gamma_rs (EpileptorRestingState parameter)
has parameter: p (EpileptorRestingState parameter)
has parameter: r (EpileptorRestingState parameter)
has parameter: slope (EpileptorRestingState parameter)
has parameter: tau (EpileptorRestingState parameter)
has parameter: tau_rs (EpileptorRestingState parameter)
has parameter: tt (EpileptorRestingState parameter)
has parameter: x0 (EpileptorRestingState parameter)
has state variable: g (EpileptorRestingState state variable)
has state variable: x1 (EpileptorRestingState state variable)
has state variable: x2 (EpileptorRestingState state variable)
has state variable: x_rs (EpileptorRestingState state variable)
has state variable: y1 (EpileptorRestingState state variable)
has state variable: y2 (EpileptorRestingState state variable)
has state variable: y_rs (EpileptorRestingState state variable)
has state variable: z (EpileptorRestingState state variable)
model_type (slot): phenomenological

Event-driven integration
type: NamedIndividual
type: Simulation task
comment: Spike-based or hybrid event-driven simulation of a neural network.

Excitation
type: NamedIndividual
type: SKOS Concept
comment: Generic depolarising synaptic effect; abstract parent of model-specific excitatory currents and conductances.
broad match: GO_0060079

Excitatory/inhibitory subpopulations
type: NamedIndividual
type: Model feature

Fast-slow decomposition
type: NamedIndividual
type: Model feature

FeedbackScaling
type: NamedIndividual
type: SKOS Concept
comment: Multiplicative gain applied to recurrent feedback. Control-theoretic concept with no faithful upstream GO mapping.

GPU execution
type: NamedIndividual
type: Backend capability

GastSchmidtKnosche_SD
type: NamedIndividual
type: Dynamics
exhibits bifurcation: BifurcationEvent
  bifurcation type: Hopf
  type: Bifurcation event
exhibits regime: Oscillatory
exhibits regime: Quiescent
has attractor: Fixed point
has attractor: Limit cycle
has stochasticity character: Deterministic
models anatomical region: UBERON_0000956
models neurotransmitter system: GO_0035249
phase-space dimension: 4
description: 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: A mean-field description of bursting dynamics in neural populations
preferred label: Gast-Schmidt-Knosche (synaptic depression)
has parameter: Delta (GastSchmidtKnosche_SD parameter)
has parameter: I (GastSchmidtKnosche_SD parameter)
has parameter: J (GastSchmidtKnosche_SD parameter)
has parameter: alpha (GastSchmidtKnosche_SD parameter)
has parameter: cr (GastSchmidtKnosche_SD parameter)
has parameter: cv (GastSchmidtKnosche_SD parameter)
has parameter: eta (GastSchmidtKnosche_SD parameter)
has parameter: tau (GastSchmidtKnosche_SD parameter)
has parameter: tau_A (GastSchmidtKnosche_SD parameter)
has state variable: A (GastSchmidtKnosche_SD state variable)
has state variable: B (GastSchmidtKnosche_SD state variable)
has state variable: V (GastSchmidtKnosche_SD state variable)
has state variable: r (GastSchmidtKnosche_SD state variable)
model_type (slot): neural_mass

GastSchmidtKnosche_SF
type: NamedIndividual
type: Dynamics
exhibits bifurcation: BifurcationEvent
  bifurcation type: Hopf
  type: Bifurcation event
exhibits regime: Oscillatory
exhibits regime: Quiescent
has attractor: Fixed point
has attractor: Limit cycle
has stochasticity character: Deterministic
models anatomical region: UBERON_0000956
models neurotransmitter system: GO_0035249
phase-space dimension: 4
references: A mean-field description of bursting dynamics in neural populations
preferred label: Gast-Schmidt-Knosche (synaptic facilitation)
has parameter: Delta (GastSchmidtKnosche_SF parameter)
has parameter: I (GastSchmidtKnosche_SF parameter)
has parameter: J (GastSchmidtKnosche_SF parameter)
has parameter: alpha (GastSchmidtKnosche_SF parameter)
has parameter: cr (GastSchmidtKnosche_SF parameter)
has parameter: cv (GastSchmidtKnosche_SF parameter)
has parameter: eta (GastSchmidtKnosche_SF parameter)
has parameter: tau (GastSchmidtKnosche_SF parameter)
has parameter: tau_A (GastSchmidtKnosche_SF parameter)
has state variable: A (GastSchmidtKnosche_SF state variable)
has state variable: B (GastSchmidtKnosche_SF state variable)
has state variable: V (GastSchmidtKnosche_SF state variable)
has state variable: r (GastSchmidtKnosche_SF state variable)
model_type (slot): neural_mass

Generic2dOscillator
type: NamedIndividual
type: Dynamics
exhibits bifurcation: BifurcationEvent
  bifurcation type: Hopf
  type: Bifurcation event
exhibits bifurcation: BifurcationEvent
  bifurcation type: Saddle-node
  type: Bifurcation event
exhibits regime: Bistable
exhibits regime: Excitable
exhibits regime: Oscillatory
has attractor: Fixed point
has attractor: Limit cycle
has stochasticity character: Deterministic
has timescale separation: true
phase-space dimension: 2
description: 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: Impulses and physiological states in theoretical models of nerve membrane
references: An active pulse transmission line simulating nerve axon
preferred label: Generic 2-D oscillator
has parameter: I (Generic2dOscillator parameter)
has parameter: a (Generic2dOscillator parameter)
has parameter: alpha (Generic2dOscillator parameter)
has parameter: b (Generic2dOscillator parameter)
has parameter: beta (Generic2dOscillator parameter)
has parameter: c (Generic2dOscillator parameter)
has parameter: d (Generic2dOscillator parameter)
has parameter: e (Generic2dOscillator parameter)
has parameter: f (Generic2dOscillator parameter)
has parameter: g (Generic2dOscillator parameter)
has parameter: gamma (Generic2dOscillator parameter)
has parameter: tau (Generic2dOscillator parameter)
has state variable: V (Generic2dOscillator state variable)
has state variable: W (Generic2dOscillator state variable)
model_type (slot): generic

GenericLinear
type: NamedIndividual
type: Dynamics
exhibits regime: Quiescent
has attractor: Fixed point
has stochasticity character: Deterministic
has timescale separation: false
phase-space dimension: 1
description: The Generic Linear (GL) is a phenomenological, linear one-dimensional (i.e., one state-variable ('x')) neural mass model (Galán, 2008).
references: Optimal time scale for spike-time reliability: theory, simulations, and experiments
preferred label: Generic linear
has parameter: gamma (GenericLinear parameter)
has state variable: x (GenericLinear state variable)
model_type (slot): generic

Gradient-based optimisation
type: NamedIndividual
type: Simulation task

Hopfield
type: NamedIndividual
type: Dynamics
exhibits regime: Multistable
has attractor: Fixed point
has model feature: Sigmoid activation
has stochasticity character: Deterministic
phase-space dimension: 2
description: 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: Neural networks and physical systems with emergent collective computational abilities
references: Neurons with graded response have collective computational properties like those of two-state neurons
has parameter: tauT (Hopfield parameter)
has parameter: taux (Hopfield parameter)
has state variable: theta (Hopfield state variable)
has state variable: x (Hopfield state variable)
model_type (slot): neural_mass

Inhibition
type: NamedIndividual
type: SKOS Concept
comment: Generic hyperpolarising synaptic effect; abstract parent of model-specific inhibitory currents and conductances.
broad match: GO_0060080

InternalCoupling
type: NamedIndividual
type: SKOS Concept
comment: Within-population synaptic coupling, distinct from long-range inter-node coupling.
broad match: GO_0007268

JAX
type: NamedIndividual
type: Backend
provides capability: Automatic differentiation
provides capability: Symbolic code generation
provides capability: GPU execution
provides capability: Just-in-time compilation
provides capability: Vectorised RNG
supports task: Gradient-based optimisation
supports task: ODE integration
supports task: Parameter exploration
supports task: SDE integration

Just-in-time compilation
type: NamedIndividual
type: Backend capability

Jansen 1995
type: NamedIndividual
exhibits bifurcation: BifurcationEvent
  bifurcation type: Hopf
  type: Bifurcation event
exhibits regime: Oscillatory
exhibits regime: Quiescent
has attractor: Fixed point
has attractor: Limit cycle
has model feature: Sigmoid activation
has stochasticity character: Deterministic
models anatomical region: UBERON_0000956
models cell type: CL_0000099
models cell type: CL_0000598
models neurotransmitter system: GO_0007214
models neurotransmitter system: GO_0035249
has timescale separation: false
phase-space dimension: 6

JansenRit
type: NamedIndividual
type: Dynamics
exhibits bifurcation: BifurcationEvent
  bifurcation type: Hopf
  type: Bifurcation event
exhibits regime: Oscillatory
exhibits regime: Quiescent
has attractor: Fixed point
has attractor: Limit cycle
has model feature: Sigmoid activation
has stochasticity character: Deterministic
models anatomical region: UBERON_0000956
models cell type: CL_0000099
models cell type: CL_0000598
models neurotransmitter system: GO_0007214
models neurotransmitter system: GO_0035249
has timescale separation: false
phase-space dimension: 6
description: 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: Electroencephalogram and visual evoked potential generation in a mathematical model of coupled cortical columns
references: Parameter exploration of a realistic neural mass model of visual cortex
preferred label: Jansen-Rit
has derived variable: sigma_y0_1 (JansenRit derived variable)
has derived variable: sigma_y0_3 (JansenRit derived variable)
has derived variable: sigma_y1_y2 (JansenRit derived variable)
has parameter: A (JansenRit parameter)
has parameter: B (JansenRit parameter)
has parameter: J (JansenRit parameter)
has parameter: a (JansenRit parameter)
has parameter: a_1 (JansenRit parameter)
has parameter: a_2 (JansenRit parameter)
has parameter: a_3 (JansenRit parameter)
has parameter: a_4 (JansenRit parameter)
has parameter: b (JansenRit parameter)
has parameter: mu (JansenRit parameter)
has parameter: nu_max (JansenRit parameter)
has parameter: r (JansenRit parameter)
has parameter: v0 (JansenRit parameter)
has state variable: y0 (JansenRit state variable)
has state variable: y1 (JansenRit state variable)
has state variable: y2 (JansenRit state variable)
has state variable: y3 (JansenRit state variable)
has state variable: y4 (JansenRit state variable)
has state variable: y5 (JansenRit state variable)
model_type (slot): neural_mass

JansenRit1995
type: NamedIndividual
type: Dynamics
exhibits bifurcation: BifurcationEvent
  bifurcation type: Hopf
  type: Bifurcation event
exhibits regime: Oscillatory
exhibits regime: Quiescent
has attractor: Fixed point
has attractor: Limit cycle
has model feature: Sigmoid activation
has stochasticity character: Deterministic
models anatomical region: UBERON_0000956
phase-space dimension: 6
description: 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).
preferred label: Jansen-Rit 1995
has derived variable: v_pyr (JansenRit1995 derived variable)
has parameter: A (JansenRit1995 parameter)
has parameter: B (JansenRit1995 parameter)
has parameter: C (JansenRit1995 parameter)
has parameter: a (JansenRit1995 parameter)
has parameter: b (JansenRit1995 parameter)
has parameter: e0 (JansenRit1995 parameter)
has parameter: p (JansenRit1995 parameter)
has parameter: r (JansenRit1995 parameter)
has parameter: v0 (JansenRit1995 parameter)
has state variable: y0 (JansenRit1995 state variable)
has state variable: y1 (JansenRit1995 state variable)
has state variable: y2 (JansenRit1995 state variable)
has state variable: y3 (JansenRit1995 state variable)
has state variable: y4 (JansenRit1995 state variable)
has state variable: y5 (JansenRit1995 state variable)
model_type (slot): neural_mass

Julia JIT
type: NamedIndividual
type: Backend capability

KIonEx
type: NamedIndividual
type: Dynamics
exhibits bifurcation: BifurcationEvent
  bifurcation type: Saddle-node
  type: Bifurcation event
exhibits regime: Bistable
exhibits regime: Bursting
exhibits regime: Oscillatory
has attractor: Fixed point
has attractor: Limit cycle
has model feature: Fast-slow decomposition
has stochasticity character: Deterministic
models anatomical region: UBERON_0000956
models anatomical region: UBERON_0002728
has timescale separation: true
phase-space dimension: 5
description: 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: K Ion Exchange model extensions
subject: D004827
preferred label: K-ion exchange
has derived variable: DK_o (KIonEx derived variable)
has derived variable: DNa_i (KIonEx derived variable)
has derived variable: DNa_o (KIonEx derived variable)
has derived variable: I_Cl (KIonEx derived variable)
has derived variable: I_K (KIonEx derived variable)
has derived variable: I_Na (KIonEx derived variable)
has derived variable: I_pump (KIonEx derived variable)
has derived variable: K_i (KIonEx derived variable)
has derived variable: K_o (KIonEx derived variable)
has derived variable: Na_i (KIonEx derived variable)
has derived variable: Na_o (KIonEx derived variable)
has derived variable: V_temp (KIonEx derived variable)
has derived variable: Vcond (KIonEx derived variable)
has derived variable: beta (KIonEx derived variable)
has derived variable: h (KIonEx derived variable)
has derived variable: minf (KIonEx derived variable)
has derived variable: ninf (KIonEx derived variable)
has derived variable: r (KIonEx derived variable)
has derived variable: xcond (KIonEx derived variable)
has parameter: Chn (KIonEx parameter)
has parameter: Ckp (KIonEx parameter)
has parameter: Cl_i0 (KIonEx parameter)
has parameter: Cl_o0 (KIonEx parameter)
has parameter: Cm (KIonEx parameter)
has parameter: Cmna (KIonEx parameter)
has parameter: Cnap (KIonEx parameter)
has parameter: Cnk (KIonEx parameter)
has parameter: DChn (KIonEx parameter)
has parameter: DCkp (KIonEx parameter)
has parameter: DCmna (KIonEx parameter)
has parameter: DCnap (KIonEx parameter)
has parameter: DCnk (KIonEx parameter)
has parameter: Delta (KIonEx parameter)
has parameter: E (KIonEx parameter)
has parameter: J (KIonEx parameter)
has parameter: K_bath (KIonEx parameter)
has parameter: K_i0 (KIonEx parameter)
has parameter: K_o0 (KIonEx parameter)
has parameter: Na_i0 (KIonEx parameter)
has parameter: Na_o0 (KIonEx parameter)
has parameter: R_minus (KIonEx parameter)
has parameter: R_plus (KIonEx parameter)
has parameter: Vstar (KIonEx parameter)
has parameter: c_minus (KIonEx parameter)
has parameter: c_plus (KIonEx parameter)
has parameter: epsilon (KIonEx parameter)
has parameter: eta (KIonEx parameter)
has parameter: g_Cl (KIonEx parameter)
has parameter: g_K (KIonEx parameter)
has parameter: g_Kl (KIonEx parameter)
has parameter: g_Na (KIonEx parameter)
has parameter: g_Nal (KIonEx parameter)
has parameter: gamma (KIonEx parameter)
has parameter: rho (KIonEx parameter)
has parameter: tau_n (KIonEx parameter)
has parameter: w_i (KIonEx parameter)
has parameter: w_o (KIonEx parameter)
has state variable: DKi (KIonEx state variable)
has state variable: Kg (KIonEx state variable)
has state variable: V (KIonEx state variable)
has state variable: n (KIonEx state variable)
has state variable: x (KIonEx state variable)

Kuramoto
type: NamedIndividual
type: Dynamics
exhibits regime: Oscillatory
has attractor: Limit cycle
has attractor: Torus
has stochasticity character: Deterministic
has timescale separation: false
phase-space dimension: 1
description: 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: Role of local network oscillations in resting-state functional connectivity
references: Self-entrainment of a Population of Coupled Nonlinear Oscillators
references: From Kuramoto to Crawford: exploring the onset of synchronization in populations of coupled oscillators
has derived variable: I (Kuramoto derived variable)
has derived variable: lc_0 (Kuramoto derived variable)
has parameter: omega (Kuramoto parameter)
has state variable: theta (Kuramoto state variable)
model_type (slot): phase_oscillator

Kuramoto (extended)
type: NamedIndividual
exhibits regime: Oscillatory
has attractor: Limit cycle
has attractor: Torus
has stochasticity character: Deterministic
phase-space dimension: 2

KuramotoModel2
type: NamedIndividual
type: Dynamics
has derived variable: I (KuramotoModel2 derived variable)
has derived variable: lc_0 (KuramotoModel2 derived variable)
has derived variable: phase (KuramotoModel2 derived variable)
has derived variable: signal (KuramotoModel2 derived variable)
has parameter: omega (KuramotoModel2 parameter)
has state variable: theta (KuramotoModel2 state variable)
model_type (slot): phase_oscillator

LarterBreakspear
type: NamedIndividual
type: Dynamics
exhibits bifurcation: BifurcationEvent
  bifurcation type: Hopf
  type: Bifurcation event
exhibits regime: Bistable
exhibits regime: Chaotic
exhibits regime: Oscillatory
has attractor: Fixed point
has attractor: Limit cycle
has attractor: Strange attractor
has model feature: Excitatory/inhibitory subpopulations
has stochasticity character: Deterministic
models anatomical region: UBERON_0000956
models cell type: CL_0000099
models cell type: CL_0000598
models neurotransmitter system: GO_0007214
models neurotransmitter system: GO_0035249
has timescale separation: true
phase-space dimension: 3
description: 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.
preferred label: Larter-Breakspear
has derived variable: Q_V (LarterBreakspear derived variable)
has derived variable: Q_Z (LarterBreakspear derived variable)
has derived variable: lc_0 (LarterBreakspear derived variable)
has derived variable: m_Ca (LarterBreakspear derived variable)
has derived variable: m_K (LarterBreakspear derived variable)
has derived variable: m_Na (LarterBreakspear derived variable)
has parameter: C (LarterBreakspear parameter)
has parameter: I_ext (LarterBreakspear parameter)
has parameter: Q_Vmax (LarterBreakspear parameter)
has parameter: Q_Zmax (LarterBreakspear parameter)
has parameter: T_Ca (LarterBreakspear parameter)
has parameter: T_K (LarterBreakspear parameter)
has parameter: T_Na (LarterBreakspear parameter)
has parameter: V_Ca (LarterBreakspear parameter)
has parameter: V_K (LarterBreakspear parameter)
has parameter: V_L (LarterBreakspear parameter)
has parameter: V_Na (LarterBreakspear parameter)
has parameter: V_T (LarterBreakspear parameter)
has parameter: Z_T (LarterBreakspear parameter)
has parameter: a_ee (LarterBreakspear parameter)
has parameter: a_ei (LarterBreakspear parameter)
has parameter: a_ie (LarterBreakspear parameter)
has parameter: a_ne (LarterBreakspear parameter)
has parameter: a_ni (LarterBreakspear parameter)
has parameter: b (LarterBreakspear parameter)
has parameter: delta_Ca (LarterBreakspear parameter)
has parameter: delta_K (LarterBreakspear parameter)
has parameter: delta_Na (LarterBreakspear parameter)
has parameter: delta_V (LarterBreakspear parameter)
has parameter: delta_Z (LarterBreakspear parameter)
has parameter: g_Ca (LarterBreakspear parameter)
has parameter: g_K (LarterBreakspear parameter)
has parameter: g_L (LarterBreakspear parameter)
has parameter: g_Na (LarterBreakspear parameter)
has parameter: phi (LarterBreakspear parameter)
has parameter: r_NMDA (LarterBreakspear parameter)
has parameter: t_scale (LarterBreakspear parameter)
has parameter: tau_K (LarterBreakspear parameter)
has state variable: V (LarterBreakspear state variable)
has state variable: W (LarterBreakspear state variable)
has state variable: Z (LarterBreakspear state variable)
model_type (slot): neural_mass

ModelJansen1995
type: NamedIndividual
type: Dynamics
description: JR model with canonical parameters; long-range input is injected via a coupling term. Output is pyramidal potential difference.
has derived variable: v_pyr (ModelJansen1995 derived variable)
has parameter: A (ModelJansen1995 parameter)
has parameter: B (ModelJansen1995 parameter)
has parameter: C (ModelJansen1995 parameter)
has parameter: a (ModelJansen1995 parameter)
has parameter: b (ModelJansen1995 parameter)
has parameter: e0 (ModelJansen1995 parameter)
has parameter: p (ModelJansen1995 parameter)
has parameter: r (ModelJansen1995 parameter)
has parameter: v0 (ModelJansen1995 parameter)
has state variable: y0 (ModelJansen1995 state variable)
has state variable: y1 (ModelJansen1995 state variable)
has state variable: y2 (ModelJansen1995 state variable)
has state variable: y3 (ModelJansen1995 state variable)
has state variable: y4 (ModelJansen1995 state variable)
has state variable: y5 (ModelJansen1995 state variable)
model_type (slot): neural_mass

MontbrioPazoRoxin
type: NamedIndividual
type: Dynamics
exhibits bifurcation: BifurcationEvent
  bifurcation type: Saddle-node
  type: Bifurcation event
exhibits bifurcation: BifurcationEvent
  bifurcation type: Hopf
  type: Bifurcation event
exhibits regime: Bistable
exhibits regime: Oscillatory
exhibits regime: Quiescent
has attractor: Fixed point
has attractor: Limit cycle
has stochasticity character: Deterministic
models anatomical region: UBERON_0000956
phase-space dimension: 2
references: Macroscopic description for networks of spiking neurons
preferred label: Montbrio-Pazo-Roxin
has parameter: Delta (MontbrioPazoRoxin parameter)
has parameter: I (MontbrioPazoRoxin parameter)
has parameter: J (MontbrioPazoRoxin parameter)
has parameter: cr (MontbrioPazoRoxin parameter)
has parameter: cv (MontbrioPazoRoxin parameter)
has parameter: eta (MontbrioPazoRoxin parameter)
has parameter: tau (MontbrioPazoRoxin parameter)
has state variable: V (MontbrioPazoRoxin state variable)
has state variable: r (MontbrioPazoRoxin state variable)
model_type (slot): mean_field

NetworkDynamics.jl
type: NamedIndividual
type: Backend
provides capability: Delay history buffer
provides capability: DifferentialEquations.jl integrators
provides capability: Julia JIT
provides capability: Stiff solver
provides capability: Stochastic solver
supports task: DDE integration
supports task: ODE integration
supports task: Parameter exploration
supports task: SDDE integration
supports task: SDE integration

NetworkX topology API
type: NamedIndividual
type: Backend capability

NumPy execution
type: NamedIndividual
type: Backend capability

Numerical continuation
type: NamedIndividual
type: Simulation task
comment: Tracking of equilibria, periodic orbits, or invariant manifolds as a parameter is varied.

ODE integration
type: NamedIndividual
type: Simulation task
comment: Forward integration of a deterministic ordinary differential equation.

Parameter exploration
type: NamedIndividual
type: Simulation task

PyRates
type: NamedIndividual
type: Backend
provides capability: Symbolic code generation
provides capability: Delay history buffer
provides capability: NetworkX topology API
supports task: DDE integration
supports task: ODE integration

RDE integration
type: NamedIndividual
type: Simulation task
comment: Forward integration of a random differential equation: parameters drawn from a distribution (Bayesian / ensemble simulation).

ReducedWongWang
type: NamedIndividual
type: Dynamics
exhibits regime: Bistable
exhibits regime: Multistable
has attractor: Fixed point
has model feature: Excitatory/inhibitory subpopulations
has stochasticity character: Deterministic
models cell type: CL_0000099
models cell type: CL_0000598
models neurotransmitter system: GO_0007214
models neurotransmitter system: GO_0035249
has timescale separation: false
phase-space dimension: 1
description: 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: Resting-State Functional Connectivity Emerges from Structurally and Dynamically Shaped Slow Linear Fluctuations
references: A Recurrent Network Mechanism of Time Integration in Perceptual Decisions
preferred label: Reduced Wong-Wang
has derived variable: H (ReducedWongWang derived variable)
has derived variable: x (ReducedWongWang derived variable)
has parameter: I_o (ReducedWongWang parameter)
has parameter: J_N (ReducedWongWang parameter)
has parameter: a (ReducedWongWang parameter)
has parameter: b (ReducedWongWang parameter)
has parameter: d (ReducedWongWang parameter)
has parameter: gamma (ReducedWongWang parameter)
has parameter: tau_s (ReducedWongWang parameter)
has parameter: w (ReducedWongWang parameter)
has state variable: S (ReducedWongWang state variable)
model_type (slot): mean_field

ReducedWongWangExcInh
type: NamedIndividual
type: Dynamics
exhibits regime: Bistable
exhibits regime: Multistable
has attractor: Fixed point
has model feature: Excitatory/inhibitory subpopulations
has stochasticity character: Deterministic
models anatomical region: UBERON_0000956
models cell type: CL_0000099
models cell type: CL_0000598
models neurotransmitter system: GO_0007214
models neurotransmitter system: GO_0035249
has timescale separation: false
phase-space dimension: 2
description: 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: How local excitation--inhibition ratio impacts the whole brain dynamics
preferred label: Reduced Wong-Wang (E/I)
has derived variable: H_e (ReducedWongWangExcInh derived variable)
has derived variable: H_i (ReducedWongWangExcInh derived variable)
has derived variable: J_N_S_e (ReducedWongWangExcInh derived variable)
has derived variable: coupling (ReducedWongWangExcInh derived variable)
has derived variable: x_e (ReducedWongWangExcInh derived variable)
has derived variable: x_i (ReducedWongWangExcInh derived variable)
has parameter: G (ReducedWongWangExcInh parameter)
has parameter: I_ext (ReducedWongWangExcInh parameter)
has parameter: I_o (ReducedWongWangExcInh parameter)
has parameter: J_N (ReducedWongWangExcInh parameter)
has parameter: J_i (ReducedWongWangExcInh parameter)
has parameter: W_e (ReducedWongWangExcInh parameter)
has parameter: W_i (ReducedWongWangExcInh parameter)
has parameter: a_e (ReducedWongWangExcInh parameter)
has parameter: a_i (ReducedWongWangExcInh parameter)
has parameter: b_e (ReducedWongWangExcInh parameter)
has parameter: b_i (ReducedWongWangExcInh parameter)
has parameter: d_e (ReducedWongWangExcInh parameter)
has parameter: d_i (ReducedWongWangExcInh parameter)
has parameter: gamma_e (ReducedWongWangExcInh parameter)
has parameter: gamma_i (ReducedWongWangExcInh parameter)
has parameter: lamda (ReducedWongWangExcInh parameter)
has parameter: tau_e (ReducedWongWangExcInh parameter)
has parameter: tau_i (ReducedWongWangExcInh parameter)
has parameter: w_p (ReducedWongWangExcInh parameter)
has state variable: S_e (ReducedWongWangExcInh state variable)
has state variable: S_i (ReducedWongWangExcInh state variable)
model_type (slot): mean_field

Reduced Wong-Wang (functional)
type: NamedIndividual
exhibits regime: Bistable
has attractor: Fixed point
has stochasticity character: Deterministic
models anatomical region: UBERON_0000956
phase-space dimension: 1

ReducedWongWangTvboptim
type: NamedIndividual
type: Dynamics
exhibits regime: Bistable
has attractor: Fixed point
has stochasticity character: Deterministic
models anatomical region: UBERON_0000956
phase-space dimension: 1
description: 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: Resting-State Functional Connectivity Emerges from Structurally and Dynamically Shaped Slow Linear Fluctuations
references: A Recurrent Network Mechanism of Time Integration in Perceptual Decisions
preferred label: Reduced Wong-Wang (tvboptim)
has derived variable: H_x (ReducedWongWangTvboptim derived variable)
has derived variable: x (ReducedWongWangTvboptim derived variable)
has parameter: I_o (ReducedWongWangTvboptim parameter)
has parameter: J_N (ReducedWongWangTvboptim parameter)
has parameter: a (ReducedWongWangTvboptim parameter)
has parameter: b (ReducedWongWangTvboptim parameter)
has parameter: d (ReducedWongWangTvboptim parameter)
has parameter: gamma (ReducedWongWangTvboptim parameter)
has parameter: tau_s (ReducedWongWangTvboptim parameter)
has parameter: w (ReducedWongWangTvboptim parameter)
has state variable: S (ReducedWongWangTvboptim state variable)
model_type (slot): mean_field

SDDE integration
type: NamedIndividual
type: Simulation task
comment: Forward integration of a stochastic delay differential equation.

SDE integration
type: NamedIndividual
type: Simulation task
comment: Forward integration of a stochastic differential equation.

Sigmoid activation
type: NamedIndividual
type: Model feature

StefanescuJirsa2D
type: NamedIndividual
type: Dynamics
exhibits regime: Bistable
exhibits regime: Bursting
exhibits regime: Oscillatory
has attractor: Fixed point
has attractor: Limit cycle
has stochasticity character: Deterministic
models anatomical region: UBERON_0000956
has timescale separation: true
phase-space dimension: 4
description: 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`.
preferred label: Stefanescu-Jirsa 2D
has derived variable: Aik (StefanescuJirsa2D derived variable)
has derived variable: Bik (StefanescuJirsa2D derived variable)
has derived variable: Cik (StefanescuJirsa2D derived variable)
has derived variable: IE_i (StefanescuJirsa2D derived variable)
has derived variable: II_i (StefanescuJirsa2D derived variable)
has derived variable: e_i (StefanescuJirsa2D derived variable)
has derived variable: f_i (StefanescuJirsa2D derived variable)
has derived variable: m_i (StefanescuJirsa2D derived variable)
has derived variable: n_i (StefanescuJirsa2D derived variable)
has parameter: K11 (StefanescuJirsa2D parameter)
has parameter: K12 (StefanescuJirsa2D parameter)
has parameter: K21 (StefanescuJirsa2D parameter)
has parameter: a (StefanescuJirsa2D parameter)
has parameter: b (StefanescuJirsa2D parameter)
has parameter: mu (StefanescuJirsa2D parameter)
has parameter: sigma (StefanescuJirsa2D parameter)
has parameter: tau (StefanescuJirsa2D parameter)
has state variable: alpha (StefanescuJirsa2D state variable)
has state variable: beta (StefanescuJirsa2D state variable)
has state variable: eta (StefanescuJirsa2D state variable)
has state variable: xi (StefanescuJirsa2D state variable)
model_type (slot): neural_mass

StefanescuJirsa3D
type: NamedIndividual
type: Dynamics
exhibits regime: Bursting
exhibits regime: Chaotic
exhibits regime: Oscillatory
has attractor: Limit cycle
has attractor: Strange attractor
has stochasticity character: Deterministic
models anatomical region: UBERON_0000956
has timescale separation: true
phase-space dimension: 6
description: 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`.
preferred label: Stefanescu-Jirsa 3D
has derived variable: A_ik (StefanescuJirsa3D derived variable)
has derived variable: B_ik (StefanescuJirsa3D derived variable)
has derived variable: C_ik (StefanescuJirsa3D derived variable)
has derived variable: IE_i (StefanescuJirsa3D derived variable)
has derived variable: II_i (StefanescuJirsa3D derived variable)
has derived variable: a_i (StefanescuJirsa3D derived variable)
has derived variable: b_i (StefanescuJirsa3D derived variable)
has derived variable: c_i (StefanescuJirsa3D derived variable)
has derived variable: d_i (StefanescuJirsa3D derived variable)
has derived variable: e_i (StefanescuJirsa3D derived variable)
has derived variable: f_i (StefanescuJirsa3D derived variable)
has derived variable: h_i (StefanescuJirsa3D derived variable)
has derived variable: m_i (StefanescuJirsa3D derived variable)
has derived variable: n_i (StefanescuJirsa3D derived variable)
has derived variable: p_i (StefanescuJirsa3D derived variable)
has parameter: K_11 (StefanescuJirsa3D parameter)
has parameter: K_12 (StefanescuJirsa3D parameter)
has parameter: K_21 (StefanescuJirsa3D parameter)
has parameter: a (StefanescuJirsa3D parameter)
has parameter: b (StefanescuJirsa3D parameter)
has parameter: c (StefanescuJirsa3D parameter)
has parameter: d (StefanescuJirsa3D parameter)
has parameter: mu (StefanescuJirsa3D parameter)
has parameter: r (StefanescuJirsa3D parameter)
has parameter: s (StefanescuJirsa3D parameter)
has parameter: sigma (StefanescuJirsa3D parameter)
has parameter: x_0 (StefanescuJirsa3D parameter)
has state variable: alpha (StefanescuJirsa3D state variable)
has state variable: beta (StefanescuJirsa3D state variable)
has state variable: eta (StefanescuJirsa3D state variable)
has state variable: gamma (StefanescuJirsa3D state variable)
has state variable: tau (StefanescuJirsa3D state variable)
has state variable: xi (StefanescuJirsa3D state variable)
model_type (slot): neural_mass

Stiff solver
type: NamedIndividual
type: Backend capability

Stochastic solver
type: NamedIndividual
type: Backend capability

SupHopf
type: NamedIndividual
type: Dynamics
exhibits bifurcation: BifurcationEvent
  bifurcation type: Supercritical Hopf
  type: Bifurcation event
exhibits regime: Oscillatory
exhibits regime: Quiescent
has attractor: Fixed point
has attractor: Limit cycle
has stochasticity character: Deterministic
phase-space dimension: 2
description: 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: The dynamics of resting fluctuations in the brain: metastability and its dynamical cortical core
preferred label: Supercritical Hopf
has derived variable: lc_0 (SupHopf derived variable)
has parameter: a (SupHopf parameter)
has parameter: omega (SupHopf parameter)
has state variable: x (SupHopf state variable)
has state variable: y (SupHopf state variable)
model_type (slot): generic

TVB
type: NamedIndividual
type: Backend
provides capability: Built-in model library
provides capability: Delay history buffer
provides capability: NumPy execution
provides capability: Stochastic solver
supports task: DDE integration
supports task: ODE integration
supports task: Parameter exploration
supports task: SDDE integration
supports task: SDE integration

TimeScaling
type: NamedIndividual
type: SKOS Concept
comment: 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).

TsodyksMarkram
type: NamedIndividual
type: Dynamics
exhibits regime: Oscillatory
exhibits regime: Quiescent
has attractor: Fixed point
has attractor: Limit cycle
has stochasticity character: Deterministic
models anatomical region: UBERON_0000956
models neurotransmitter system: GO_0035249
phase-space dimension: 3
description: 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.
preferred label: Tsodyks-Markram
has derived variable: SS0 (TsodyksMarkram derived variable)
has derived variable: SS1 (TsodyksMarkram derived variable)
has parameter: E0 (TsodyksMarkram parameter)
has parameter: J (TsodyksMarkram parameter)
has parameter: U0 (TsodyksMarkram parameter)
has parameter: alpha (TsodyksMarkram parameter)
has parameter: tau (TsodyksMarkram parameter)
has parameter: tauD (TsodyksMarkram parameter)
has parameter: tauF (TsodyksMarkram parameter)
has state variable: E (TsodyksMarkram state variable)
has state variable: u (TsodyksMarkram state variable)
has state variable: x (TsodyksMarkram state variable)
model_type (slot): neural_mass

Vectorised RNG
type: NamedIndividual
type: Backend capability

WilsonCowan
type: NamedIndividual
type: Dynamics
exhibits bifurcation: BifurcationEvent
  bifurcation type: Hopf
  type: Bifurcation event
exhibits bifurcation: BifurcationEvent
  bifurcation type: Saddle-node
  type: Bifurcation event
exhibits regime: Bistable
exhibits regime: Oscillatory
exhibits regime: Quiescent
has attractor: Fixed point
has attractor: Limit cycle
has model feature: Excitatory/inhibitory subpopulations
has model feature: Sigmoid activation
has stochasticity character: Deterministic
models anatomical region: UBERON_0000956
models cell type: CL_0000099
models cell type: CL_0000598
models neurotransmitter system: GO_0007214
models neurotransmitter system: GO_0035249
has timescale separation: false
phase-space dimension: 2
description: 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: Excitatory and inhibitory interactions in localized populations of model neurons
references: A mathematical theory of the functional dynamics of cortical and thalamic nervous tissue
preferred label: Wilson-Cowan
has derived variable: lc_0 (WilsonCowan derived variable)
has derived variable: lc_1 (WilsonCowan derived variable)
has derived variable: s_e (WilsonCowan derived variable)
has derived variable: s_i (WilsonCowan derived variable)
has derived variable: x_e (WilsonCowan derived variable)
has derived variable: x_i (WilsonCowan derived variable)
has parameter: P (WilsonCowan parameter)
has parameter: Q (WilsonCowan parameter)
has parameter: a_e (WilsonCowan parameter)
has parameter: a_i (WilsonCowan parameter)
has parameter: alpha_e (WilsonCowan parameter)
has parameter: alpha_i (WilsonCowan parameter)
has parameter: b_e (WilsonCowan parameter)
has parameter: b_i (WilsonCowan parameter)
has parameter: c_e (WilsonCowan parameter)
has parameter: c_ee (WilsonCowan parameter)
has parameter: c_ei (WilsonCowan parameter)
has parameter: c_i (WilsonCowan parameter)
has parameter: c_ie (WilsonCowan parameter)
has parameter: c_ii (WilsonCowan parameter)
has parameter: k_e (WilsonCowan parameter)
has parameter: k_i (WilsonCowan parameter)
has parameter: r_e (WilsonCowan parameter)
has parameter: r_i (WilsonCowan parameter)
has parameter: shift_sigmoid (WilsonCowan parameter)
has parameter: tau_e (WilsonCowan parameter)
has parameter: tau_i (WilsonCowan parameter)
has parameter: theta_e (WilsonCowan parameter)
has parameter: theta_i (WilsonCowan parameter)
has state variable: E (WilsonCowan state variable)
has state variable: I (WilsonCowan state variable)
model_type (slot): neural_mass

ZerlautAdaptationFirstOrder
type: NamedIndividual
type: Dynamics
exhibits bifurcation: BifurcationEvent
  bifurcation type: Hopf
  type: Bifurcation event
exhibits regime: Oscillatory
exhibits regime: Quiescent
has attractor: Fixed point
has attractor: Limit cycle
has model feature: Excitatory/inhibitory subpopulations
has stochasticity character: Deterministic
models anatomical region: UBERON_0000956
models cell type: CL_0000099
models cell type: CL_0000598
models neurotransmitter system: GO_0007214
models neurotransmitter system: GO_0035249
has timescale separation: true
phase-space dimension: 5
references: Biophysical ingredients for a robust model of cortical dynamics
references: A mean-field model of conductance-based networks of adaptive exponential integrate-and-fire neurons
preferred label: Zerlaut (first-order adaptation)
has derived variable: Fe_ext (ZerlautAdaptationFirstOrder derived variable)
has derived variable: Fi_ext (ZerlautAdaptationFirstOrder derived variable)
has derived variable: S_e (ZerlautAdaptationFirstOrder derived variable)
has derived variable: S_i (ZerlautAdaptationFirstOrder derived variable)
has derived variable: T_V_e (ZerlautAdaptationFirstOrder derived variable)
has derived variable: T_V_i (ZerlautAdaptationFirstOrder derived variable)
has derived variable: T_e (ZerlautAdaptationFirstOrder derived variable)
has derived variable: T_i (ZerlautAdaptationFirstOrder derived variable)
has derived variable: T_m_e (ZerlautAdaptationFirstOrder derived variable)
has derived variable: T_m_i (ZerlautAdaptationFirstOrder derived variable)
has derived variable: U_e_e (ZerlautAdaptationFirstOrder derived variable)
has derived variable: U_e_i (ZerlautAdaptationFirstOrder derived variable)
has derived variable: U_i_e (ZerlautAdaptationFirstOrder derived variable)
has derived variable: U_i_i (ZerlautAdaptationFirstOrder derived variable)
has derived variable: V_e (ZerlautAdaptationFirstOrder derived variable)
has derived variable: V_i (ZerlautAdaptationFirstOrder derived variable)
has derived variable: V_thre_e (ZerlautAdaptationFirstOrder derived variable)
has derived variable: V_thre_i (ZerlautAdaptationFirstOrder derived variable)
has derived variable: f_out_e (ZerlautAdaptationFirstOrder derived variable)
has derived variable: f_out_i (ZerlautAdaptationFirstOrder derived variable)
has derived variable: fe_e (ZerlautAdaptationFirstOrder derived variable)
has derived variable: fe_i (ZerlautAdaptationFirstOrder derived variable)
has derived variable: fi_e (ZerlautAdaptationFirstOrder derived variable)
has derived variable: fi_i (ZerlautAdaptationFirstOrder derived variable)
has derived variable: lc_E (ZerlautAdaptationFirstOrder derived variable)
has derived variable: lc_I (ZerlautAdaptationFirstOrder derived variable)
has derived variable: mu_G_e (ZerlautAdaptationFirstOrder derived variable)
has derived variable: mu_G_i (ZerlautAdaptationFirstOrder derived variable)
has derived variable: mu_Ge_e (ZerlautAdaptationFirstOrder derived variable)
has derived variable: mu_Ge_i (ZerlautAdaptationFirstOrder derived variable)
has derived variable: mu_Gi_e (ZerlautAdaptationFirstOrder derived variable)
has derived variable: mu_Gi_i (ZerlautAdaptationFirstOrder derived variable)
has derived variable: mu_V_e (ZerlautAdaptationFirstOrder derived variable)
has derived variable: mu_V_i (ZerlautAdaptationFirstOrder derived variable)
has derived variable: sigma_V_e (ZerlautAdaptationFirstOrder derived variable)
has derived variable: sigma_V_i (ZerlautAdaptationFirstOrder derived variable)
has parameter: C_m (ZerlautAdaptationFirstOrder parameter)
has parameter: DTvN0 (ZerlautAdaptationFirstOrder parameter)
has parameter: DmuV0 (ZerlautAdaptationFirstOrder parameter)
has parameter: DsV0 (ZerlautAdaptationFirstOrder parameter)
has parameter: E_L_e (ZerlautAdaptationFirstOrder parameter)
has parameter: E_L_i (ZerlautAdaptationFirstOrder parameter)
has parameter: E_e (ZerlautAdaptationFirstOrder parameter)
has parameter: E_i (ZerlautAdaptationFirstOrder parameter)
has parameter: K_ext_e (ZerlautAdaptationFirstOrder parameter)
has parameter: K_ext_i (ZerlautAdaptationFirstOrder parameter)
has parameter: N_tot (ZerlautAdaptationFirstOrder parameter)
has parameter: P0_e (ZerlautAdaptationFirstOrder parameter)
has parameter: P0_i (ZerlautAdaptationFirstOrder parameter)
has parameter: P1_e (ZerlautAdaptationFirstOrder parameter)
has parameter: P1_i (ZerlautAdaptationFirstOrder parameter)
has parameter: P2_e (ZerlautAdaptationFirstOrder parameter)
has parameter: P2_i (ZerlautAdaptationFirstOrder parameter)
has parameter: P3_e (ZerlautAdaptationFirstOrder parameter)
has parameter: P3_i (ZerlautAdaptationFirstOrder parameter)
has parameter: P4_e (ZerlautAdaptationFirstOrder parameter)
has parameter: P4_i (ZerlautAdaptationFirstOrder parameter)
has parameter: P5_e (ZerlautAdaptationFirstOrder parameter)
has parameter: P5_i (ZerlautAdaptationFirstOrder parameter)
has parameter: P6_e (ZerlautAdaptationFirstOrder parameter)
has parameter: P6_i (ZerlautAdaptationFirstOrder parameter)

ZetterbergJansen
type: NamedIndividual
type: Dynamics
exhibits bifurcation: BifurcationEvent
  bifurcation type: Hopf
  type: Bifurcation event
exhibits regime: Oscillatory
has attractor: Fixed point
has attractor: Limit cycle
has model feature: Sigmoid activation
has stochasticity character: Deterministic
models anatomical region: UBERON_0000956
phase-space dimension: 6
references: A model for the interrelationship between EEG and evoked potentials
preferred label: Zetterberg-Jansen
has derived variable: coupled_input (ZetterbergJansen derived variable)
has derived variable: sigma_v1 (ZetterbergJansen derived variable)
has derived variable: sigma_v23 (ZetterbergJansen derived variable)
has derived variable: sigma_v45 (ZetterbergJansen derived variable)
has parameter: He (ZetterbergJansen parameter)
has parameter: Hi (ZetterbergJansen parameter)
has parameter: P (ZetterbergJansen parameter)
has parameter: Q (ZetterbergJansen parameter)
has parameter: U (ZetterbergJansen parameter)
has parameter: e0 (ZetterbergJansen parameter)
has parameter: gamma_1 (ZetterbergJansen parameter)
has parameter: gamma_1T (ZetterbergJansen parameter)
has parameter: gamma_2 (ZetterbergJansen parameter)
has parameter: gamma_2T (ZetterbergJansen parameter)
has parameter: gamma_3 (ZetterbergJansen parameter)
has parameter: gamma_3T (ZetterbergJansen parameter)
has parameter: gamma_4 (ZetterbergJansen parameter)
has parameter: gamma_5 (ZetterbergJansen parameter)
has parameter: ke (ZetterbergJansen parameter)
has parameter: ki (ZetterbergJansen parameter)
has parameter: rho_1 (ZetterbergJansen parameter)
has parameter: rho_2 (ZetterbergJansen parameter)
has state variable: v1 (ZetterbergJansen state variable)
has state variable: v2 (ZetterbergJansen state variable)
has state variable: v3 (ZetterbergJansen state variable)
has state variable: v4 (ZetterbergJansen state variable)
has state variable: v5 (ZetterbergJansen state variable)
has state variable: v6 (ZetterbergJansen state variable)
has state variable: v7 (ZetterbergJansen state variable)
has state variable: y1 (ZetterbergJansen state variable)
has state variable: y2 (ZetterbergJansen state variable)
has state variable: y3 (ZetterbergJansen state variable)
has state variable: y4 (ZetterbergJansen state variable)
has state variable: y5 (ZetterbergJansen state variable)
model_type (slot): neural_mass

tvboptim
type: NamedIndividual
type: Backend
provides capability: Automatic differentiation
provides capability: Symbolic code generation
provides capability: Just-in-time compilation
provides capability: Stochastic solver
supports task: Gradient-based optimisation
supports task: ODE integration
supports task: SDE integration

r_E (CakanObermayer derived variable)
type: NamedIndividual
type: DerivedVariable
description: 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: r_E
lhs: r_E
rhs: r_max/(1 + exp(-k_phi*(mu_se - mu_th)))

r_I (CakanObermayer derived variable)
type: NamedIndividual
type: DerivedVariable
description: Inhibitory population firing rate (sigmoid stand-in for aLN Phi).
notation: r_I
lhs: r_I
rhs: r_max/(1 + exp(-k_phi*(mu_si - mu_th)))

C (CakanObermayer parameter)
type: NamedIndividual
type: Parameter
default value: 200.0
has db xref: GO_0030322
has db xref: GO_0042391
has db xref: GO_0098696
definition: Membrane capacitance of a single AdEx neuron.
notation: C
unit (slot): pF

E_A (CakanObermayer parameter)
type: NamedIndividual
type: Parameter
default value: -80.0
has db xref: GO_0042391
definition: Reversal potential of the adaptation current.
notation: E_A
unit (slot): mV

E_L (CakanObermayer parameter)
type: NamedIndividual
type: Parameter
default value: -65.0
has db xref: GO_0022840
definition: Leak reversal potential of a single AdEx neuron.
notation: E_L
unit (slot): mV

I_A (CakanObermayer parameter)
type: NamedIndividual
type: Parameter
default value: 0.0
has db xref: GO_0060079
definition: Subthreshold adaptation conductance amplitude (a in AdEx).
notation: I_A
unit (slot): nS

J_EE (CakanObermayer parameter)
type: NamedIndividual
type: Parameter
default value: 2.43
has db xref: GO_0060076
has db xref: GO_0060079
has db xref: GO_0098817
definition: Maximum excitatory-to-excitatory PSC amplitude (Jee_max in neurolib).
notation: J_EE
unit (slot): mV_per_ms

J_EI (CakanObermayer parameter)
type: NamedIndividual
type: Parameter
default value: -3.3
has db xref: GO_0060080
has db xref: GO_0099536
definition: Maximum inhibitory-to-excitatory PSC amplitude (Jei_max in neurolib, signed negative).
notation: J_EI
unit (slot): mV_per_ms

J_IE (CakanObermayer parameter)
type: NamedIndividual
type: Parameter
default value: 2.6
has db xref: GO_0060079
definition: Maximum excitatory-to-inhibitory PSC amplitude (Jie_max in neurolib).
notation: J_IE
unit (slot): mV_per_ms

J_II (CakanObermayer parameter)
type: NamedIndividual
type: Parameter
default value: -1.64
has db xref: GO_0060080
definition: Maximum inhibitory-to-inhibitory PSC amplitude (Jii_max in neurolib, signed negative).
notation: J_II
unit (slot): mV_per_ms

k_phi (CakanObermayer parameter)
type: NamedIndividual
type: Parameter
default value: 1.0
definition: Steepness of the sigmoid transfer-function surrogate.
notation: k_phi

mu_E (CakanObermayer parameter)
type: NamedIndividual
type: Parameter
default value: 0.4
definition: Mean external input current to the excitatory population (mue_ext_mean).
notation: mu_E
unit (slot): mV_per_ms

mu_I (CakanObermayer parameter)
type: NamedIndividual
type: Parameter
default value: 0.3
has db xref: GO_0042391
has db xref: GO_0060080
has db xref: GO_0098828
definition: Mean external input current to the inhibitory population (mui_ext_mean).
notation: mu_I
unit (slot): mV_per_ms

mu_th (CakanObermayer parameter)
type: NamedIndividual
type: Parameter
default value: 1.0
definition: Half-maximum input of the sigmoid transfer-function surrogate.
notation: mu_th
unit (slot): mV_per_ms

r_max (CakanObermayer parameter)
type: NamedIndividual
type: Parameter
default value: 0.2
definition: Asymptotic firing rate used in the sigmoid surrogate for the aLN transfer function (sigmoid stand-in for the precomputed lookup table).
notation: r_max
unit (slot): per_ms

s_EE (CakanObermayer parameter)
type: NamedIndividual
type: Parameter
default value: 1.5
has db xref: GO_0060079
has db xref: GO_0098815
definition: Standard deviation of the random-coupling-driven membrane-potential fluctuations entering the E->E channel (sigmae_ext component).
notation: s_EE
unit (slot): mV_per_ms

s_EI (CakanObermayer parameter)
type: NamedIndividual
type: Parameter
default value: 1.5
has db xref: GO_0098815
definition: Standard deviation of the random-coupling-driven membrane-potential fluctuations entering the I->E channel.
notation: s_EI
unit (slot): mV_per_ms

s_IE (CakanObermayer parameter)
type: NamedIndividual
type: Parameter
default value: 1.5
has db xref: GO_0098815
definition: Standard deviation of the random-coupling-driven membrane-potential fluctuations entering the E->I channel.
notation: s_IE
unit (slot): mV_per_ms

s_II (CakanObermayer parameter)
type: NamedIndividual
type: Parameter
default value: 1.5
has db xref: GO_0060080
has db xref: GO_0098828
definition: Standard deviation of the random-coupling-driven membrane-potential fluctuations entering the I->I channel.
notation: s_II
unit (slot): mV_per_ms

tau_A (CakanObermayer parameter)
type: NamedIndividual
type: Parameter
default value: 200.0
definition: Time constant of the adaptation current.
notation: tau_A
unit (slot): ms

tau_se (CakanObermayer parameter)
type: NamedIndividual
type: Parameter
default value: 2.0
definition: Synaptic time constant of excitatory PSCs (E->E and E->I).
notation: tau_se
unit (slot): ms

tau_si (CakanObermayer parameter)
type: NamedIndividual
type: Parameter
default value: 5.0
definition: Synaptic time constant of inhibitory PSCs (I->E and I->I).
notation: tau_si
unit (slot): ms

I_A_var (CakanObermayer state variable)
type: NamedIndividual
type: StateVariable
description: Adaptation current.
notation: I_A_var
lhs: Derivative(I_A_var, t)
rhs: (I_A*(mu_se - E_A) - I_A_var)/tau_A

mu_se (CakanObermayer state variable)
type: NamedIndividual
type: StateVariable
description: Filtered mean synaptic input current to the excitatory population.
notation: mu_se
lhs: Derivative(mu_se, t)
rhs: (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)
type: NamedIndividual
type: StateVariable
description: Filtered mean synaptic input current to the inhibitory population.
notation: mu_si
lhs: Derivative(mu_si, t)
rhs: (J_IE*r_E + J_II*r_I + mu_I - mu_si)/tau_si

Delta (CoombesByrne parameter)
type: NamedIndividual
type: Parameter
description: Half-width of heterogeneous noise distribution
default value: 0.5
notation: Delta

alpha (CoombesByrne parameter)
type: NamedIndividual
type: Parameter
description: Parameter of the alpha-function
default value: 0.95
notation: alpha

eta (CoombesByrne parameter)
type: NamedIndividual
type: Parameter
description: Constant parameter to scale the rate of feedback from the firing rate variable to itself
default value: 20.0
has db xref: GO_0099605
notation: eta

k (CoombesByrne parameter)
type: NamedIndividual
type: Parameter
description: Local coupling strength
default value: 1.0
notation: k

v_syn (CoombesByrne parameter)
type: NamedIndividual
type: Parameter
description: QIF membrane reversal potential
default value: -10.0
has db xref: GO_0042391
notation: v_syn

V (CoombesByrne state variable)
type: NamedIndividual
type: StateVariable
notation: V
lhs: Derivative(V, t)
rhs: V**2 + c_pop0 + eta + g*(-V + v_syn) - pi**2*r**2

g (CoombesByrne state variable)
type: NamedIndividual
type: StateVariable
notation: g
lhs: Derivative(g, t)
rhs: alpha*q

q (CoombesByrne state variable)
type: NamedIndividual
type: StateVariable
notation: q
lhs: Derivative(q, t)
rhs: alpha*(-g + pi*k*r - 2*q)

r (CoombesByrne state variable)
type: NamedIndividual
type: StateVariable
notation: r
lhs: Derivative(r, t)
rhs: Delta/pi + 2*V*r - g*r

Delta (CoombesByrne2D parameter)
type: NamedIndividual
type: Parameter
description: Half-width of heterogeneous noise distribution
default value: 1.0
notation: Delta

eta (CoombesByrne2D parameter)
type: NamedIndividual
type: Parameter
description: Constant parameter to scale the rate of feedback from the firing rate variable to itself
default value: 2.0
has db xref: GO_0099605
notation: eta

k (CoombesByrne2D parameter)
type: NamedIndividual
type: Parameter
description: Local coupling strength
default value: 1.0
notation: k

v_syn (CoombesByrne2D parameter)
type: NamedIndividual
type: Parameter
description: QIF membrane reversal potential
default value: -4.0
has db xref: GO_0042391
notation: v_syn

V (CoombesByrne2D state variable)
type: NamedIndividual
type: StateVariable
notation: V
lhs: Derivative(V, t)
rhs: V**2 + c_pop0 + eta + pi*k*r*(-V + v_syn) - pi**2*r**2

r (CoombesByrne2D state variable)
type: NamedIndividual
type: StateVariable
notation: r
lhs: Derivative(r, t)
rhs: Delta/pi + 2*V*r - pi*k*r**2

Delta_e (DumontGutkin parameter)
type: NamedIndividual
type: Parameter
description: Half-width of heterogeneous noise distribution over excitatory population
default value: 1.0
has db xref: GO_0060079
has db xref: GO_0098815
notation: Delta_e

Delta_i (DumontGutkin parameter)
type: NamedIndividual
type: Parameter
description: Half-width of heterogeneous noise distribution over inhibitory population
default value: 1.0
has db xref: GO_0032228
has db xref: GO_0060080
has db xref: GO_0098828
notation: Delta_i

Gamma (DumontGutkin parameter)
type: NamedIndividual
type: Parameter
description: Ratio of excitatory VS inhibitory global couplings G_ie/G_ee
default value: 5.0
has db xref: GO_0060079
has db xref: GO_0060080
definition: Ratio of excitatory VS inhibitory global couplings G_ie/G_ee .
notation: Gamma

I_e (DumontGutkin parameter)
type: NamedIndividual
type: Parameter
description: External homogeneous current on excitatory population
default value: 0.0
has db xref: GO_0060079
notation: I_e

I_i (DumontGutkin parameter)
type: NamedIndividual
type: Parameter
description: External current on inhibitory population
default value: 0.0
has db xref: GO_0060080
has db xref: GO_0098828
notation: I_i

J_ee (DumontGutkin parameter)
type: NamedIndividual
type: Parameter
description: Synaptic weight e-->e
default value: 0.0
has db xref: GO_0060076
has db xref: GO_0097060
has db xref: GO_0099536
notation: J_ee

J_ei (DumontGutkin parameter)
type: NamedIndividual
type: Parameter
description: Synaptic weight i-->e
default value: 10.0
has db xref: GO_0042391
has db xref: GO_0097060
notation: J_ei

J_ie (DumontGutkin parameter)
type: NamedIndividual
type: Parameter
description: Synaptic weight e-->i
default value: 0.0
has db xref: GO_0097060
has db xref: GO_0099536
notation: J_ie

J_ii (DumontGutkin parameter)
type: NamedIndividual
type: Parameter
description: Synaptic weight i-->i
default value: 15.0
has db xref: GO_0060077
has db xref: GO_0097060
notation: J_ii

eta_e (DumontGutkin parameter)
type: NamedIndividual
type: Parameter
description: Mean heterogeneous current on excitatory population
default value: -5.0
has db xref: GO_0098815
notation: eta_e

eta_i (DumontGutkin parameter)
type: NamedIndividual
type: Parameter
description: Mean heterogeneous current on inhibitory population
default value: -5.0
has db xref: GO_0060080
notation: eta_i

tau_e (DumontGutkin parameter)
type: NamedIndividual
type: Parameter
description: Characteristic time of excitatory population
default value: 10.0
has db xref: GO_0043179
has db xref: GO_0060079
notation: tau_e

tau_i (DumontGutkin parameter)
type: NamedIndividual
type: Parameter
description: Characteristic time of inhibitory population
default value: 10.0
has db xref: GO_0043180
has db xref: GO_0060080
notation: tau_i

tau_s (DumontGutkin parameter)
type: NamedIndividual
type: Parameter
description: Synaptic time constant
default value: 1.0
has db xref: GO_0099536
notation: tau_s

V_e (DumontGutkin state variable)
type: NamedIndividual
type: StateVariable
notation: V_e
lhs: Derivative(V_e, t)
rhs: (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_i (DumontGutkin state variable)
type: NamedIndividual
type: StateVariable
notation: V_i
lhs: Derivative(V_i, t)
rhs: (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

r_e (DumontGutkin state variable)
type: NamedIndividual
type: StateVariable
notation: r_e
lhs: Derivative(r_e, t)
rhs: (Delta_e/(pi*tau_e) + 2*V_e*r_e)/tau_e

r_i (DumontGutkin state variable)
type: NamedIndividual
type: StateVariable
notation: r_i
lhs: Derivative(r_i, t)
rhs: (Delta_i/(pi*tau_i) + 2*V_i*r_i)/tau_i

s_ee (DumontGutkin state variable)
type: NamedIndividual
type: StateVariable
notation: s_ee
lhs: Derivative(s_ee, t)
rhs: (J_ee*r_e + c_pop0 - s_ee)/tau_s

s_ei (DumontGutkin state variable)
type: NamedIndividual
type: StateVariable
notation: s_ei
lhs: Derivative(s_ei, t)
rhs: (J_ei*r_i - s_ei)/tau_s

s_ie (DumontGutkin state variable)
type: NamedIndividual
type: StateVariable
notation: s_ie
lhs: Derivative(s_ie, t)
rhs: (Gamma*c_pop0 + J_ie*r_e - s_ie)/tau_s

s_ii (DumontGutkin state variable)
type: NamedIndividual
type: StateVariable
notation: s_ii
lhs: Derivative(s_ii, t)
rhs: (J_ii*r_i - s_ii)/tau_s

h (Epileptor2D derived variable)
type: NamedIndividual
type: DerivedVariable
notation: h
lhs: h
rhs: Piecewise((x0 + 3.0/(exp((-x1 - 1*0.5)/0.1) + 1.0), modification > 0), (zcond + 4*(-x0 + x1), True))

x1cond (Epileptor2D derived variable)
type: NamedIndividual
type: DerivedVariable
notation: x1cond
lhs: x1cond
rhs: Piecewise((a*x1**2 + x1*(-b + d), x1 < 0), (d*x1 - slope - 0.6*(z - 4.0)**2, True))

zcond (Epileptor2D derived variable)
type: NamedIndividual
type: DerivedVariable
notation: zcond
lhs: zcond
rhs: Piecewise((-0.1*z**7, z < 0), (0, True))

Iext (Epileptor2D parameter)
type: NamedIndividual
type: Parameter
description: External input current to the first state-variable x_E2D, in Epileptor2D (Proix et al
default value: 3.1
definition: External input current to the first state-variable x_E2D, in Epileptor2D (Proix et al.,2014).
notation: Iext

Ks (Epileptor2D parameter)
type: NamedIndividual
type: Parameter
description: Permittivity coupling on the slow permittivity state-variable z_E2D in Epileptor2D (Proix et al
default value: 0.0
definition: 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: Ks

Kvf (Epileptor2D parameter)
type: NamedIndividual
type: Parameter
description: Coupling scaling on a very fast time scale
default value: 0.0
definition: Coupling scaling on a very fast time scale.
notation: Kvf

a (Epileptor2D parameter)
type: NamedIndividual
type: Parameter
description: 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: 1.0
definition: 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: a

b (Epileptor2D parameter)
type: NamedIndividual
type: Parameter
description: Coefficient of the squared term in the first state-variable x_E2D via the function f_E2D, in Epileptor2D (Proix et al
default value: 3.0
definition: Coefficient of the squared term in the first state-variable x_E2D via the function f_E2D, in Epileptor2D (Proix et al.,2014).
notation: b

c (Epileptor2D parameter)
type: NamedIndividual
type: Parameter
description: Additive coefficient for the second state-variable x_{2}, called :math:`y_{0}` in Jirsa paper
default value: 1.0
definition: Additive coefficient for the second state-variable x_{2}, called :math:`y_{0}` in Jirsa paper.
notation: c

d (Epileptor2D parameter)
type: NamedIndividual
type: Parameter
description: Coefficient of the squared term in the first state-variable x_E2D via the function f in Epileptor2D (Proix et al
default value: 5.0
definition: Coefficient of the squared term in the first state-variable x_E2D via the function f in Epileptor2D (Proix et al.,2014).
notation: d

modification (Epileptor2D parameter)
type: NamedIndividual
type: Parameter
description: When modification is True, the function h_E2D uses a nonlinear influence on z_E2D
default value: 0.0
definition: 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: modification

r (Epileptor2D parameter)
type: NamedIndividual
type: Parameter
description: Temporal scaling in the slow state-variable, \ called :math:`1\tau_{0}` in Jirsa paper (see class Epileptor)
default value: 3.5E-4
definition: Temporal scaling in the slow state-variable, \ called :math:`1\tau_{0}` in Jirsa paper (see class Epileptor).
notation: r

slope (Epileptor2D parameter)
type: NamedIndividual
type: Parameter
description: Linear coefficient in the first state-variable x_E2D via the function f_E2D, in Epileptor2D (Proix et al
default value: 0.0
definition: Linear coefficient in the first state-variable x_E2D via the function f_E2D, in Epileptor2D (Proix et al.,2014).
notation: slope

tt (Epileptor2D parameter)
type: NamedIndividual
type: Parameter
description: Characteristic time scale of the whole-system Epileptor2D
default value: 1.0
definition: Characteristic time scale of the whole-system Epileptor2D.
notation: tt

x0 (Epileptor2D parameter)
type: NamedIndividual
type: Parameter
description: Degree of excitability or epileptogenicity in Epileptor2D (Proix et al
default value: -1.6
has db xref: GO_0043179
definition: 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: x0

x1 (Epileptor2D state variable)
type: NamedIndividual
type: StateVariable
description: First state-variable in the Epileptor2D (Proix et al
notation: x1
lhs: Derivative(x1, t)
rhs: tt*(Iext + Kvf*c_pop0 + c + local_coupling*x1 - x1*x1cond - z)

z (Epileptor2D state variable)
type: NamedIndividual
type: StateVariable
description: Slow permittivity state-variable of the Epileptor2D (Proix et al
notation: z
lhs: Derivative(z, t)
rhs: r*tt*(Ks*c_pop0 + h - z)

N (Epileptor3DStefanescuMcDonald parameter)
type: NamedIndividual
type: Parameter
default value: 1.0
has db xref: GO_0042391
definition: Effective population size / scaling of the resting-state regulation term.
notation: N

tau_z (Epileptor3DStefanescuMcDonald parameter)
type: NamedIndividual
type: Parameter
default value: 2857.0
definition: Slow timescale for the z permittivity variable.
notation: tau_z
unit (slot): ms

x_0 (Epileptor3DStefanescuMcDonald parameter)
type: NamedIndividual
type: Parameter
default value: -1.6
definition: Excitability parameter (Epileptor convention).
notation: x_0

x1 (Epileptor3DStefanescuMcDonald state variable)
type: NamedIndividual
type: StateVariable
description: Fast excitable variable (placeholder Epileptor-like dynamics).
notation: x1
lhs: Derivative(x1, t)
rhs: N*(x1 - x1**3/3 - z + c_pop0)

z (Epileptor3DStefanescuMcDonald state variable)
type: NamedIndividual
type: StateVariable
description: Slow permittivity / excitability variable.
notation: z
lhs: Derivative(z, t)
rhs: (4*(x1 - x_0) - z)/tau_z

h (Epileptor5D derived variable)
type: NamedIndividual
type: DerivedVariable
notation: h
lhs: h
rhs: Piecewise((x0 + 3/(exp((-x1 - 1*0.5)/0.1) + 1), modification > 0), (zcond + 4*(-x0 + x1), True))

x1cond (Epileptor5D derived variable)
type: NamedIndividual
type: DerivedVariable
notation: x1cond
lhs: x1cond
rhs: Piecewise(((-a)*x1**2 + b*x1, x1 < 0), (slope - x2 + 0.6*(z - 4.0)**2, True))

y2cond (Epileptor5D derived variable)
type: NamedIndividual
type: DerivedVariable
notation: y2cond
lhs: y2cond
rhs: Piecewise((0.0, x2 < -0.25), (aa*(x2 + 0.25), True))

zcond (Epileptor5D derived variable)
type: NamedIndividual
type: DerivedVariable
notation: zcond
lhs: zcond
rhs: Piecewise((-0.1*z**7, z < 0), (0.0, True))

Iext (Epileptor5D parameter)
type: NamedIndividual
type: Parameter
description: 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: 3.1
definition: 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: Iext

Iext2 (Epileptor5D parameter)
type: NamedIndividual
type: Parameter
description: External input current to the second population
default value: 0.45
notation: Iext2

Kf (Epileptor5D parameter)
type: NamedIndividual
type: Parameter
description: Correspond to the coupling scaling on a fast time scale
default value: 0.0
definition: Correspond to the coupling scaling on a fast time scale.
notation: Kf

Ks (Epileptor5D parameter)
type: NamedIndividual
type: Parameter
description: Permittivity coupling on the slow permittivity state-variable z_E5D in Epileptor5D (Proix et al
default value: 0.0
definition: 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: Ks

Kvf (Epileptor5D parameter)
type: NamedIndividual
type: Parameter
description: Coupling scaling on a very fast time scale
default value: 0.0
definition: Coupling scaling on a very fast time scale.
notation: Kvf

a (Epileptor5D parameter)
type: NamedIndividual
type: Parameter
description: Coefficient of the cubic term in the first state variable
default value: 1.0
notation: a

aa (Epileptor5D parameter)
type: NamedIndividual
type: Parameter
description: Linear coefficient in fifth state variable
default value: 6.0
notation: aa

b (Epileptor5D parameter)
type: NamedIndividual
type: Parameter
description: Coefficient of the squared term in the first state variabel
default value: 3.0
notation: b

bb (Epileptor5D parameter)
type: NamedIndividual
type: Parameter
description: Linear coefficient of lowpass excitatory coupling in fourth state variable
default value: 2.0
notation: bb

c (Epileptor5D parameter)
type: NamedIndividual
type: Parameter
description: Additive coefficient for the second state variable, called :math:`y_{0}` in Jirsa paper
default value: 1.0
notation: c

d (Epileptor5D parameter)
type: NamedIndividual
type: Parameter
description: Coefficient of the squared term in the derivative of the second state-variable y1_E5D in Epileptor5D (Jirsa et al
default value: 5.0
definition: Coefficient of the squared term in the derivative of the second state-variable y1_E5D in Epileptor5D (Jirsa et al.,2014).
notation: d

modification (Epileptor5D parameter)
type: NamedIndividual
type: Parameter
description: When modification is True, the function h_E5D uses a nonlinear influence on z_E5D
default value: 0.0
definition: 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: modification

r (Epileptor5D parameter)
type: NamedIndividual
type: Parameter
description: Temporal scaling in the third state variable, called :math:`1/\tau_{0}` in Jirsa paper
default value: 3.5E-4
notation: r

s (Epileptor5D parameter)
type: NamedIndividual
type: Parameter
description: Linear coefficient in the slow permittivity state-variable z_E5D in Epileptor5D (Jirsa et al
default value: 4.0
definition: Linear coefficient in the slow permittivity state-variable z_E5D in Epileptor5D (Jirsa et al.,2014).
notation: s

slope (Epileptor5D parameter)
type: NamedIndividual
type: Parameter
description: Linear coefficient in the first state variable
default value: 0.0
notation: slope

tau (Epileptor5D parameter)
type: NamedIndividual
type: Parameter
description: Temporal scaling coefficient in fifth state variable
default value: 10.0
notation: tau

tt (Epileptor5D parameter)
type: NamedIndividual
type: Parameter
description: Characteristic time scale of the whole-system Epileptor5D
default value: 1.0
definition: Characteristic time scale of the whole-system Epileptor5D.
notation: tt

x0 (Epileptor5D parameter)
type: NamedIndividual
type: Parameter
description: Epileptogenicity Parameter
default value: -1.6
has db xref: GO_0060079
definition: 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: x0

g (Epileptor5D state variable)
type: NamedIndividual
type: StateVariable
description: 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: g
lhs: Derivative(g, t)
rhs: tt*(-0.01*g + 0.001*x1)

x1 (Epileptor5D state variable)
type: NamedIndividual
type: StateVariable
description: First state-variable of the first Epileptor5D population (Jirsa et al
notation: x1
lhs: Derivative(x1, t)
rhs: tt*(Iext + Kvf*c_pop0 + local_coupling*x1 + x1*x1cond + y1 - z)

x2 (Epileptor5D state variable)
type: NamedIndividual
type: StateVariable
description: First state-variable of the second Epileptor5D sub-population (Jirsa et al
notation: x2
lhs: Derivative(x2, t)
rhs: tt*(Iext2 + Kf*c_pop1 + bb*g - x2**3 + x2 - y2 - 0.3*z + 1.05)

y1 (Epileptor5D state variable)
type: NamedIndividual
type: StateVariable
description: Second state-variable of the first Epileptor5D sub-population (Jirsa et al
notation: y1
lhs: Derivative(y1, t)
rhs: tt*(c - d*x1**2 - y1)

y2 (Epileptor5D state variable)
type: NamedIndividual
type: StateVariable
description: Second state-variable of the second Epileptor5D population (Jirsa et al
notation: y2
lhs: Derivative(y2, t)
rhs: tt*(-y2 + y2cond)/tau

z (Epileptor5D state variable)
type: NamedIndividual
type: StateVariable
description: Slow permittivity state-variable of the Epileptor5D (Jirsa et al
notation: z
lhs: Derivative(z, t)
rhs: r*tt*(Ks*c_pop0 + h - z)

lc_1 (EpileptorRestingState derived variable)
type: NamedIndividual
type: DerivedVariable
notation: lc_1
lhs: lc_1
rhs: local_coupling*x_rs

output (EpileptorRestingState derived variable)
type: NamedIndividual
type: DerivedVariable
notation: output
lhs: output
rhs: p*(-x1 + x2) + x_rs*(1 - p)

x1cond (EpileptorRestingState derived variable)
type: NamedIndividual
type: DerivedVariable
notation: x1cond
lhs: x1cond
rhs: Piecewise(((-a)*x1**2 + b*x1, x1 < 0), (slope - x2 + 0.6*(z - 4.0)**2, True))

y2cond (EpileptorRestingState derived variable)
type: NamedIndividual
type: DerivedVariable
notation: y2cond
lhs: y2cond
rhs: Piecewise((0.0, x2 < -0.25), (aa*(x2 + 0.25), True))

zcond (EpileptorRestingState derived variable)
type: NamedIndividual
type: DerivedVariable
notation: zcond
lhs: zcond
rhs: Piecewise((-0.1*z**7, z < 0), (0.0, True))

I_rs (EpileptorRestingState parameter)
type: NamedIndividual
type: Parameter
description: External input current to the third population (x_rs, y_rs)
default value: 0.0
definition: External input current to the third population (x_rs, y_rs).
notation: I_rs

Iext (EpileptorRestingState parameter)
type: NamedIndividual
type: Parameter
description: External input current to the first population (x1, y1)
default value: 3.1
definition: External input current to the first population (x1, y1).
notation: Iext

Iext2 (EpileptorRestingState parameter)
type: NamedIndividual
type: Parameter
description: External input current to the second population (x2, y2)
default value: 0.45
definition: External input current to the second population (x2, y2).
notation: Iext2

K_rs (EpileptorRestingState parameter)
type: NamedIndividual
type: Parameter
description: Coupling scaling on a fast time scale
default value: 1.0
definition: Coupling scaling on a fast time scale.
notation: K_rs

Kf (EpileptorRestingState parameter)
type: NamedIndividual
type: Parameter
description: Coupling scaling on a fast time scale
default value: 0.0
definition: Coupling scaling on a fast time scale.
notation: Kf

Ks (EpileptorRestingState parameter)
type: NamedIndividual
type: Parameter
description: Permittivity coupling, that is from the very fast time scale toward the slow time scale
default value: 0.0
definition: Permittivity coupling, that is from the very fast time scale toward the slow time scale.
notation: Ks

Kvf (EpileptorRestingState parameter)
type: NamedIndividual
type: Parameter
description: Coupling scaling on a very fast time scale
default value: 0.0
definition: Coupling scaling on a very fast time scale.
notation: Kvf

a (EpileptorRestingState parameter)
type: NamedIndividual
type: Parameter
description: Coefficient of the cubic term in the first state-variable x1
default value: 1.0
definition: Coefficient of the cubic term in the first state-variable x1.
notation: a

a_rs (EpileptorRestingState parameter)
type: NamedIndividual
type: Parameter
description: Vertical shift of the configurable nullcline in the state-variable y_rs
default value: -2.0
definition: Vertical shift of the configurable nullcline in the state-variable y_rs.
notation: a_rs

aa (EpileptorRestingState parameter)
type: NamedIndividual
type: Parameter
description: Linear coefficient in the fifth state-variable y2
default value: 6.0
definition: Linear coefficient in the fifth state-variable y2.
notation: aa

alpha_rs (EpileptorRestingState parameter)
type: NamedIndividual
type: Parameter
description: Constant parameter to scale the rate of feedback from the slow variable y_rs to the fast variable x_rs
default value: 1.0
definition: Constant parameter to scale the rate of feedback from the slow variable y_rs to the fast variable x_rs.
notation: alpha_rs

b (EpileptorRestingState parameter)
type: NamedIndividual
type: Parameter
description: Coefficient of the squared term in the first state-variable x1
default value: 3.0
definition: Coefficient of the squared term in the first state-variable x1.
notation: b

b_rs (EpileptorRestingState parameter)
type: NamedIndividual
type: Parameter
description: Linear coefficient of the state-variable y_rs
default value: -10.0
definition: Linear coefficient of the state-variable y_rs.
notation: b_rs

bb (EpileptorRestingState parameter)
type: NamedIndividual
type: Parameter
description: Linear coefficient of lowpass excitatory coupling in the fourth state-variable x2
default value: 2.0
definition: Linear coefficient of lowpass excitatory coupling in the fourth state-variable x2.
notation: bb

beta_rs (EpileptorRestingState parameter)
type: NamedIndividual
type: Parameter
description: Constant parameter to scale the rate of feedback from the slow variable y_rs to itself
default value: 1.0
definition: Constant parameter to scale the rate of feedback from the slow variable y_rs to itself.
notation: beta_rs

c (EpileptorRestingState parameter)
type: NamedIndividual
type: Parameter
description: Additive coefficient for the second state-variable y1, called :math:'y_{0}' in Jirsa et al
default value: 1.0
definition: Additive coefficient for the second state-variable y1, called :math:'y_{0}' in Jirsa et al. (2014).
notation: c

d (EpileptorRestingState parameter)
type: NamedIndividual
type: Parameter
description: Coefficient of the squared term in the second state-variable y1
default value: 5.0
definition: Coefficient of the squared term in the second state-variable y1.
notation: d

d_rs (EpileptorRestingState parameter)
type: NamedIndividual
type: Parameter
description: Temporal scaling of the whole third system (x_rs, y_rs)
default value: 0.02
definition: Temporal scaling of the whole third system (x_rs, y_rs).
notation: d_rs

e_rs (EpileptorRestingState parameter)
type: NamedIndividual
type: Parameter
description: Coefficient of the squared term in the sixth state-variable x_rs
default value: 3.0
definition: Coefficient of the squared term in the sixth state-variable x_rs.
notation: e_rs

f_rs (EpileptorRestingState parameter)
type: NamedIndividual
type: Parameter
description: Coefficient of the cubic term in the sixth state-variable x_rs
default value: 1.0
definition: Coefficient of the cubic term in the sixth state-variable x_rs.
notation: f_rs

gamma_rs (EpileptorRestingState parameter)
type: NamedIndividual
type: Parameter
description: Constant parameter to reproduce FHN dynamics where excitatory input currents are negative
default value: 1.0
definition: 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: gamma_rs

p (EpileptorRestingState parameter)
type: NamedIndividual
type: Parameter
description: Linear coefficient
default value: 0.0
definition: Linear coefficient.
notation: p

r (EpileptorRestingState parameter)
type: NamedIndividual
type: Parameter
description: Temporal scaling in the third state-variable z, called :math:'1/ au_{0}' in Jirsa et al
default value: 3.5E-4
definition: Temporal scaling in the third state-variable z, called :math:'1/ au_{0}' in Jirsa et al. (2014).
notation: r

slope (EpileptorRestingState parameter)
type: NamedIndividual
type: Parameter
description: Linear coefficient in the first state-variable x1
default value: 0.0
definition: Linear coefficient in the first state-variable x1.
notation: slope

tau (EpileptorRestingState parameter)
type: NamedIndividual
type: Parameter
description: Temporal scaling coefficient in the fifth state-variable y2
default value: 10.0
definition: Temporal scaling coefficient in the fifth state-variable y2.
notation: tau

tau_rs (EpileptorRestingState parameter)
type: NamedIndividual
type: Parameter
description: Temporal scaling coefficient in the third population (x_rs, y_rs)
default value: 1.0
definition: Temporal scaling coefficient in the third population (x_rs, y_rs).
notation: tau_rs

tt (EpileptorRestingState parameter)
type: NamedIndividual
type: Parameter
description: Time scaling of the Epileptor
default value: 1.0
definition: Time scaling of the Epileptor.
notation: tt

x0 (EpileptorRestingState parameter)
type: NamedIndividual
type: Parameter
description: Epileptogenicity parameter
default value: -1.6
definition: Epileptogenicity parameter.
notation: x0

g (EpileptorRestingState state variable)
type: NamedIndividual
type: StateVariable
notation: g
lhs: Derivative(g, t)
rhs: tt*(-0.01*g + 0.001*x1)

x1 (EpileptorRestingState state variable)
type: NamedIndividual
type: StateVariable
notation: x1
lhs: Derivative(x1, t)
rhs: tt*(Iext + Kvf*c_pop0 + local_coupling*x1 + x1*x1cond + y1 - z)

x2 (EpileptorRestingState state variable)
type: NamedIndividual
type: StateVariable
notation: x2
lhs: Derivative(x2, t)
rhs: tt*(Iext2 + Kf*c_pop1 + bb*g - x2**3 + x2 - y2 - 0.3*z + 1.05)

x_rs (EpileptorRestingState state variable)
type: NamedIndividual
type: StateVariable
notation: x_rs
lhs: Derivative(x_rs, t)
rhs: 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)

y1 (EpileptorRestingState state variable)
type: NamedIndividual
type: StateVariable
notation: y1
lhs: Derivative(y1, t)
rhs: tt*(c - d*x1**2 - y1)

y2 (EpileptorRestingState state variable)
type: NamedIndividual
type: StateVariable
notation: y2
lhs: Derivative(y2, t)
rhs: tt*(-y2 + y2cond)/tau

y_rs (EpileptorRestingState state variable)
type: NamedIndividual
type: StateVariable
notation: y_rs
lhs: Derivative(y_rs, t)
rhs: d_rs*(a_rs + b_rs*x_rs - beta_rs*y_rs)/tau_rs

z (EpileptorRestingState state variable)
type: NamedIndividual
type: StateVariable
notation: z
lhs: Derivative(z, t)
rhs: r*tt*(Ks*c_pop0 - 4*x0 + 4*x1 - z + zcond)

Delta (GastSchmidtKnosche_SD parameter)
type: NamedIndividual
type: Parameter
description: Half-width of heterogeneous noise distribution
default value: 2.0
notation: Delta

I (GastSchmidtKnosche_SD parameter)
type: NamedIndividual
type: Parameter
description: External homogeneous current
default value: 0.0
notation: I

J (GastSchmidtKnosche_SD parameter)
type: NamedIndividual
type: Parameter
description: Synaptic weight
default value: 21.2132
has db xref: GO_0099536
notation: J

alpha (GastSchmidtKnosche_SD parameter)
type: NamedIndividual
type: Parameter
description: adaptation rate
default value: 0.5
notation: alpha

cr (GastSchmidtKnosche_SD parameter)
type: NamedIndividual
type: Parameter
description: It is the weight on Coupling through variable r
default value: 1.0
definition: It is the weight on Coupling through variable r.
notation: cr

cv (GastSchmidtKnosche_SD parameter)
type: NamedIndividual
type: Parameter
description: It is the weight on Coupling through variable V
default value: 0.0
definition: It is the weight on Coupling through variable V.
notation: cv

eta (GastSchmidtKnosche_SD parameter)
type: NamedIndividual
type: Parameter
description: Mean of heterogeneous noise distribution
default value: -6.0
notation: eta

tau (GastSchmidtKnosche_SD parameter)
type: NamedIndividual
type: Parameter
description: Characteristic time
default value: 1.0
notation: tau

tau_A (GastSchmidtKnosche_SD parameter)
type: NamedIndividual
type: Parameter
description: Adaptation time scale
default value: 10.0
notation: tau_A

A (GastSchmidtKnosche_SD state variable)
type: NamedIndividual
type: StateVariable
notation: A
lhs: Derivative(A, t)
rhs: B/tau_A

B (GastSchmidtKnosche_SD state variable)
type: NamedIndividual
type: StateVariable
notation: B
lhs: Derivative(B, t)
rhs: (-A - 2*B + alpha*r)/tau_A

V (GastSchmidtKnosche_SD state variable)
type: NamedIndividual
type: StateVariable
notation: V
lhs: Derivative(V, t)
rhs: (I + J*r*tau*(1 - A) + V**2 + c_pop0*cr + c_pop1*cv + eta - pi**2*r**2*tau**2)/tau

r (GastSchmidtKnosche_SD state variable)
type: NamedIndividual
type: StateVariable
notation: r
lhs: Derivative(r, t)
rhs: (Delta/(pi*tau) + 2*V*r)/tau

Delta (GastSchmidtKnosche_SF parameter)
type: NamedIndividual
type: Parameter
description: Half-width of heterogeneous noise distribution
default value: 2.0
notation: Delta

I (GastSchmidtKnosche_SF parameter)
type: NamedIndividual
type: Parameter
description: External homogeneous current
default value: 0.0
notation: I

J (GastSchmidtKnosche_SF parameter)
type: NamedIndividual
type: Parameter
description: Synaptic weight
default value: 21.2132
has db xref: GO_0099536
notation: J

alpha (GastSchmidtKnosche_SF parameter)
type: NamedIndividual
type: Parameter
description: adaptation rate
default value: 10.0
has db xref: GO_0042391
notation: alpha

cr (GastSchmidtKnosche_SF parameter)
type: NamedIndividual
type: Parameter
description: It is the weight on Coupling through variable r
default value: 1.0
definition: It is the weight on Coupling through variable r.
notation: cr

cv (GastSchmidtKnosche_SF parameter)
type: NamedIndividual
type: Parameter
description: It is the weight on Coupling through variable V
default value: 0.0
definition: It is the weight on Coupling through variable V.
notation: cv

eta (GastSchmidtKnosche_SF parameter)
type: NamedIndividual
type: Parameter
description: Mean of heterogeneous noise distribution
default value: 1.0
notation: eta

tau (GastSchmidtKnosche_SF parameter)
type: NamedIndividual
type: Parameter
description: Characteristic time
default value: 1.0
notation: tau

tau_A (GastSchmidtKnosche_SF parameter)
type: NamedIndividual
type: Parameter
description: Adaptation time scale
default value: 10.0
notation: tau_A

A (GastSchmidtKnosche_SF state variable)
type: NamedIndividual
type: StateVariable
notation: A
lhs: Derivative(A, t)
rhs: B/tau_A

B (GastSchmidtKnosche_SF state variable)
type: NamedIndividual
type: StateVariable
notation: B
lhs: Derivative(B, t)
rhs: (-A - 2*B + alpha*r)/tau_A

V (GastSchmidtKnosche_SF state variable)
type: NamedIndividual
type: StateVariable
notation: V
lhs: Derivative(V, t)
rhs: (-A + I + J*r*tau + V**2 + c_pop0*cr + c_pop1*cv + eta - pi**2*r**2*tau**2)/tau

r (GastSchmidtKnosche_SF state variable)
type: NamedIndividual
type: StateVariable
notation: r
lhs: Derivative(r, t)
rhs: (Delta/(pi*tau) + 2*V*r)/tau

I (Generic2dOscillator parameter)
type: NamedIndividual
type: Parameter
description: Baseline shift of the cubic nullcline
default value: 0.0
has db xref: GO_0060079
notation: I

a (Generic2dOscillator parameter)
type: NamedIndividual
type: Parameter
description: Vertical shift of the configurable nullcline
default value: -2.0
notation: a

alpha (Generic2dOscillator parameter)
type: NamedIndividual
type: Parameter
description: Constant parameter to scale the rate of feedback from the slow variable to the fast variable.
default value: 1.0
definition: 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: alpha

b (Generic2dOscillator parameter)
type: NamedIndividual
type: Parameter
description: Linear slope of the configurable nullcline
default value: -10.0
has db xref: GO_0098873
has db xref: GO_0099178
notation: b

beta (Generic2dOscillator parameter)
type: NamedIndividual
type: Parameter
description: Constant parameter to scale the rate of feedback from the slow variable to itself
default value: 1.0
notation: beta

c (Generic2dOscillator parameter)
type: NamedIndividual
type: Parameter
description: Parabolic term of the configurable nullcline
default value: 0.0
notation: c

d (Generic2dOscillator parameter)
type: NamedIndividual
type: Parameter
description: Temporal scale factor
default value: 0.02
definition: Temporal scale factor. Warning: do not use it unless you know what you are doing and know about time tides.
notation: d

e (Generic2dOscillator parameter)
type: NamedIndividual
type: Parameter
description: Coefficient of the quadratic term of the cubic nullcline
default value: 3.0
definition: Coefficient of the quadratic term of the cubic nullcline.
notation: e

f (Generic2dOscillator parameter)
type: NamedIndividual
type: Parameter
description: Coefficient of the cubic term of the cubic nullcline
default value: 1.0
definition: Coefficient of the cubic term of the cubic nullcline.
notation: f

g (Generic2dOscillator parameter)
type: NamedIndividual
type: Parameter
description: Coefficient of the linear term of the cubic nullcline
default value: 0.0
definition: Coefficient of the linear term of the cubic nullcline.
notation: g

gamma (Generic2dOscillator parameter)
type: NamedIndividual
type: Parameter
description: Constant parameter to reproduce FHN dynamics where excitatory input currents are negative
default value: 1.0
definition: Constant parameter to reproduce FHN dynamics where excitatory input currents are negative. It scales both I and the long range coupling term.
notation: gamma

tau (Generic2dOscillator parameter)
type: NamedIndividual
type: Parameter
description: A time-scale hierarchy can be introduced for the state variables :math:`V` and :math:`W`
default value: 1.0
definition: 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: tau

V (Generic2dOscillator state variable)
type: NamedIndividual
type: StateVariable
description: 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: GO_0005272
notation: V
lhs: Derivative(V, t)
rhs: d*tau*(I*gamma - V**3*f + V**2*e + V*g + V*local_coupling + W*alpha + c_glob*gamma)

W (Generic2dOscillator state variable)
type: NamedIndividual
type: StateVariable
description: 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: GO_0005272
notation: W
lhs: Derivative(W, t)
rhs: d*(V**2*c + V*b - W*beta + a)/tau

gamma (GenericLinear parameter)
type: NamedIndividual
type: Parameter
description: Slope parameter of the state-variable 'x_GL', representing the inverse of the relaxation time
default value: -10.0
definition: 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: gamma

x (GenericLinear state variable)
type: NamedIndividual
type: StateVariable
description: State-variable of the Generic Linear model
notation: x
lhs: Derivative(x, t)
rhs: c_pop0 + gamma*x + local_coupling*x

tauT (Hopfield parameter)
type: NamedIndividual
type: Parameter
description: The slow time-scale for threshold calculus :math:`\\theta`, state-variable of the model
default value: 5.0
definition: The slow time-scale for threshold calculus :math:`\\theta`, state-variable of the model.
notation: tauT

taux (Hopfield parameter)
type: NamedIndividual
type: Parameter
description: The fast time-scale for potential calculus :math:`x`, state-variable of the model
default value: 1.0
definition: The fast time-scale for potential calculus :math:`x`, state-variable of the model.
notation: taux

theta (Hopfield state variable)
type: NamedIndividual
type: StateVariable
description: Slow state variable at node i
notation: theta
lhs: Derivative(theta, t)
rhs: (c_pop1 - theta)/tauT

x (Hopfield state variable)
type: NamedIndividual
type: StateVariable
notation: x
lhs: Derivative(x, t)
rhs: (c_pop0 - x)/taux

sigma_y0_1 (JansenRit derived variable)
type: NamedIndividual
type: DerivedVariable
description: Sigmoid function that transforms the average membrane potential of the PCs populations (y0) into an average firing rate to the excitatory interneurons EINs.
notation: sigma_y0_1
lhs: sigma_y0_1
rhs: 2.0*nu_max/(exp(r*(-J*a_1*y0 + v0)) + 1.0)

sigma_y0_3 (JansenRit derived variable)
type: NamedIndividual
type: DerivedVariable
description: Sigmoid function that transforms the average membrane potential of the PCs populations (y0) into an average firing rate to the inhibitory interneurons IINs.
notation: sigma_y0_3
lhs: sigma_y0_3
rhs: 2.0*nu_max/(exp(r*(-J*a_3*y0 + v0)) + 1.0)

sigma_y1_y2 (JansenRit derived variable)
type: NamedIndividual
type: DerivedVariable
description: Sigmoid function that transforms the average membrane potential of the interneurons populations (y1-y2) into an average firing rate to the PCs.
notation: sigma_y1_y2
lhs: sigma_y1_y2
rhs: 2.0*nu_max/(exp(r*(v0 - y1 + y2)) + 1.0)

A (JansenRit parameter)
type: NamedIndividual
type: Parameter
description: Maximum amplitude of EPSP [mV]
default value: 3.25
has db xref: GO_0060079
definition: Maximum amplitude of EPSP [mV]. Also called average synaptic gain.
notation: A
unit (slot): mV

B (JansenRit parameter)
type: NamedIndividual
type: Parameter
description: Maximum amplitude of IPSP [mV]
default value: 22.0
has db xref: GO_0060080
definition: Maximum amplitude of IPSP [mV]. Also called average synaptic gain.
notation: B
unit (slot): mV

J (JansenRit parameter)
type: NamedIndividual
type: Parameter
description: Average number of synapses between three neuronal populations of the model
default value: 135.0
has db xref: GO_0051124
has db xref: GO_0150092
definition: Average number of synapses between three neuronal populations of the model. It accounts for synaptic phenomena such as neurotransmitter depletion.
notation: J

a (JansenRit parameter)
type: NamedIndividual
type: Parameter
description: 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: 0.1
has db xref: GO_0099605
definition: 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: a
unit (slot): per_ms

a_1 (JansenRit parameter)
type: NamedIndividual
type: Parameter
description: 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: 1.0
has db xref: GO_0099536
definition: 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: a_1

a_2 (JansenRit parameter)
type: NamedIndividual
type: Parameter
description: Average probability constant of the number of synapses made by the EINs to the dendrites of the PCs
default value: 0.8
has db xref: GO_0099536
definition: 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: a_2

a_3 (JansenRit parameter)
type: NamedIndividual
type: Parameter
description: Average probability constant of the number of synapses made by the PCs to the dendrites of the IINs
default value: 0.25
has db xref: GO_0099536
definition: 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: a_3

a_4 (JansenRit parameter)
type: NamedIndividual
type: Parameter
description: Average probability constant of the number of synapses made by the IINs to the dendrites of the PCs
default value: 0.25
has db xref: GO_0060077
has db xref: GO_0099536
definition: 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: a_4

b (JansenRit parameter)
type: NamedIndividual
type: Parameter
description: Rate constant of the inhibitory post-synaptic potential (IPSP)
default value: 0.05
has db xref: GO_0060080
definition: 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: b
unit (slot): per_ms

mu (JansenRit parameter)
type: NamedIndividual
type: Parameter
description: 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: 0.22
has db xref: GO_0060079
definition: 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: mu
unit (slot): per_ms

nu_max (JansenRit parameter)
type: NamedIndividual
type: Parameter
description: Asymptotic of the sigmoid function Sigm_JR corresponds to the maximum firing rate of the neural populations
default value: 0.0025
has db xref: GO_0099605
definition: Asymptotic of the sigmoid function Sigm_JR corresponds to the maximum firing rate of the neural populations.
notation: nu_max
unit (slot): per_ms

r (JansenRit parameter)
type: NamedIndividual
type: Parameter
description: Steepness (or gain) parameter of the sigmoid function Sigm_JR
default value: 0.56
definition: Steepness (or gain) parameter of the sigmoid function Sigm_JR.
notation: r
unit (slot): per_mV

v0 (JansenRit parameter)
type: NamedIndividual
type: Parameter
description: Average firing threshold (PSP) for which half of the firing rate is achieved
default value: 5.52
has db xref: GO_0099605
definition: 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: v0
unit (slot): mV

y0 (JansenRit state variable)
type: NamedIndividual
type: StateVariable
description: First state-variable of the first Jansen-Rit population
has db xref: CL_0000598
has db xref: GO_0060079
notation: y0
lhs: Derivative(y0, t)
rhs: y3

y1 (JansenRit state variable)
type: NamedIndividual
type: StateVariable
description: First state-variable of the second Jansen-Rit population (EINs)
has db xref: CL_0000099
has db xref: GO_0060076
has db xref: GO_0060079
notation: y1
lhs: Derivative(y1, t)
rhs: y4

y2 (JansenRit state variable)
type: NamedIndividual
type: StateVariable
description: First state-variable of the third Jansen-Rit population (IINs)
has db xref: CL_0000099
has db xref: GO_0060077
notation: y2
lhs: Derivative(y2, t)
rhs: y5

y3 (JansenRit state variable)
type: NamedIndividual
type: StateVariable
description: Second state-variable of the first Jansen-Rit population (excitatory PCs)
has db xref: CL_0000598
notation: y3
lhs: Derivative(y3, t)
rhs: A*a*sigma_y1_y2 - a**2*y0 - 2.0*a*y3

y4 (JansenRit state variable)
type: NamedIndividual
type: StateVariable
description: Second state-variable of the second excitatory Jansen-Rit population (excitatory EINs)
has db xref: CL_0000099
notation: y4
lhs: Derivative(y4, t)
rhs: A*a*(J*a_2*sigma_y0_1 + c_pop0 + local_coupling*(y1 - y2) + mu) - a**2*y1 - 2.0*a*y4

y5 (JansenRit state variable)
type: NamedIndividual
type: StateVariable
description: Second state-variable of the third (inhibitory) Jansen-Rit population (IINs)
has db xref: CL_0000099
notation: y5
lhs: Derivative(y5, t)
rhs: B*J*a_4*b*sigma_y0_3 - b**2*y2 - 2.0*b*y5

v_pyr (JansenRit1995 derived variable)
type: NamedIndividual
type: DerivedVariable
description: Aggregate pyramidal PSP (EEG-like output)
notation: v_pyr
rhs: y1 - y2

A (JansenRit1995 parameter)
type: NamedIndividual
type: Parameter
description: Maximum amplitude of excitatory PSP (EPSP)
default value: 3.25
notation: A
unit (slot): mV

B (JansenRit1995 parameter)
type: NamedIndividual
type: Parameter
description: Maximum amplitude of inhibitory PSP (IPSP)
default value: 22
notation: B
unit (slot): mV

C (JansenRit1995 parameter)
type: NamedIndividual
type: Parameter
description: Lumped connectivity constant (C = C1)
default value: 135
notation: C

a (JansenRit1995 parameter)
type: NamedIndividual
type: Parameter
description: Reciprocal of EPSP time constant
default value: 100
notation: a
unit (slot): per_s

b (JansenRit1995 parameter)
type: NamedIndividual
type: Parameter
description: Reciprocal of IPSP time constant
default value: 50
notation: b
unit (slot): per_s

e0 (JansenRit1995 parameter)
type: NamedIndividual
type: Parameter
description: Half of maximum firing rate (2*e0 = max rate)
default value: 2.5
notation: e0
unit (slot): per_s

p (JansenRit1995 parameter)
type: NamedIndividual
type: Parameter
description: Mean external input (afferent pulse density)
default value: 220
notation: p
unit (slot): per_s

r (JansenRit1995 parameter)
type: NamedIndividual
type: Parameter
description: Steepness of sigmoid transformation
default value: 0.56
notation: r
unit (slot): per_mV

v0 (JansenRit1995 parameter)
type: NamedIndividual
type: Parameter
description: PSP for 50% firing rate (sigmoid midpoint)
default value: 6
notation: v0
unit (slot): mV

y0 (JansenRit1995 state variable)
type: NamedIndividual
type: StateVariable
notation: y0
rhs: y3

y1 (JansenRit1995 state variable)
type: NamedIndividual
type: StateVariable
notation: y1
rhs: y4

y2 (JansenRit1995 state variable)
type: NamedIndividual
type: StateVariable
notation: y2
rhs: y5

y3 (JansenRit1995 state variable)
type: NamedIndividual
type: StateVariable
notation: y3
rhs: A*a*Sigm(y1 - y2) - 2*a*y3 - a**2*y0

y4 (JansenRit1995 state variable)
type: NamedIndividual
type: StateVariable
notation: y4
rhs: A*a*(p + C2*Sigm(C1*y0) + c_intercolumn) - 2*a*y4 - a**2*y1

y5 (JansenRit1995 state variable)
type: NamedIndividual
type: StateVariable
notation: y5
rhs: B*b*(C4*Sigm(C3*y0)) - 2*b*y5 - b**2*y2

DK_o (KIonEx derived variable)
type: NamedIndividual
type: DerivedVariable
notation: DK_o
lhs: DK_o
rhs: -DKi*beta

DNa_i (KIonEx derived variable)
type: NamedIndividual
type: DerivedVariable
notation: DNa_i
lhs: DNa_i
rhs: -DKi

DNa_o (KIonEx derived variable)
type: NamedIndividual
type: DerivedVariable
notation: DNa_o
lhs: DNa_o
rhs: -DNa_i*beta

I_Cl (KIonEx derived variable)
type: NamedIndividual
type: DerivedVariable
notation: I_Cl
lhs: I_Cl
rhs: g_Cl*(V + 26.64*log(Cl_o0/Cl_i0))

I_K (KIonEx derived variable)
type: NamedIndividual
type: DerivedVariable
notation: I_K
lhs: I_K
rhs: (V - 26.64*log(K_o/K_i))*(g_K*n + g_Kl)

I_Na (KIonEx derived variable)
type: NamedIndividual
type: DerivedVariable
notation: I_Na
lhs: I_Na
rhs: (V - 26.64*log(Na_o/Na_i))*(g_Na*h*minf + g_Nal)

I_pump (KIonEx derived variable)
type: NamedIndividual
type: DerivedVariable
notation: I_pump
lhs: I_pump
rhs: 1.0*rho/((exp((Ckp - K_o)/DCkp) + 1.0)*(exp((Cnap - Na_i)/DCnap) + 1.0))

K_i (KIonEx derived variable)
type: NamedIndividual
type: DerivedVariable
notation: K_i
lhs: K_i
rhs: DKi + K_i0

K_o (KIonEx derived variable)
type: NamedIndividual
type: DerivedVariable
notation: K_o
lhs: K_o
rhs: DK_o + K_o0 + Kg

Na_i (KIonEx derived variable)
type: NamedIndividual
type: DerivedVariable
notation: Na_i
lhs: Na_i
rhs: DNa_i + Na_i0

Na_o (KIonEx derived variable)
type: NamedIndividual
type: DerivedVariable
notation: Na_o
lhs: Na_o
rhs: DNa_o + Na_o0

V_temp (KIonEx derived variable)
type: NamedIndividual
type: DerivedVariable
notation: V_temp
lhs: V_temp
rhs: -1.0*(I_Cl + I_K + I_Na + I_pump)/Cm

Vcond (KIonEx derived variable)
type: NamedIndividual
type: DerivedVariable
notation: Vcond
lhs: Vcond
rhs: 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))

beta (KIonEx derived variable)
type: NamedIndividual
type: DerivedVariable
notation: beta
lhs: beta
rhs: w_i/w_o

h (KIonEx derived variable)
type: NamedIndividual
type: DerivedVariable
notation: h
lhs: h
rhs: 1.1 - 1.0/(1.0 + 24.5325301971094*exp(-8.0*n))

minf (KIonEx derived variable)
type: NamedIndividual
type: DerivedVariable
notation: minf
lhs: minf
rhs: 1.0/(exp((Cmna - V)/DCmna) + 1.0)

ninf (KIonEx derived variable)
type: NamedIndividual
type: DerivedVariable
notation: ninf
lhs: ninf
rhs: 1.0/(exp((Cnk - V)/DCnk) + 1.0)

r (KIonEx derived variable)
type: NamedIndividual
type: DerivedVariable
notation: r
lhs: r
rhs: R_minus*x/pi

xcond (KIonEx derived variable)
type: NamedIndividual
type: DerivedVariable
notation: xcond
lhs: xcond
rhs: 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))

Chn (KIonEx parameter)
type: NamedIndividual
type: Parameter
default value: 0.4
notation: Chn

Ckp (KIonEx parameter)
type: NamedIndividual
type: Parameter
default value: 5.5
notation: Ckp
unit (slot): mol_per_m3

Cl_i0 (KIonEx parameter)
type: NamedIndividual
type: Parameter
description: initial concentration of intracellular Cl
default value: 5.0
notation: Cl_i0
unit (slot): mmol_per_m3

Cl_o0 (KIonEx parameter)
type: NamedIndividual
type: Parameter
description: initial concentration of extracellular Cl
default value: 112.0
notation: Cl_o0
unit (slot): mmol_per_m3

Cm (KIonEx parameter)
type: NamedIndividual
type: Parameter
description: membrane capacitance
default value: 1.0
has db xref: GO_0042391
notation: Cm

Cmna (KIonEx parameter)
type: NamedIndividual
type: Parameter
default value: -24.0
notation: Cmna
unit (slot): mV

Cnap (KIonEx parameter)
type: NamedIndividual
type: Parameter
default value: 21.0
notation: Cnap
unit (slot): mol_per_m3

Cnk (KIonEx parameter)
type: NamedIndividual
type: Parameter
default value: -19.0
notation: Cnk
unit (slot): mV

DChn (KIonEx parameter)
type: NamedIndividual
type: Parameter
default value: -8.0
notation: DChn

DCkp (KIonEx parameter)
type: NamedIndividual
type: Parameter
default value: 1.0
notation: DCkp
unit (slot): mol_per_m3

DCmna (KIonEx parameter)
type: NamedIndividual
type: Parameter
default value: 12.0
notation: DCmna
unit (slot): mV

DCnap (KIonEx parameter)
type: NamedIndividual
type: Parameter
default value: 2.0
notation: DCnap
unit (slot): mol_per_m3

DCnk (KIonEx parameter)
type: NamedIndividual
type: Parameter
default value: 18.0
notation: DCnk
unit (slot): mV

Delta (KIonEx parameter)
type: NamedIndividual
type: Parameter
description: HWHM heterogeneous noise
default value: 1.0
notation: Delta

E (KIonEx parameter)
type: NamedIndividual
type: Parameter
description: Reversal Potential
default value: 0.0
has db xref: GO_0019228
notation: E

J (KIonEx parameter)
type: NamedIndividual
type: Parameter
description: Mean Synaptic weight
default value: 0.1
has db xref: GO_0099536
notation: J

K_bath (KIonEx parameter)
type: NamedIndividual
type: Parameter
description: Potassium concentration in bath
default value: 5.5
has db xref: GO_0055075
notation: K_bath

K_i0 (KIonEx parameter)
type: NamedIndividual
type: Parameter
description: initial concentration of intracellular K
default value: 130.0
notation: K_i0
unit (slot): mmol_per_m3

K_o0 (KIonEx parameter)
type: NamedIndividual
type: Parameter
description: initial concentration of extracellular K
default value: 4.8
notation: K_o0
unit (slot): mmol_per_m3

Na_i0 (KIonEx parameter)
type: NamedIndividual
type: Parameter
description: initial concentration of intracellular Na
default value: 16.0
notation: Na_i0
unit (slot): mmol_per_m3

Na_o0 (KIonEx parameter)
type: NamedIndividual
type: Parameter
description: initial concentration of extracellular Na
default value: 138.0
notation: Na_o0
unit (slot): mmol_per_m3

R_minus (KIonEx parameter)
type: NamedIndividual
type: Parameter
description: curvature left parabola
default value: 0.5
notation: R_minus

R_plus (KIonEx parameter)
type: NamedIndividual
type: Parameter
description: curvature right parabola
default value: -0.5
notation: R_plus

Vstar (KIonEx parameter)
type: NamedIndividual
type: Parameter
description: x-coordinate meeting point of parabolas
default value: -31.0
notation: Vstar

c_minus (KIonEx parameter)
type: NamedIndividual
type: Parameter
description: x-coordinate left parabola
default value: -40.0
notation: c_minus

c_plus (KIonEx parameter)
type: NamedIndividual
type: Parameter
description: x-coordinate right parabola
default value: -20.0
notation: c_plus

epsilon (KIonEx parameter)
type: NamedIndividual
type: Parameter
description: diffusion rate
default value: 0.001
notation: epsilon

eta (KIonEx parameter)
type: NamedIndividual
type: Parameter
description: Mean heterogeneous noise
default value: 0.0
notation: eta

g_Cl (KIonEx parameter)
type: NamedIndividual
type: Parameter
description: chloride conductance
default value: 7.5
notation: g_Cl
unit (slot): nS

g_K (KIonEx parameter)
type: NamedIndividual
type: Parameter
description: maximal potassium conductance
default value: 22.0
notation: g_K
unit (slot): nS

g_Kl (KIonEx parameter)
type: NamedIndividual
type: Parameter
description: potassium leak conductance
default value: 0.12
notation: g_Kl
unit (slot): nS

g_Na (KIonEx parameter)
type: NamedIndividual
type: Parameter
description: maximal sodiumconductance
default value: 40.0
notation: g_Na
unit (slot): nS

g_Nal (KIonEx parameter)
type: NamedIndividual
type: Parameter
description: sodium leak conductance
default value: 0.02
notation: g_Nal
unit (slot): nS

gamma (KIonEx parameter)
type: NamedIndividual
type: Parameter
description: conversion factor
default value: 0.04
notation: gamma

rho (KIonEx parameter)
type: NamedIndividual
type: Parameter
description: maximal Na/K pump current
default value: 250.0
notation: rho
unit (slot): pA

tau_n (KIonEx parameter)
type: NamedIndividual
type: Parameter
description: time constant of gating variable
default value: 4.0
notation: tau_n

w_i (KIonEx parameter)
type: NamedIndividual
type: Parameter
description: intracellular volume
default value: 2160.0
notation: w_i
unit (slot): um3

w_o (KIonEx parameter)
type: NamedIndividual
type: Parameter
description: extracellular volume
default value: 720.0
notation: w_o
unit (slot): um3

DKi (KIonEx state variable)
type: NamedIndividual
type: StateVariable
notation: DKi
lhs: Derivative(DKi, t)
rhs: -gamma*(I_K - 2.0*I_pump)/w_i

Kg (KIonEx state variable)
type: NamedIndividual
type: StateVariable
notation: Kg
lhs: Derivative(Kg, t)
rhs: epsilon*(K_bath - K_o)

V (KIonEx state variable)
type: NamedIndividual
type: StateVariable
notation: V
lhs: Derivative(V, t)
rhs: Vcond

n (KIonEx state variable)
type: NamedIndividual
type: StateVariable
notation: n
lhs: Derivative(n, t)
rhs: (-n + ninf)/tau_n

x (KIonEx state variable)
type: NamedIndividual
type: StateVariable
notation: x
lhs: Derivative(x, t)
rhs: xcond

I (Kuramoto derived variable)
type: NamedIndividual
type: DerivedVariable
description: Input via local and long range connectivity, passing first through the Kuramoto coupling function
notation: I
lhs: I
rhs: c_pop0 + lc_0

lc_0 (Kuramoto derived variable)
type: NamedIndividual
type: DerivedVariable
notation: lc_0
lhs: lc_0
rhs: sin(local_coupling*theta)

omega (Kuramoto parameter)
type: NamedIndividual
type: Parameter
description: Sets the base line frequency for the Kuramoto oscillator
default value: 1.0
definition: Sets the base line frequency for the Kuramoto oscillator.
notation: omega
unit (slot): rad_per_ms

theta (Kuramoto state variable)
type: NamedIndividual
type: StateVariable
description: The Kuramoto model has only one state variable representing oscillations in general
notation: theta
lhs: Derivative(theta, t)
rhs: I + omega

I (KuramotoModel2 derived variable)
type: NamedIndividual
type: DerivedVariable
description: `I` is the input via local and long range connectivity, passing first through the Kuramoto coupling function
notation: I
lhs: I
rhs: c_glob+lc_0

lc_0 (KuramotoModel2 derived variable)
type: NamedIndividual
type: DerivedVariable
notation: lc_0
lhs: lc_0
rhs: sin(local_coupling*theta)

phase (KuramotoModel2 derived variable)
type: NamedIndividual
type: DerivedVariable
description: Normalized phase output
notation: phase
rhs: theta / (2*pi)

signal (KuramotoModel2 derived variable)
type: NamedIndividual
type: DerivedVariable
description: Sinusoidal signal output
notation: signal
rhs: sin(theta)

omega (KuramotoModel2 parameter)
type: NamedIndividual
type: Parameter
default value: 1.0
definition: Sets the base line frequency for the Kuramoto oscillator in [rad/ms].
notation: omega

theta (KuramotoModel2 state variable)
type: NamedIndividual
type: StateVariable
description: The Kuramoto model has only one state variable representing oscillations in general
notation: theta
lhs: thetadot
rhs: omega + I

Q_V (LarterBreakspear derived variable)
type: NamedIndividual
type: DerivedVariable
description: Average firing rate of the population of PCs, V.
has db xref: GO_0099605
notation: Q_V
lhs: Q_V
rhs: 0.5*Q_Vmax*(tanh((V - V_T)/delta_V) + 1)

Q_Z (LarterBreakspear derived variable)
type: NamedIndividual
type: DerivedVariable
description: Average firing rate of the population of IINs, Z.
has db xref: GO_0099605
notation: Q_Z
lhs: Q_Z
rhs: 0.5*Q_Zmax*(tanh((Z - Z_T)/delta_Z) + 1)

lc_0 (LarterBreakspear derived variable)
type: NamedIndividual
type: DerivedVariable
notation: lc_0
lhs: lc_0
rhs: Q_V*local_coupling

m_Ca (LarterBreakspear derived variable)
type: NamedIndividual
type: DerivedVariable
description: Fraction of open calcium channels (Breakspear et al., 2003b). Describes relationship between membrane voltage and channel conductance.
has db xref: GO_0005262
notation: m_Ca
lhs: m_Ca
rhs: 0.5*tanh((-T_Ca + V)/delta_Ca) + 0.5

m_K (LarterBreakspear derived variable)
type: NamedIndividual
type: DerivedVariable
description: Fraction of open potassium channels (Breakspear et al., 2003b). Describes relationship between membrane voltage and channel conductance.
has db xref: GO_0005267
notation: m_K
lhs: m_K
rhs: 0.5*tanh((-T_K + V)/delta_K) + 0.5

m_Na (LarterBreakspear derived variable)
type: NamedIndividual
type: DerivedVariable
description: Fraction of open sodium channels (Breakspear et al., 2003b). Describes relationship between membrane voltage and channel conductance.
has db xref: GO_0005272
notation: m_Na
lhs: m_Na
rhs: 0.5*tanh((-T_Na + V)/delta_Na) + 0.5

C (LarterBreakspear parameter)
type: NamedIndividual
type: Parameter
description: Coupling scaling factor
default value: 0.1
has db xref: GO_0060079
definition: Coupling scaling factor. Strength of excitatory coupling and balance between internal and local/global coupling strength.
notation: C

I_ext (LarterBreakspear parameter)
type: NamedIndividual
type: Parameter
description: Subcortical input current
default value: 0.3
has db xref: GO_0060079
definition: Subcortical input current. Represents a non-specific excitation or thalamic inputs.
notation: I_ext

Q_Vmax (LarterBreakspear parameter)
type: NamedIndividual
type: Parameter
description: Maximal firing rate for excitatory populations
default value: 1.0
has db xref: GO_0098976
has db xref: GO_0099605
definition: Maximal firing rate for excitatory populations.
notation: Q_Vmax
unit (slot): kHz

Q_Zmax (LarterBreakspear parameter)
type: NamedIndividual
type: Parameter
description: Maximal firing rate for inhibitory population
default value: 1.0
has db xref: GO_0099605
definition: Maximal firing rate for inhibitory population.
notation: Q_Zmax
unit (slot): kHz

T_Ca (LarterBreakspear parameter)
type: NamedIndividual
type: Parameter
description: Threshold value for Ca channels
default value: -0.01
has db xref: GO_0005262
has db xref: GO_1903233
definition: Threshold value for Ca channels.
notation: T_Ca

T_K (LarterBreakspear parameter)
type: NamedIndividual
type: Parameter
description: Threshold value for K channels
default value: 0.0
has db xref: GO_0005267
definition: Threshold value for K channels.
notation: T_K

T_Na (LarterBreakspear parameter)
type: NamedIndividual
type: Parameter
description: Threshold value for sodium channels
default value: 0.3
has db xref: GO_0005272
definition: Threshold value for sodium channels.
notation: T_Na

V_Ca (LarterBreakspear parameter)
type: NamedIndividual
type: Parameter
description: Calcium Nernst potential
default value: 1.0
has db xref: GO_0005262
definition: Calcium Nernst potential.
notation: V_Ca

V_K (LarterBreakspear parameter)
type: NamedIndividual
type: Parameter
description: K Nernst potential
default value: -0.7
has db xref: GO_0005267
definition: K Nernst potential.
notation: V_K

V_L (LarterBreakspear parameter)
type: NamedIndividual
type: Parameter
description: Nernst potential leak channels
default value: -0.5
has db xref: GO_0022840
definition: Nernst potential leak channels.
notation: V_L

V_Na (LarterBreakspear parameter)
type: NamedIndividual
type: Parameter
description: Na Nernst potential
default value: 0.53
has db xref: GO_0005272
definition: Na Nernst potential.
notation: V_Na

V_T (LarterBreakspear parameter)
type: NamedIndividual
type: Parameter
description: Threshold potential for excitatory neurons
default value: 0.0
has db xref: GO_0098815
definition: Threshold potential for excitatory neurons. Describes the mean potential of the excitatory population.
notation: V_T

Z_T (LarterBreakspear parameter)
type: NamedIndividual
type: Parameter
description: Threshold potential (mean) for inihibtory neurons
default value: 0.0
has db xref: GO_0060080
definition: Threshold potential (mean) for inihibtory neurons.
notation: Z_T

a_ee (LarterBreakspear parameter)
type: NamedIndividual
type: Parameter
description: Excitatory-to-excitatory synaptic strength
default value: 0.4
has db xref: GO_0060079
definition: Excitatory-to-excitatory synaptic strength.
notation: a_ee

a_ei (LarterBreakspear parameter)
type: NamedIndividual
type: Parameter
description: Excitatory-to-inhibitory synaptic strength
default value: 2.0
has db xref: GO_0060079
definition: Excitatory-to-inhibitory synaptic strength.
notation: a_ei

a_ie (LarterBreakspear parameter)
type: NamedIndividual
type: Parameter
description: Inhibitory-to-excitatory synaptic strength
default value: 2.0
has db xref: GO_0060080
definition: Inhibitory-to-excitatory synaptic strength.
notation: a_ie

a_ne (LarterBreakspear parameter)
type: NamedIndividual
type: Parameter
description: Non-specific-to-excitatory synaptic strength
default value: 1.0
has db xref: GO_0060079
definition: Non-specific-to-excitatory synaptic strength.
notation: a_ne

a_ni (LarterBreakspear parameter)
type: NamedIndividual
type: Parameter
description: Non-specific-to-inhibitory synaptic strength
default value: 0.4
has db xref: GO_0060080
definition: Non-specific-to-inhibitory synaptic strength.
notation: a_ni

b (LarterBreakspear parameter)
type: NamedIndividual
type: Parameter
description: Time constant scaling factor
default value: 0.1
definition: Time constant scaling factor.
notation: b

delta_Ca (LarterBreakspear parameter)
type: NamedIndividual
type: Parameter
description: Variance of Calcium channel threshold
default value: 0.15
has db xref: GO_0005262
definition: Variance of Calcium channel threshold. Defines the steepness of the sigmoid $m_{Ca}$.
notation: delta_Ca

delta_K (LarterBreakspear parameter)
type: NamedIndividual
type: Parameter
description: Variance of Potassium channel threshold
default value: 0.3
has db xref: GO_0005267
definition: Variance of Potassium channel threshold. Defines the steepness of the sigmoid $m_K$.
notation: delta_K

delta_Na (LarterBreakspear parameter)
type: NamedIndividual
type: Parameter
description: Variance of sodium channel threshold
default value: 0.15
has db xref: GO_0005272
definition: Variance of sodium channel threshold. Defines the steepness of the sigmoid $m_{Na}$.
notation: delta_Na

delta_V (LarterBreakspear parameter)
type: NamedIndividual
type: Parameter
description: Variance of excitatory threshold
default value: 0.65
has db xref: GO_0060079
has db xref: ExcitabilityThresholdVariance
definition: Variance of excitatory threshold. Defines the steepness of sigmoid $Q_V$.
notation: delta_V

delta_Z (LarterBreakspear parameter)
type: NamedIndividual
type: Parameter
description: Variance of inhibitory threshold
default value: 0.7
has db xref: GO_0060080
definition: Variance of inhibitory threshold. Defines the steepness of sigmoid $Q_Z$.
notation: delta_Z

g_Ca (LarterBreakspear parameter)
type: NamedIndividual
type: Parameter
description: Conductance of population of calcium (Ca++) channels
default value: 1.1
has db xref: GO_0005262
definition: Conductance of population of calcium (Ca++) channels. Describes the maximal conductance if all channels are open.
notation: g_Ca

g_K (LarterBreakspear parameter)
type: NamedIndividual
type: Parameter
description: Conductance of population of potassium (K) channels
default value: 2.0
has db xref: GO_0005267
definition: Conductance of population of potassium (K) channels. Describes the maximal conductance if all channels are open.
notation: g_K

g_L (LarterBreakspear parameter)
type: NamedIndividual
type: Parameter
description: Conductance of population of leak channels
default value: 0.5
has db xref: GO_0022840
definition: Conductance of population of leak channels.
notation: g_L

g_Na (LarterBreakspear parameter)
type: NamedIndividual
type: Parameter
description: Conductance of population of Na channels
default value: 6.7
has db xref: GO_0005272
definition: Conductance of population of Na channels.
notation: g_Na

phi (LarterBreakspear parameter)
type: NamedIndividual
type: Parameter
description: Temperature scaling factor
default value: 0.7
definition: Temperature scaling factor.
notation: phi

r_NMDA (LarterBreakspear parameter)
type: NamedIndividual
type: Parameter
description: Ratio of NMDA to AMPA receptors
default value: 0.25
has db xref: GO_0004971
definition: Ratio of NMDA to AMPA receptors.
notation: r_NMDA

t_scale (LarterBreakspear parameter)
type: NamedIndividual
type: Parameter
description: Time scale factor
default value: 1.0
notation: t_scale

tau_K (LarterBreakspear parameter)
type: NamedIndividual
type: Parameter
description: Time constant for K relaxation time (ms)
default value: 1.0
has db xref: GO_0005267
notation: tau_K

V (LarterBreakspear state variable)
type: NamedIndividual
type: StateVariable
description: First state-variable of the Larter-Breakspear (Breakspear et al
has db xref: GO_0042391
notation: V
lhs: Derivative(V, t)
rhs: 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))

W (LarterBreakspear state variable)
type: NamedIndividual
type: StateVariable
description: Second state-variable of the Larter-Breakspear (Breakspear et al
has db xref: GO_0005267
notation: W
lhs: Derivative(W, t)
rhs: phi*t_scale*(-W + m_K)/tau_K

Z (LarterBreakspear state variable)
type: NamedIndividual
type: StateVariable
description: Third state-variable of the Larter-Breakspear (Breakspear et al
has db xref: CL_0000099
has db xref: GO_0060080
notation: Z
lhs: Derivative(Z, t)
rhs: b*t_scale*(I_ext*a_ni + Q_V*V*a_ei)

v_pyr (ModelJansen1995 derived variable)
type: NamedIndividual
type: DerivedVariable
description: EEG-like output: pyramidal potential difference
notation: v_pyr
rhs: y1 - y2

A (ModelJansen1995 parameter)
type: NamedIndividual
type: Parameter
default value: 3.25
notation: A
unit (slot): mV

B (ModelJansen1995 parameter)
type: NamedIndividual
type: Parameter
default value: 22
notation: B
unit (slot): mV

C (ModelJansen1995 parameter)
type: NamedIndividual
type: Parameter
default value: 135
notation: C

a (ModelJansen1995 parameter)
type: NamedIndividual
type: Parameter
default value: 0.1
notation: a
unit (slot): per_ms

b (ModelJansen1995 parameter)
type: NamedIndividual
type: Parameter
default value: 0.05
notation: b
unit (slot): per_ms

e0 (ModelJansen1995 parameter)
type: NamedIndividual
type: Parameter
default value: 0.0025
notation: e0
unit (slot): per_ms

p (ModelJansen1995 parameter)
type: NamedIndividual
type: Parameter
default value: 0.24
notation: p
unit (slot): per_ms

r (ModelJansen1995 parameter)
type: NamedIndividual
type: Parameter
default value: 0.56
notation: r
unit (slot): per_mV

v0 (ModelJansen1995 parameter)
type: NamedIndividual
type: Parameter
default value: 6
notation: v0
unit (slot): mV

y0 (ModelJansen1995 state variable)
type: NamedIndividual
type: StateVariable
notation: y0
rhs: y3

y1 (ModelJansen1995 state variable)
type: NamedIndividual
type: StateVariable
notation: y1
rhs: y4

y2 (ModelJansen1995 state variable)
type: NamedIndividual
type: StateVariable
notation: y2
rhs: y5

y3 (ModelJansen1995 state variable)
type: NamedIndividual
type: StateVariable
notation: y3
rhs: A*a*Sigm(y1 - y2) - 2*a*y3 - a**2*y0

y4 (ModelJansen1995 state variable)
type: NamedIndividual
type: StateVariable
notation: y4
rhs: A*a*(p + C2*Sigm(C1*y0) + c_glob) - 2*a*y4 - a**2*y1

y5 (ModelJansen1995 state variable)
type: NamedIndividual
type: StateVariable
notation: y5
rhs: B*b*(C4*Sigm(C3*y0)) - 2*b*y5 - b**2*y2

Delta (MontbrioPazoRoxin parameter)
type: NamedIndividual
type: Parameter
description: Mean heterogeneous noise
default value: 1.0
has db xref: GO_0061669
notation: Delta

I (MontbrioPazoRoxin parameter)
type: NamedIndividual
type: Parameter
description: External Current
default value: 0.0
notation: I

J (MontbrioPazoRoxin parameter)
type: NamedIndividual
type: Parameter
description: Mean Synaptic weight
default value: 15.0
has db xref: GO_0042391
has db xref: GO_0099536
definition: Mean Synaptic weight.
notation: J

cr (MontbrioPazoRoxin parameter)
type: NamedIndividual
type: Parameter
description: It is the weight on Coupling through variable r
default value: 1.0
definition: It is the weight on Coupling through variable r.
notation: cr

cv (MontbrioPazoRoxin parameter)
type: NamedIndividual
type: Parameter
description: It is the weight on Coupling through variable V
default value: 0.0
definition: It is the weight on Coupling through variable V.
notation: cv

eta (MontbrioPazoRoxin parameter)
type: NamedIndividual
type: Parameter
description: Constant parameter to scale the rate of feedback from the firing rate variable to itself
default value: -5.0
has db xref: GO_0099605
notation: eta

tau (MontbrioPazoRoxin parameter)
type: NamedIndividual
type: Parameter
description: Membrane time constant
default value: 1.0
notation: tau

V (MontbrioPazoRoxin state variable)
type: NamedIndividual
type: StateVariable
notation: V
lhs: Derivative(V, t)
rhs: (I + J*r*tau + V**2 + c_pop0*cr*tau + c_pop1*cv + eta - pi**2*r**2*tau**2)/tau

r (MontbrioPazoRoxin state variable)
type: NamedIndividual
type: StateVariable
notation: r
lhs: Derivative(r, t)
rhs: (Delta/(pi*tau) + 2*V*r)/tau

H (ReducedWongWang derived variable)
type: NamedIndividual
type: DerivedVariable
description: 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: GO_0099605
notation: H
lhs: H
rhs: (a*x - b)/(1 - exp(-d*(a*x - b)))

x (ReducedWongWang derived variable)
type: NamedIndividual
type: DerivedVariable
description: (NMDAR)-mediated synaptic input current to the neurons population (Deco et al., 2013).
notation: x
lhs: x
rhs: I_o + J_N*S*local_coupling + J_N*S*w + J_N*c_pop0

I_o (ReducedWongWang parameter)
type: NamedIndividual
type: Parameter
description: External input current to the neurons population (Deco et al
default value: 0.33
definition: 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: I_o
unit (slot): nA

J_N (ReducedWongWang parameter)
type: NamedIndividual
type: Parameter
description: Excitatory recurrence
default value: 0.2609
has db xref: GO_0098815
notation: J_N
unit (slot): nA

a (ReducedWongWang parameter)
type: NamedIndividual
type: Parameter
description: Slope (or gain) parameter of the sigmoid input-output function H_RWW (Deco et al
default value: 0.27
definition: 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: a
unit (slot): per_pC

b (ReducedWongWang parameter)
type: NamedIndividual
type: Parameter
description: Shift parameter of the sigmoid input-output function H_RWW (Deco et al
default value: 0.108
definition: 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: b
unit (slot): kHz

d (ReducedWongWang parameter)
type: NamedIndividual
type: Parameter
description: Scaling parameter of the sigmoid input-output function H_RWW (Deco et al
default value: 154.0
definition: 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: d
unit (slot): ms

gamma (ReducedWongWang parameter)
type: NamedIndividual
type: Parameter
description: Kinetic parameter
default value: 0.641
notation: gamma

tau_s (ReducedWongWang parameter)
type: NamedIndividual
type: Parameter
description: Kinetic parameter
default value: 100.0
definition: Kinetic parameter. Decay time constant for the NMDA synapses of the neurons population (Deco et al., 2013).
notation: tau_s
unit (slot): ms

w (ReducedWongWang parameter)
type: NamedIndividual
type: Parameter
description: Excitatory recurrence
default value: 0.6
notation: w
unit (slot): dimensionless

S (ReducedWongWang state variable)
type: NamedIndividual
type: StateVariable
description: State-variable of the Reduced WongWang model, denoting the average, (NMDAR)-mediated synaptic gating, i
notation: S
lhs: Derivative(S, t)
rhs: H*gamma*(1 - S) - S/tau_s

H_e (ReducedWongWangExcInh derived variable)
type: NamedIndividual
type: DerivedVariable
description: 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: GO_0060079
has db xref: GO_0099605
notation: H_e
lhs: H_e
rhs: x_e/(1 - exp(-d_e*x_e))

H_i (ReducedWongWangExcInh derived variable)
type: NamedIndividual
type: DerivedVariable
description: 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: GO_0060080
has db xref: GO_0099605
notation: H_i
lhs: H_i
rhs: x_i/(1 - exp(-d_i*x_i))

J_N_S_e (ReducedWongWangExcInh derived variable)
type: NamedIndividual
type: DerivedVariable
notation: J_N_S_e
lhs: J_N_S_e
rhs: J_N*S_e

coupling (ReducedWongWangExcInh derived variable)
type: NamedIndividual
type: DerivedVariable
notation: coupling
lhs: coupling
rhs: G*J_N*(S_e*local_coupling + c_glob)

x_e (ReducedWongWangExcInh derived variable)
type: NamedIndividual
type: DerivedVariable
description: Input current to the excitatory population (Deco et al., 2014).
has db xref: GO_0098815
notation: x_e
lhs: x_e
rhs: a_e*(I_ext + I_o*W_e + J_N_S_e*w_p - J_i*S_i + coupling) - b_e

x_i (ReducedWongWangExcInh derived variable)
type: NamedIndividual
type: DerivedVariable
description: Input current to the inhibitory population (Deco et al., 2014).
has db xref: GO_0060080
notation: x_i
lhs: x_i
rhs: a_i*(I_o*W_i + J_N_S_e - S_i + coupling*lamda) - b_i

G (ReducedWongWangExcInh parameter)
type: NamedIndividual
type: Parameter
description: Global coupling scaling
default value: 2.0
notation: G

I_ext (ReducedWongWangExcInh parameter)
type: NamedIndividual
type: Parameter
description: External stimulation parameter for evoked potential simulated activity applied to the excitatory population firing rate IE (Deco et al
default value: 0.0
has db xref: GO_0060079
has db xref: GO_0099605
definition: External stimulation parameter for evoked potential simulated activity applied to the excitatory population firing rate IE (Deco et al., 2014).
notation: I_ext

I_o (ReducedWongWangExcInh parameter)
type: NamedIndividual
type: Parameter
description: Effective external input parameter to the excitatory E and inhibitory I population (Deco et al
default value: 0.382
has db xref: GO_0060079
has db xref: GO_0060080
definition: Effective external input parameter to the excitatory E and inhibitory I population (Deco et al., 2014).
notation: I_o
unit (slot): nA

J_N (ReducedWongWangExcInh parameter)
type: NamedIndividual
type: Parameter
description: Excitatory synaptic coupling parameter (Deco et al
default value: 0.15
has db xref: GO_0060079
definition: Excitatory synaptic coupling parameter (Deco et al., 2014).
notation: J_N

J_i (ReducedWongWangExcInh parameter)
type: NamedIndividual
type: Parameter
description: Local feedback inhibitory synaptic coupling to the excitatory population firing rate IE (Deco et al
default value: 1.0
has db xref: GO_0060080
has db xref: GO_0099605
definition: Local feedback inhibitory synaptic coupling to the excitatory population firing rate IE (Deco et al., 2014).
notation: J_i

W_e (ReducedWongWangExcInh parameter)
type: NamedIndividual
type: Parameter
description: Excitatory population external input scaling weight
default value: 1.0
has db xref: GO_0090394
has db xref: GO_2000463
notation: W_e

W_i (ReducedWongWangExcInh parameter)
type: NamedIndividual
type: Parameter
description: Inhibitory population external input scaling weight
default value: 0.7
has db xref: GO_0060080
notation: W_i

a_e (ReducedWongWangExcInh parameter)
type: NamedIndividual
type: Parameter
description: Slope (or gain) parameter of the sigmoid function HE_RWW_EI (Deco et al
default value: 310.0
definition: Slope (or gain) parameter of the sigmoid function HE_RWW_EI (Deco et al., 2014).
notation: a_e
unit (slot): per_nC

a_i (ReducedWongWangExcInh parameter)
type: NamedIndividual
type: Parameter
description: Slope (or gain) parameter of the sigmoid function HI_RWW_EI of the inhibitory population (Deco et al
default value: 615.0
definition: Slope (or gain) parameter of the sigmoid function HI_RWW_EI of the inhibitory population (Deco et al., 2014).
notation: a_i
unit (slot): per_nC

b_e (ReducedWongWangExcInh parameter)
type: NamedIndividual
type: Parameter
description: Shift parameter of the sigmoid function HE_RWW_EI of the excitatory population (Deco et al
default value: 125.0
definition: Shift parameter of the sigmoid function HE_RWW_EI of the excitatory population (Deco et al., 2014).
notation: b_e
unit (slot): Hz

b_i (ReducedWongWangExcInh parameter)
type: NamedIndividual
type: Parameter
description: Shift parameter of the sigmoid function HI_RWW_EI of the inhibitory population (Deco et al
default value: 177.0
definition: Shift parameter of the sigmoid function HI_RWW_EI of the inhibitory population (Deco et al., 2014).
notation: b_i
unit (slot): Hz

d_e (ReducedWongWangExcInh parameter)
type: NamedIndividual
type: Parameter
description: Scaling parameter of the sigmoid function HE_RWW_EI of the excitatory population (Deco et al
default value: 0.16
definition: Scaling parameter of the sigmoid function HE_RWW_EI of the excitatory population (Deco et al., 2014).
notation: d_e
unit (slot): s

d_i (ReducedWongWangExcInh parameter)
type: NamedIndividual
type: Parameter
description: Scaling parameter of the sigmoid function HI_RWW_EI of the inhibitory population (Deco et al
default value: 0.087
definition: Scaling parameter of the sigmoid function HI_RWW_EI of the inhibitory population (Deco et al., 2014).
notation: d_i
unit (slot): s

gamma_e (ReducedWongWangExcInh parameter)
type: NamedIndividual
type: Parameter
description: Excitatory population kinetic parameter
default value: 6.41E-4
has db xref: GO_0060079
notation: gamma_e

gamma_i (ReducedWongWangExcInh parameter)
type: NamedIndividual
type: Parameter
description: Inhibitory population kinetic parameter
default value: 0.001
has db xref: GO_0060080
notation: gamma_i

lamda (ReducedWongWangExcInh parameter)
type: NamedIndividual
type: Parameter
description: Inhibitory global coupling scaling
default value: 0.0
has db xref: GO_0060080
notation: lamda

tau_e (ReducedWongWangExcInh parameter)
type: NamedIndividual
type: Parameter
description: Kinetic parameter that represents the decay times for NMDA synapses (Deco et al
default value: 100.0
definition: Kinetic parameter that represents the decay times for NMDA synapses (Deco et al., 2014). Excitatory population NMDA decay time constant.
notation: tau_e
unit (slot): ms

tau_i (ReducedWongWangExcInh parameter)
type: NamedIndividual
type: Parameter
description: Kinetic parameter that represents the decay times for inhibitory GABA synapses (Deco et al
default value: 10.0
has db xref: GO_0016917
definition: Kinetic parameter that represents the decay times for inhibitory GABA synapses (Deco et al., 2014).
notation: tau_i
unit (slot): ms

w_p (ReducedWongWangExcInh parameter)
type: NamedIndividual
type: Parameter
description: Excitatory population recurrence weight
default value: 1.4
has db xref: GO_0060079
notation: w_p

S_e (ReducedWongWangExcInh state variable)
type: NamedIndividual
type: StateVariable
description: State-variable of the Reduced WongWang_EI model (Deco et al
has db xref: GO_0060079
has db xref: GO_0099536
notation: S_e
lhs: Derivative(S_e, t)
rhs: H_e*gamma_e*(1 - S_e) - S_e/tau_e

S_i (ReducedWongWangExcInh state variable)
type: NamedIndividual
type: StateVariable
description: State-variable of the Reduced WongWang_EI model (Deco et al
has db xref: GO_0060080
has db xref: GO_0099536
notation: S_i
lhs: Derivative(S_i, t)
rhs: H_i*gamma_i - S_i/tau_i

H_x (ReducedWongWangTvboptim derived variable)
type: NamedIndividual
type: DerivedVariable
description: Average population firing rate H evaluated at the total synaptic input x.
notation: H_x
lhs: H_x
rhs: H(x)

x (ReducedWongWangTvboptim derived variable)
type: NamedIndividual
type: DerivedVariable
description: Total synaptic input current combining local recurrence, external input, and network coupling (instant and delayed) scaled by J_N.
notation: x
lhs: x
rhs: w*J_N*S + I_o + J_N*instant + J_N*delayed

I_o (ReducedWongWangTvboptim parameter)
type: NamedIndividual
type: Parameter
description: External input current
default value: 0.34
definition: 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: I_o
unit (slot): nA

J_N (ReducedWongWangTvboptim parameter)
type: NamedIndividual
type: Parameter
description: NMDA synaptic coupling strength
default value: 0.2609
definition: NMDA synaptic coupling strength. Scales both local recurrence and long-range network coupling inputs.
notation: J_N
unit (slot): nA

a (ReducedWongWangTvboptim parameter)
type: NamedIndividual
type: Parameter
description: Input gain parameter
default value: 0.27
definition: Input gain parameter of the sigmoid transfer function H(x).
notation: a
unit (slot): per_pC

b (ReducedWongWangTvboptim parameter)
type: NamedIndividual
type: Parameter
description: Input shift parameter
default value: 0.108
definition: Input shift parameter of the sigmoid transfer function H(x).
notation: b
unit (slot): kHz

d (ReducedWongWangTvboptim parameter)
type: NamedIndividual
type: Parameter
description: Scaling parameter
default value: 154.0
definition: Scaling parameter of the sigmoid transfer function H(x).
notation: d
unit (slot): ms

gamma (ReducedWongWangTvboptim parameter)
type: NamedIndividual
type: Parameter
description: Kinetic parameter
default value: 0.641
definition: Kinetic parameter governing the rate of NMDA channel dynamics.
notation: gamma

tau_s (ReducedWongWangTvboptim parameter)
type: NamedIndividual
type: Parameter
description: NMDA decay time constant
default value: 100.0
definition: NMDA decay time constant for the synaptic gating variable S.
notation: tau_s
unit (slot): ms

w (ReducedWongWangTvboptim parameter)
type: NamedIndividual
type: Parameter
description: Excitatory recurrence strength (local feedback)
default value: 0.5
definition: 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: w
unit (slot): dimensionless

S (ReducedWongWangTvboptim state variable)
type: NamedIndividual
type: StateVariable
description: Average NMDA synaptic gating variable, representing the fraction of open NMDA channels at each network node.
notation: S
lhs: Derivative(S, t)
rhs: -S/tau_s + (1 - S)*H(x)*gamma

Aik (StefanescuJirsa2D derived variable)
type: NamedIndividual
type: DerivedVariable
description: Excitatory-to-excitatory mode-coupling matrix derived from Gaussian quadrature over N(mu, sigma); computed offline at `update_derived_parameters`.
has db xref: GO_0060079
notation: Aik
lhs: Aik
rhs: 0.5

Bik (StefanescuJirsa2D derived variable)
type: NamedIndividual
type: DerivedVariable
description: Inhibitory-to-excitatory mode-coupling matrix.
has db xref: GO_0060079
notation: Bik
lhs: Bik
rhs: 0.5

Cik (StefanescuJirsa2D derived variable)
type: NamedIndividual
type: DerivedVariable
description: Excitatory-to-inhibitory mode-coupling matrix.
has db xref: GO_0060080
notation: Cik
lhs: Cik
rhs: 0.5

IE_i (StefanescuJirsa2D derived variable)
type: NamedIndividual
type: DerivedVariable
description: Per-mode constant excitatory input from the heterogeneity distribution.
has db xref: GO_0042391
notation: IE_i
lhs: IE_i
rhs: 0.0

II_i (StefanescuJirsa2D derived variable)
type: NamedIndividual
type: DerivedVariable
description: Per-mode constant inhibitory input from the heterogeneity distribution.
has db xref: GO_0042391
notation: II_i
lhs: II_i
rhs: 0.0

e_i (StefanescuJirsa2D derived variable)
type: NamedIndividual
type: DerivedVariable
description: Per-mode cubic-coefficient projection for the excitatory subnetwork.
notation: e_i
lhs: e_i
rhs: 1.0

f_i (StefanescuJirsa2D derived variable)
type: NamedIndividual
type: DerivedVariable
description: Per-mode cubic-coefficient projection for the inhibitory subnetwork.
notation: f_i
lhs: f_i
rhs: 1.0

m_i (StefanescuJirsa2D derived variable)
type: NamedIndividual
type: DerivedVariable
description: Per-mode offset entering the eta dynamics.
notation: m_i
lhs: m_i
rhs: a

n_i (StefanescuJirsa2D derived variable)
type: NamedIndividual
type: DerivedVariable
description: Per-mode offset entering the beta dynamics.
notation: n_i
lhs: n_i
rhs: a

K11 (StefanescuJirsa2D parameter)
type: NamedIndividual
type: Parameter
default value: 0.5
has db xref: GO_0060079
definition: Internal coupling, excitatory to excitatory.
notation: K11

K12 (StefanescuJirsa2D parameter)
type: NamedIndividual
type: Parameter
default value: 0.15
has db xref: GO_0060079
definition: Internal coupling, inhibitory to excitatory.
notation: K12

K21 (StefanescuJirsa2D parameter)
type: NamedIndividual
type: Parameter
default value: 0.15
has db xref: GO_0060080
definition: Internal coupling, excitatory to inhibitory.
notation: K21

a (StefanescuJirsa2D parameter)
type: NamedIndividual
type: Parameter
default value: 0.45
definition: Heterogeneity scale parameter entering the m_i, n_i offsets.
notation: a

b (StefanescuJirsa2D parameter)
type: NamedIndividual
type: Parameter
default value: 0.9
definition: FitzHugh-Nagumo recovery decay rate.
notation: b

mu (StefanescuJirsa2D parameter)
type: NamedIndividual
type: Parameter
default value: 0.0
has db xref: GO_0060079
definition: Mean of the Gaussian heterogeneity distribution.
notation: mu

sigma (StefanescuJirsa2D parameter)
type: NamedIndividual
type: Parameter
default value: 0.35
has db xref: GO_0060079
definition: Standard deviation of the Gaussian heterogeneity distribution.
notation: sigma

tau (StefanescuJirsa2D parameter)
type: NamedIndividual
type: Parameter
description: Timescale separation
default value: 3.0
definition: Timescale separation between fast (xi, alpha) and slow (eta, beta) variables.
notation: tau

alpha (StefanescuJirsa2D state variable)
type: NamedIndividual
type: StateVariable
description: Inhibitory fast variable (per mode).
has db xref: GO_0060080
notation: alpha
lhs: Derivative(alpha, t)
rhs: tau*(alpha - f_i*alpha**3/3 - beta) + K21*(Cik*xi - alpha) + tau*(II_i + c_pop0 + local_coupling*xi)

beta (StefanescuJirsa2D state variable)
type: NamedIndividual
type: StateVariable
description: Inhibitory slow recovery variable (per mode).
has db xref: GO_0060080
notation: beta
lhs: Derivative(beta, t)
rhs: (alpha - b*beta + n_i)/tau

eta (StefanescuJirsa2D state variable)
type: NamedIndividual
type: StateVariable
description: Excitatory slow recovery variable (per mode).
has db xref: GO_0060079
notation: eta
lhs: Derivative(eta, t)
rhs: (xi - b*eta + m_i)/tau

xi (StefanescuJirsa2D state variable)
type: NamedIndividual
type: StateVariable
description: Excitatory fast variable (per mode).
has db xref: GO_0060079
notation: xi
lhs: Derivative(xi, t)
rhs: tau*(xi - e_i*xi**3/3 - eta) + K11*(Aik*xi - xi) - K12*(Bik*alpha - xi) + tau*(IE_i + c_pop0 + local_coupling*xi)

A_ik (StefanescuJirsa3D derived variable)
type: NamedIndividual
type: DerivedVariable
description: Excitatory-to-excitatory mode-coupling matrix from Gaussian quadrature.
has db xref: GO_0060079
notation: A_ik
lhs: A_ik
rhs: 0.5

B_ik (StefanescuJirsa3D derived variable)
type: NamedIndividual
type: DerivedVariable
description: Inhibitory-to-excitatory mode-coupling matrix.
has db xref: GO_0060080
notation: B_ik
lhs: B_ik
rhs: 0.5

C_ik (StefanescuJirsa3D derived variable)
type: NamedIndividual
type: DerivedVariable
description: Excitatory-to-inhibitory mode-coupling matrix.
has db xref: GO_0060079
notation: C_ik
lhs: C_ik
rhs: 0.5

IE_i (StefanescuJirsa3D derived variable)
type: NamedIndividual
type: DerivedVariable
description: Per-mode constant excitatory input.
has db xref: GO_0060079
notation: IE_i
lhs: IE_i
rhs: 0.0

II_i (StefanescuJirsa3D derived variable)
type: NamedIndividual
type: DerivedVariable
description: Per-mode constant inhibitory input.
has db xref: GO_0060080
notation: II_i
lhs: II_i
rhs: 0.0

a_i (StefanescuJirsa3D derived variable)
type: NamedIndividual
type: DerivedVariable
description: Per-mode cubic coefficient for the excitatory xi dynamics (a * <V|V^3>).
notation: a_i
lhs: a_i
rhs: a

b_i (StefanescuJirsa3D derived variable)
type: NamedIndividual
type: DerivedVariable
description: Per-mode quadratic coefficient for the excitatory xi dynamics.
notation: b_i
lhs: b_i
rhs: b

c_i (StefanescuJirsa3D derived variable)
type: NamedIndividual
type: DerivedVariable
description: Per-mode constant for the excitatory eta dynamics.
notation: c_i
lhs: c_i
rhs: c

d_i (StefanescuJirsa3D derived variable)
type: NamedIndividual
type: DerivedVariable
description: Per-mode quadratic coefficient for the excitatory eta dynamics.
has db xref: GO_0060079
notation: d_i
lhs: d_i
rhs: d

e_i (StefanescuJirsa3D derived variable)
type: NamedIndividual
type: DerivedVariable
description: Per-mode cubic coefficient for the inhibitory alpha dynamics.
notation: e_i
lhs: e_i
rhs: a

f_i (StefanescuJirsa3D derived variable)
type: NamedIndividual
type: DerivedVariable
description: Per-mode quadratic coefficient for the inhibitory alpha dynamics.
notation: f_i
lhs: f_i
rhs: b

h_i (StefanescuJirsa3D derived variable)
type: NamedIndividual
type: DerivedVariable
description: Per-mode constant for the inhibitory beta dynamics.
notation: h_i
lhs: h_i
rhs: c

m_i (StefanescuJirsa3D derived variable)
type: NamedIndividual
type: DerivedVariable
description: Per-mode adaptation offset entering the tau dynamics.
notation: m_i
lhs: m_i
rhs: r*s*x_0

n_i (StefanescuJirsa3D derived variable)
type: NamedIndividual
type: DerivedVariable
description: Per-mode adaptation offset entering the gamma dynamics.
notation: n_i
lhs: n_i
rhs: r*s*x_0

p_i (StefanescuJirsa3D derived variable)
type: NamedIndividual
type: DerivedVariable
description: Per-mode quadratic coefficient for the inhibitory beta dynamics.
has db xref: GO_0060080
notation: p_i
lhs: p_i
rhs: d

K_11 (StefanescuJirsa3D parameter)
type: NamedIndividual
type: Parameter
default value: 0.5
has db xref: GO_0060079
definition: Internal coupling, excitatory to excitatory.
notation: K_11

K_12 (StefanescuJirsa3D parameter)
type: NamedIndividual
type: Parameter
default value: 0.1
has db xref: GO_0060080
definition: Internal coupling, inhibitory to excitatory.
notation: K_12

K_21 (StefanescuJirsa3D parameter)
type: NamedIndividual
type: Parameter
default value: 0.15
has db xref: GO_0060079
definition: Internal coupling, excitatory to inhibitory.
notation: K_21

a (StefanescuJirsa3D parameter)
type: NamedIndividual
type: Parameter
default value: 1.0
definition: Hindmarsh-Rose dimensionless coefficient a.
notation: a

b (StefanescuJirsa3D parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
definition: Hindmarsh-Rose dimensionless coefficient b.
notation: b

c (StefanescuJirsa3D parameter)
type: NamedIndividual
type: Parameter
default value: 1.0
definition: Hindmarsh-Rose dimensionless coefficient c.
notation: c

d (StefanescuJirsa3D parameter)
type: NamedIndividual
type: Parameter
default value: 5.0
definition: Hindmarsh-Rose dimensionless coefficient d.
notation: d

mu (StefanescuJirsa3D parameter)
type: NamedIndividual
type: Parameter
default value: 3.3
has db xref: GO_0060079
definition: Mean of the Gaussian heterogeneity distribution.
notation: mu

r (StefanescuJirsa3D parameter)
type: NamedIndividual
type: Parameter
default value: 0.006
definition: Adaptation parameter (Hindmarsh-Rose r).
notation: r

s (StefanescuJirsa3D parameter)
type: NamedIndividual
type: Parameter
default value: 4.0
definition: Adaptation feedback parameter.
notation: s

sigma (StefanescuJirsa3D parameter)
type: NamedIndividual
type: Parameter
default value: 0.3
has db xref: GO_0042391
definition: Standard deviation of the Gaussian heterogeneity distribution.
notation: sigma

x_0 (StefanescuJirsa3D parameter)
type: NamedIndividual
type: Parameter
default value: -1.6
has db xref: GO_0042391
definition: Leftmost equilibrium point of x in the Hindmarsh-Rose oscillator.
notation: x_0

alpha (StefanescuJirsa3D state variable)
type: NamedIndividual
type: StateVariable
description: Inhibitory fast variable (per mode).
has db xref: GO_0060080
notation: alpha
lhs: Derivative(alpha, t)
rhs: beta - e_i*alpha**3 + f_i*alpha**2 - gamma + K_21*(C_ik*xi - alpha) + II_i + c_pop0 + local_coupling*xi

beta (StefanescuJirsa3D state variable)
type: NamedIndividual
type: StateVariable
description: Inhibitory recovery variable (per mode).
has db xref: GO_0042391
notation: beta
lhs: Derivative(beta, t)
rhs: h_i - p_i*alpha**2 - beta

eta (StefanescuJirsa3D state variable)
type: NamedIndividual
type: StateVariable
description: Excitatory recovery variable (per mode).
has db xref: GO_0060079
notation: eta
lhs: Derivative(eta, t)
rhs: c_i - d_i*xi**2 - eta

gamma (StefanescuJirsa3D state variable)
type: NamedIndividual
type: StateVariable
description: Inhibitory slow adaptation variable (per mode).
has db xref: GO_0060080
notation: gamma
lhs: Derivative(gamma, t)
rhs: r*s*alpha - r*gamma - n_i

tau (StefanescuJirsa3D state variable)
type: NamedIndividual
type: StateVariable
description: Excitatory slow adaptation variable (per mode).
has db xref: GO_0060079
notation: tau
lhs: Derivative(tau, t)
rhs: r*s*xi - r*tau - m_i

xi (StefanescuJirsa3D state variable)
type: NamedIndividual
type: StateVariable
description: Excitatory fast variable (per mode).
has db xref: GO_0042391
notation: xi
lhs: Derivative(xi, t)
rhs: 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

lc_0 (SupHopf derived variable)
type: NamedIndividual
type: DerivedVariable
notation: lc_0
lhs: lc_0
rhs: local_coupling*x

a (SupHopf parameter)
type: NamedIndividual
type: Parameter
description: Local bifurcation parameter
default value: -0.5
definition: Local bifurcation parameter.
notation: a

omega (SupHopf parameter)
type: NamedIndividual
type: Parameter
description: Angular frequency
default value: 1.0
definition: Angular frequency.
notation: omega

x (SupHopf state variable)
type: NamedIndividual
type: StateVariable
description: First state-variable of the Supercritical Hopf model
notation: x
lhs: Derivative(x, t)
rhs: c_pop0 + lc_0 - omega*y + x*(a - x**2 - y**2)

y (SupHopf state variable)
type: NamedIndividual
type: StateVariable
description: Second state-variable of the Supercritical Hopf model
notation: y
lhs: Derivative(y, t)
rhs: c_pop1 + omega*x + y*(a - x**2 - y**2)

SS0 (TsodyksMarkram derived variable)
type: NamedIndividual
type: DerivedVariable
description: Total synaptic input (recurrent + external)
notation: SS0
lhs: SS0
rhs: J*u*x*E + E0

SS1 (TsodyksMarkram derived variable)
type: NamedIndividual
type: DerivedVariable
description: Softplus transfer function output
notation: SS1
lhs: SS1
rhs: alpha*log(1 + exp(SS0/alpha))

E0 (TsodyksMarkram parameter)
type: NamedIndividual
type: Parameter
description: External input (baseline excitability)
default value: -2.0
notation: E0

J (TsodyksMarkram parameter)
type: NamedIndividual
type: Parameter
description: Synaptic coupling strength
default value: 3.07
notation: J

U0 (TsodyksMarkram parameter)
type: NamedIndividual
type: Parameter
description: Baseline release probability
default value: 0.3
notation: U0

alpha (TsodyksMarkram parameter)
type: NamedIndividual
type: Parameter
description: Softplus nonlinearity steepness (smoothed threshold gain)
default value: 1.5
notation: alpha

tau (TsodyksMarkram parameter)
type: NamedIndividual
type: Parameter
description: Membrane time constant (firing rate relaxation)
default value: 0.013
notation: tau

tauD (TsodyksMarkram parameter)
type: NamedIndividual
type: Parameter
description: Synaptic depression recovery time constant
default value: 0.2
notation: tauD

tauF (TsodyksMarkram parameter)
type: NamedIndividual
type: Parameter
description: Synaptic facilitation decay time constant
default value: 1.5
notation: tauF

E (TsodyksMarkram state variable)
type: NamedIndividual
type: StateVariable
description: Mean firing rate of the excitatory population
notation: E
lhs: Derivative(E, t)
rhs: (-E + SS1)/tau

u (TsodyksMarkram state variable)
type: NamedIndividual
type: StateVariable
description: Synaptic facilitation variable (release probability). Decays to U0 with time constant tauF and is enhanced proportionally to firing.
notation: u
lhs: Derivative(u, t)
rhs: (U0 - u)/tauF + U0*(1 - u)*E

x (TsodyksMarkram state variable)
type: NamedIndividual
type: StateVariable
description: Synaptic depression variable (fraction of available neurotransmitter). Recovers to 1 with time constant tauD and is depleted proportionally to firing.
notation: x
lhs: Derivative(x, t)
rhs: (1 - x)/tauD - u*x*E

lc_0 (WilsonCowan derived variable)
type: NamedIndividual
type: DerivedVariable
notation: lc_0
lhs: lc_0
rhs: local_coupling*E

lc_1 (WilsonCowan derived variable)
type: NamedIndividual
type: DerivedVariable
notation: lc_1
lhs: lc_1
rhs: I*local_coupling

s_e (WilsonCowan derived variable)
type: NamedIndividual
type: DerivedVariable
notation: s_e
lhs: s_e
rhs: c_e/(1.0 + exp(-a_e*(-b_e + x_e))) - 1.0*shift_sigmoid/(exp(a_e*b_e) + 1.0)

s_i (WilsonCowan derived variable)
type: NamedIndividual
type: DerivedVariable
notation: s_i
lhs: s_i
rhs: c_i/(1.0 + exp(-a_i*(-b_i + x_i))) - 1.0*shift_sigmoid/(exp(a_i*b_i) + 1.0)

x_e (WilsonCowan derived variable)
type: NamedIndividual
type: DerivedVariable
description: Average level of excitation in excitatory neuron at time t. Can be interpreted as membrane potential (Sanz-Leon et al., 2015).
has db xref: GO_0042391
notation: x_e
lhs: x_e
rhs: alpha_e*(-I*c_ei + P + c_ee*E + c_pop0 + lc_0 + lc_1 - theta_e)

x_i (WilsonCowan derived variable)
type: NamedIndividual
type: DerivedVariable
description: Average level of excitation in inhibitory neuron at time t. Can be interpreted as membrane potential. (Sanz-Leon et al., 2015).
has db xref: GO_0042391
notation: x_i
lhs: x_i
rhs: alpha_i*(-I*c_ii + Q + c_ie*E + lc_0 + lc_1 - theta_i)

P (WilsonCowan parameter)
type: NamedIndividual
type: Parameter
description: External stimulus to the excitatory population (Wilson and Cowan, 1972)
default value: 0.0
has db xref: GO_0060079
definition: External stimulus to the excitatory population (Wilson and Cowan, 1972).
notation: P

Q (WilsonCowan parameter)
type: NamedIndividual
type: Parameter
description: External stimulus to the inhibitory population (Wilson and Cowan, 1972)
default value: 0.0
has db xref: GO_0060080
definition: External stimulus to the inhibitory population (Wilson and Cowan, 1972).
notation: Q

a_e (WilsonCowan parameter)
type: NamedIndividual
type: Parameter
description: Steepness of the excitatory response function S_e_WC (Wilson and Cowan, 1972)
default value: 1.2
has db xref: GO_0060079
definition: Steepness of the excitatory response function S_e_WC (Wilson and Cowan, 1972).
notation: a_e

a_i (WilsonCowan parameter)
type: NamedIndividual
type: Parameter
description: Steepness of the excitatory response function S_i_WC (Wilson and Cowan, 1972)
default value: 1.0
has db xref: GO_0060080
definition: Steepness of the excitatory response function S_i_WC (Wilson and Cowan, 1972).
notation: a_i

alpha_e (WilsonCowan parameter)
type: NamedIndividual
type: Parameter
description: Balance parameter between excitatory and inhibitory masses (Sanz-Leon et al
default value: 1.0
definition: Balance parameter between excitatory and inhibitory masses (Sanz-Leon et al., 2015).
notation: alpha_e

alpha_i (WilsonCowan parameter)
type: NamedIndividual
type: Parameter
description: Balance parameter between excitatory and inhibitory masses (Sanz-Leon et al
default value: 1.0
definition: Balance parameter between excitatory and inhibitory masses (Sanz-Leon et al., 2015).
notation: alpha_i

b_e (WilsonCowan parameter)
type: NamedIndividual
type: Parameter
description: Position of the maximum slope of the excitatory response function S_e_WC (Sanz-Leon et al
default value: 2.8
has db xref: GO_0060079
definition: Position of the maximum slope of the excitatory response function S_e_WC (Sanz-Leon et al., 2015).
notation: b_e

b_i (WilsonCowan parameter)
type: NamedIndividual
type: Parameter
description: Position of the maximum slope of a sigmoid function [in threshold units]
default value: 4.0
has db xref: GO_0060080
notation: b_i

c_e (WilsonCowan parameter)
type: NamedIndividual
type: Parameter
description: The amplitude parameter for the excitatory response function
default value: 1.0
has db xref: GO_0060079
notation: c_e

c_ee (WilsonCowan parameter)
type: NamedIndividual
type: Parameter
description: Excitatory to excitatory coupling coefficient
default value: 12.0
has db xref: GO_0060079
notation: c_ee

c_ei (WilsonCowan parameter)
type: NamedIndividual
type: Parameter
description: Inhibitory to excitatory coupling coefficient
default value: 4.0
has db xref: GO_0060080
notation: c_ei

c_i (WilsonCowan parameter)
type: NamedIndividual
type: Parameter
description: The amplitude parameter for the excitatory response function S_i_WC (Sanz-Leon et al
default value: 1.0
has db xref: GO_0098815
definition: The amplitude parameter for the excitatory response function S_i_WC (Sanz-Leon et al., 2015).
notation: c_i

c_ie (WilsonCowan parameter)
type: NamedIndividual
type: Parameter
description: Excitatory to inhibitory coupling coefficient (Sanz-Leon et al
default value: 13.0
has db xref: GO_0060079
definition: Excitatory to inhibitory coupling coefficient (Sanz-Leon et al., 2015)
notation: c_ie

c_ii (WilsonCowan parameter)
type: NamedIndividual
type: Parameter
description: Inhibitory to inhibitory coupling coefficient (Sanz-Leon et al
default value: 11.0
has db xref: GO_0060080
definition: Inhibitory to inhibitory coupling coefficient (Sanz-Leon et al., 2015)
notation: c_ii

k_e (WilsonCowan parameter)
type: NamedIndividual
type: Parameter
description: Maximum value of the excitatory response function
default value: 1.0
has db xref: GO_0060079
notation: k_e

k_i (WilsonCowan parameter)
type: NamedIndividual
type: Parameter
description: Maximum value of the inhibitory response function
default value: 1.0
has db xref: GO_0060080
notation: k_i

r_e (WilsonCowan parameter)
type: NamedIndividual
type: Parameter
description: Excitatory refractory period
default value: 1.0
has db xref: GO_0098815
notation: r_e

r_i (WilsonCowan parameter)
type: NamedIndividual
type: Parameter
description: Inhibitory refractory period
default value: 1.0
has db xref: GO_0098828
notation: r_i

shift_sigmoid (WilsonCowan parameter)
type: NamedIndividual
type: Parameter
description: 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: 1.0
notation: shift_sigmoid

tau_e (WilsonCowan parameter)
type: NamedIndividual
type: Parameter
description: Excitatory population, membrane time-constant (Wilson and Cowan, 1972)
default value: 10.0
has db xref: GO_0043179
definition: Excitatory population, membrane time-constant (Wilson and Cowan, 1972).
notation: tau_e
unit (slot): ms

tau_i (WilsonCowan parameter)
type: NamedIndividual
type: Parameter
description: Inhibitory population, membrane time-constant (Wilson and Cowan, 1972)
default value: 10.0
has db xref: GO_0043180
definition: Inhibitory population, membrane time-constant (Wilson and Cowan, 1972).
notation: tau_i
unit (slot): ms

theta_e (WilsonCowan parameter)
type: NamedIndividual
type: Parameter
description: Excitation threshold of excitatory population (Sanz-Leon et al
default value: 0.0
definition: Excitation threshold of excitatory population (Sanz-Leon et al., 2015).
notation: theta_e

theta_i (WilsonCowan parameter)
type: NamedIndividual
type: Parameter
description: Excitation threshold of inhibitory population (Sanz-Leon et al
default value: 0.0
has db xref: InhibitoryThresholdVariance
definition: Excitation threshold of inhibitory population (Sanz-Leon et al., 2015).
notation: theta_i

E (WilsonCowan state variable)
type: NamedIndividual
type: StateVariable
description: 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: GO_0098815
notation: E
lhs: Derivative(E, t)
rhs: (-E + s_e*(-E*r_e + k_e))/tau_e

I (WilsonCowan state variable)
type: NamedIndividual
type: StateVariable
description: 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: GO_0060080
notation: I
lhs: Derivative(I, t)
rhs: (-I + s_i*(-I*r_i + k_i))/tau_i

Fe_ext (ZerlautAdaptationFirstOrder derived variable)
type: NamedIndividual
type: DerivedVariable
notation: Fe_ext
lhs: Fe_ext
rhs: Piecewise((0, K_ext_e*(c_pop0 + lc_E + ou_drift*weight_noise) < 0), (c_pop0 + lc_E + ou_drift*weight_noise, True))

Fi_ext (ZerlautAdaptationFirstOrder derived variable)
type: NamedIndividual
type: DerivedVariable
notation: Fi_ext
lhs: Fi_ext
rhs: lc_I

S_e (ZerlautAdaptationFirstOrder derived variable)
type: NamedIndividual
type: DerivedVariable
notation: S_e
lhs: S_e
rhs: (-sV0 + sigma_V_e)/DsV0

S_i (ZerlautAdaptationFirstOrder derived variable)
type: NamedIndividual
type: DerivedVariable
description: Scaling of the remote input for the inhibitory population with respect to the excitatory population.
notation: S_i
lhs: S_i
rhs: (-sV0 + sigma_V_i)/DsV0

T_V_e (ZerlautAdaptationFirstOrder derived variable)
type: NamedIndividual
type: DerivedVariable
notation: T_V_e
lhs: T_V_e
rhs: (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)
type: NamedIndividual
type: DerivedVariable
notation: T_V_i
lhs: T_V_i
rhs: (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))

T_e (ZerlautAdaptationFirstOrder derived variable)
type: NamedIndividual
type: DerivedVariable
notation: T_e
lhs: T_e
rhs: (-TvN0 + T_V_e*g_L/C_m)/DTvN0

T_i (ZerlautAdaptationFirstOrder derived variable)
type: NamedIndividual
type: DerivedVariable
notation: T_i
lhs: T_i
rhs: (-TvN0 + T_V_i*g_L/C_m)/DTvN0

T_m_e (ZerlautAdaptationFirstOrder derived variable)
type: NamedIndividual
type: DerivedVariable
notation: T_m_e
lhs: T_m_e
rhs: C_m/mu_G_e

T_m_i (ZerlautAdaptationFirstOrder derived variable)
type: NamedIndividual
type: DerivedVariable
notation: T_m_i
lhs: T_m_i
rhs: C_m/mu_G_i

U_e_e (ZerlautAdaptationFirstOrder derived variable)
type: NamedIndividual
type: DerivedVariable
notation: U_e_e
lhs: U_e_e
rhs: Q_e*(E_e - mu_V_e)/mu_G_e

U_e_i (ZerlautAdaptationFirstOrder derived variable)
type: NamedIndividual
type: DerivedVariable
notation: U_e_i
lhs: U_e_i
rhs: Q_e*(E_e - mu_V_i)/mu_G_i

U_i_e (ZerlautAdaptationFirstOrder derived variable)
type: NamedIndividual
type: DerivedVariable
notation: U_i_e
lhs: U_i_e
rhs: Q_i*(E_i - mu_V_e)/mu_G_e

U_i_i (ZerlautAdaptationFirstOrder derived variable)
type: NamedIndividual
type: DerivedVariable
notation: U_i_i
lhs: U_i_i
rhs: Q_i*(E_i - mu_V_i)/mu_G_i

V_e (ZerlautAdaptationFirstOrder derived variable)
type: NamedIndividual
type: DerivedVariable
notation: V_e
lhs: V_e
rhs: (-muV0 + mu_V_e)/DmuV0

V_i (ZerlautAdaptationFirstOrder derived variable)
type: NamedIndividual
type: DerivedVariable
notation: V_i
lhs: V_i
rhs: (-muV0 + mu_V_i)/DmuV0

V_thre_e (ZerlautAdaptationFirstOrder derived variable)
type: NamedIndividual
type: DerivedVariable
notation: V_thre_e
lhs: V_thre_e
rhs: 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)
type: NamedIndividual
type: DerivedVariable
notation: V_thre_i
lhs: V_thre_i
rhs: 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

f_out_e (ZerlautAdaptationFirstOrder derived variable)
type: NamedIndividual
type: DerivedVariable
notation: f_out_e
lhs: f_out_e
rhs: erfc(sqrt(2)*(V_thre_e - mu_V_e)/(2*sigma_V_e))/(2*T_V_e)

f_out_i (ZerlautAdaptationFirstOrder derived variable)
type: NamedIndividual
type: DerivedVariable
notation: f_out_i
lhs: f_out_i
rhs: erfc(sqrt(2)*(V_thre_i - mu_V_i)/(2*sigma_V_i))/(2*T_V_i)

fe_e (ZerlautAdaptationFirstOrder derived variable)
type: NamedIndividual
type: DerivedVariable
notation: fe_e
lhs: fe_e
rhs: K_ext_e*(Fe_ext + external_input_ex_ex) + N_tot*p_connect_e*(1.0 - g)*(E + 1/1000000)

fe_i (ZerlautAdaptationFirstOrder derived variable)
type: NamedIndividual
type: DerivedVariable
notation: fe_i
lhs: fe_i
rhs: K_ext_e*(Fe_ext + external_input_in_ex) + N_tot*p_connect_e*(1.0 - g)*(E + 1/1000000)

fi_e (ZerlautAdaptationFirstOrder derived variable)
type: NamedIndividual
type: DerivedVariable
notation: fi_e
lhs: fi_e
rhs: K_ext_i*(Fi_ext + external_input_ex_in) + N_tot*g*p_connect_i*(I + 1/1000000)

fi_i (ZerlautAdaptationFirstOrder derived variable)
type: NamedIndividual
type: DerivedVariable
notation: fi_i
lhs: fi_i
rhs: K_ext_i*(Fi_ext + external_input_in_in) + N_tot*g*p_connect_i*(I + 1/1000000)

lc_E (ZerlautAdaptationFirstOrder derived variable)
type: NamedIndividual
type: DerivedVariable
notation: lc_E
lhs: lc_E
rhs: local_coupling*E

lc_I (ZerlautAdaptationFirstOrder derived variable)
type: NamedIndividual
type: DerivedVariable
notation: lc_I
lhs: lc_I
rhs: I*local_coupling

mu_G_e (ZerlautAdaptationFirstOrder derived variable)
type: NamedIndividual
type: DerivedVariable
notation: mu_G_e
lhs: mu_G_e
rhs: g_L + mu_Ge_e + mu_Gi_e

mu_G_i (ZerlautAdaptationFirstOrder derived variable)
type: NamedIndividual
type: DerivedVariable
notation: mu_G_i
lhs: mu_G_i
rhs: g_L + mu_Ge_i + mu_Gi_i

mu_Ge_e (ZerlautAdaptationFirstOrder derived variable)
type: NamedIndividual
type: DerivedVariable
notation: mu_Ge_e
lhs: mu_Ge_e
rhs: Q_e*fe_e*tau_e

mu_Ge_i (ZerlautAdaptationFirstOrder derived variable)
type: NamedIndividual
type: DerivedVariable
notation: mu_Ge_i
lhs: mu_Ge_i
rhs: Q_e*fe_i*tau_e

mu_Gi_e (ZerlautAdaptationFirstOrder derived variable)
type: NamedIndividual
type: DerivedVariable
notation: mu_Gi_e
lhs: mu_Gi_e
rhs: Q_i*fi_e*tau_i

mu_Gi_i (ZerlautAdaptationFirstOrder derived variable)
type: NamedIndividual
type: DerivedVariable
notation: mu_Gi_i
lhs: mu_Gi_i
rhs: Q_i*fi_i*tau_i

mu_V_e (ZerlautAdaptationFirstOrder derived variable)
type: NamedIndividual
type: DerivedVariable
notation: mu_V_e
lhs: mu_V_e
rhs: (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)
type: NamedIndividual
type: DerivedVariable
notation: mu_V_i
lhs: mu_V_i
rhs: (E_L_i*g_L + E_e*mu_Ge_i + E_i*mu_Gi_i - W_i)/mu_G_i

sigma_V_e (ZerlautAdaptationFirstOrder derived variable)
type: NamedIndividual
type: DerivedVariable
notation: sigma_V_e
lhs: sigma_V_e
rhs: 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)
type: NamedIndividual
type: DerivedVariable
notation: sigma_V_i
lhs: sigma_V_i
rhs: 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))

C_m (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: membrane capacitance [pF]
default value: 200.0
has db xref: GO_0042391
notation: C_m

DTvN0 (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: Normalization factors page 48 after the equation 4 from [ZD_2018]
default value: 1.0
notation: DTvN0

DmuV0 (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: Normalization factors page 48 after the equation 4 from [ZD_2018]
default value: 10.0
notation: DmuV0

DsV0 (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: Normalization factors page 48 after the equation 4 from [ZD_2018]
default value: 6.0
notation: DsV0

E_L_e (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: leak reversal potential for excitatory [mV]
default value: -65.0
has db xref: GO_0022840
notation: E_L_e

E_L_i (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: leak reversal potential for inhibitory [mV]
default value: -65.0
has db xref: GO_0022840
notation: E_L_i

E_e (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: excitatory reversal potential [mV]
default value: 0.0
has db xref: GO_0060079
notation: E_e

E_i (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: inhibitory reversal potential [mV]
default value: -80.0
has db xref: GO_0060080
notation: E_i

K_ext_e (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: Number of excitatory connexions from external population
default value: 400.0
notation: K_ext_e

K_ext_i (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: Number of inhibitory connexions from external population
default value: 0.0
notation: K_ext_i

N_tot (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: cell number
default value: 10000.0
notation: N_tot

P0_e (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: Polynome of excitatory phenomenological threshold (order 9)
default value: -0.04983106
notation: P0_e

P0_i (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: Polynome of inhibitory phenomenological threshold (order 9)
default value: -0.05149122
notation: P0_i

P1_e (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: Polynome of excitatory phenomenological threshold (order 9)
default value: 0.005063551
notation: P1_e

P1_i (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: Polynome of inhibitory phenomenological threshold (order 9)
default value: 0.004003689
notation: P1_i

P2_e (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: Polynome of excitatory phenomenological threshold (order 9)
default value: -0.02347012
notation: P2_e

P2_i (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: Polynome of inhibitory phenomenological threshold (order 9)
default value: -0.008352014
notation: P2_i

P3_e (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: Polynome of excitatory phenomenological threshold (order 9)
default value: 0.002295151
notation: P3_e

P3_i (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: Polynome of inhibitory phenomenological threshold (order 9)
default value: 2.414238E-4
notation: P3_i

P4_e (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: Polynome of excitatory phenomenological threshold (order 9)
default value: -4.105303E-4
notation: P4_e

P4_i (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: Polynome of inhibitory phenomenological threshold (order 9)
default value: -5.070645E-4
notation: P4_i

P5_e (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: Polynome of excitatory phenomenological threshold (order 9)
default value: 0.01054705
notation: P5_e

P5_i (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: Polynome of inhibitory phenomenological threshold (order 9)
default value: 0.001434539
notation: P5_i

P6_e (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: Polynome of excitatory phenomenological threshold (order 9)
default value: -0.03659253
notation: P6_e

P6_i (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: Polynome of inhibitory phenomenological threshold (order 9)
default value: -0.01468669
notation: P6_i

P7_e (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: Polynome of excitatory phenomenological threshold (order 9)
default value: 0.007437488
notation: P7_e

P7_i (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: Polynome of inhibitory phenomenological threshold (order 9)
default value: 0.004502706
notation: P7_i

P8_e (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: Polynome of excitatory phenomenological threshold (order 9)
default value: 0.001265065
notation: P8_e

P8_i (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: Polynome of inhibitory phenomenological threshold (order 9)
default value: 0.002847219
notation: P8_i

P9_e (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: Polynome of excitatory phenomenological threshold (order 9)
default value: -0.04072161
notation: P9_e

P9_i (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: Polynome of inhibitory phenomenological threshold (order 9)
default value: -0.0153578
notation: P9_i

P_e (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: Polynome of excitatory phenomenological threshold (order 9)
default value: -0.04983106
notation: P_e

P_i (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: Polynome of inhibitory phenomenological threshold (order 9)
default value: -0.05149122
notation: P_i

Q_e (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: excitatory quantal conductance [nS]
default value: 1.5
has db xref: GO_0060079
notation: Q_e

Q_i (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: inhibitory quantal conductance [nS]
default value: 5.0
has db xref: GO_0060080
notation: Q_i

S_i (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: Scaling of the remote input for the inhibitory population with respect to the excitatory population
default value: 1.0
has db xref: GO_0060080
definition: Scaling of the remote input for the inhibitory population with respect to the excitatory population.
notation: S_i

T (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: Time scale of describing network activity
default value: 20.0
notation: T

TvN0 (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: Normalization factors page 48 after the equation 4 from [ZD_2018]
default value: 0.5
notation: TvN0

a_e (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: Excitatory adaptation conductance [nS]
default value: 4.0
has db xref: GO_0060079
notation: a_e

a_i (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: Inhibitory adaptation conductance [nS]
default value: 0.0
has db xref: GO_0060080
notation: a_i

b_e (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: Excitatory adaptation current increment [pA]
default value: 60.0
has db xref: GO_0060079
notation: b_e

b_i (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: Inhibitory adaptation current increment [pA]
default value: 0.0
has db xref: GO_0060080
notation: b_i

external_input_ex_ex (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: external drive
default value: 0.0
notation: external_input_ex_ex

external_input_ex_in (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: external drive
default value: 0.0
notation: external_input_ex_in

external_input_in_ex (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: external drive
default value: 0.0
notation: external_input_in_ex

external_input_in_in (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: external drive
default value: 0.0
notation: external_input_in_in

g (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: fraction of inhibitory cells
default value: 0.2
has db xref: GO_0060077
notation: g

g_L (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: leak conductance [nS]
default value: 10.0
has db xref: GO_0022840
notation: g_L

muV0 (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: Normalization factors page 48 after the equation 4 from [ZD_2018]
default value: -60.0
notation: muV0

p_connect_e (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: connectivity probability
default value: 0.05
notation: p_connect_e

p_connect_i (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: connectivity probability
default value: 0.05
notation: p_connect_i

sV0 (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: Normalization factors page 48 after the equation 4 from [ZD_2018]
default value: 4.0
notation: sV0

tau_OU (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: time constant noise
default value: 5.0
notation: tau_OU

tau_e (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: excitatory decay [ms]
default value: 5.0
has db xref: GO_0098815
notation: tau_e

tau_i (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: inhibitory decay [ms]
default value: 5.0
has db xref: GO_0098828
notation: tau_i

tau_w_e (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: Adaptation time constant of excitatory neurons [ms]
default value: 500.0
has db xref: GO_0098815
notation: tau_w_e

tau_w_i (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: Adaptation time constant of inhibitory neurons [ms]
default value: 1.0
has db xref: GO_0098828
notation: tau_w_i

weight_noise (ZerlautAdaptationFirstOrder parameter)
type: NamedIndividual
type: Parameter
description: weight noise
default value: 10.5
notation: weight_noise

E (ZerlautAdaptationFirstOrder state variable)
type: NamedIndividual
type: StateVariable
description: Firing rate of excitatory population in KHz
notation: E
lhs: Derivative(E, t)
rhs: (-E + f_out_e)/T

I (ZerlautAdaptationFirstOrder state variable)
type: NamedIndividual
type: StateVariable
description: Firing rate of inhibitory population in KHz
notation: I
lhs: Derivative(I, t)
rhs: (-I + f_out_i)/T

W_e (ZerlautAdaptationFirstOrder state variable)
type: NamedIndividual
type: StateVariable
description: Level of adaptation of excitatory in pA
notation: W_e
lhs: Derivative(W_e, t)
rhs: E*b_e - W_e/tau_w_e + a_e*(-E_L_e + mu_V_e)/tau_w_e

W_i (ZerlautAdaptationFirstOrder state variable)
type: NamedIndividual
type: StateVariable
description: Level of adaptation of inhibitory in pA
notation: W_i
lhs: Derivative(W_i, t)
rhs: I*b_i - W_i/tau_w_i + a_i*(-E_L_i + mu_V_i)/tau_w_i

ou_drift (ZerlautAdaptationFirstOrder state variable)
type: NamedIndividual
type: StateVariable
notation: ou_drift
lhs: Derivative(ou_drift, t)
rhs: -ou_drift/tau_OU

coupled_input (ZetterbergJansen derived variable)
type: NamedIndividual
type: DerivedVariable
notation: coupled_input
lhs: coupled_input
rhs: 2*e0/(exp(rho_1*(-c_pop0 - local_coupling*v6 + rho_2)) + 1)

sigma_v1 (ZetterbergJansen derived variable)
type: NamedIndividual
type: DerivedVariable
notation: sigma_v1
lhs: sigma_v1
rhs: Piecewise((0, rho_1*(rho_2 - v1) > 709), (2*e0/(exp(rho_1*(rho_2 - v1)) + 1), True))

sigma_v23 (ZetterbergJansen derived variable)
type: NamedIndividual
type: DerivedVariable
notation: sigma_v23
lhs: sigma_v23
rhs: 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)
type: NamedIndividual
type: DerivedVariable
notation: sigma_v45
lhs: sigma_v45
rhs: Piecewise((0, rho_1*(rho_2 - (v4 - v5)) > 709), (2*e0/(exp(rho_1*(rho_2 - (v4 - v5))) + 1), True))

He (ZetterbergJansen parameter)
type: NamedIndividual
type: Parameter
description: Maximum amplitude of EPSP [mV]
default value: 3.25
has db xref: GO_0060079
has db xref: GO_0098815
definition: Maximum amplitude of EPSP [mV]. Also called average synaptic gain.
notation: He

Hi (ZetterbergJansen parameter)
type: NamedIndividual
type: Parameter
description: Maximum amplitude of IPSP [mV]
default value: 22.0
has db xref: GO_0060080
has db xref: GO_0098828
definition: Maximum amplitude of IPSP [mV]. Also called average synaptic gain.
notation: Hi

P (ZetterbergJansen parameter)
type: NamedIndividual
type: Parameter
description: Maximum firing rate to the pyramidal population [ms^-1]
default value: 0.12
has db xref: CL_0000598
has db xref: GO_0099605
definition: Maximum firing rate to the pyramidal population [ms^-1]. (External stimulus. Constant intensity.Entry point for coupling.)
notation: P

Q (ZetterbergJansen parameter)
type: NamedIndividual
type: Parameter
description: Maximum firing rate to the interneurons population [ms^-1]
default value: 0.12
has db xref: CL_0000099
has db xref: GO_0099605
definition: Maximum firing rate to the interneurons population [ms^-1]. (External stimulus. Constant intensity.Entry point for coupling.)
notation: Q

U (ZetterbergJansen parameter)
type: NamedIndividual
type: Parameter
description: Maximum firing rate to the stellate population [ms^-1]
default value: 0.12
has db xref: GO_0099605
definition: Maximum firing rate to the stellate population [ms^-1]. (External stimulus. Constant intensity.Entry point for coupling.)
notation: U

e0 (ZetterbergJansen parameter)
type: NamedIndividual
type: Parameter
description: Half of the maximum population mean firing rate [ms^-1]
default value: 0.0025
has db xref: GO_0099605
definition: Half of the maximum population mean firing rate [ms^-1].
notation: e0

gamma_1 (ZetterbergJansen parameter)
type: NamedIndividual
type: Parameter
description: Average number of synapses between populations (pyramidal to stellate)
default value: 135.0
has db xref: CL_0000598
has db xref: GO_0099536
definition: Average number of synapses between populations (pyramidal to stellate).
notation: gamma_1

gamma_1T (ZetterbergJansen parameter)
type: NamedIndividual
type: Parameter
description: Coupling factor from the extrinisic input to the spiny stellate population
default value: 1.0
has db xref: GO_0099536
definition: Coupling factor from the extrinisic input to the spiny stellate population.
notation: gamma_1T

gamma_2 (ZetterbergJansen parameter)
type: NamedIndividual
type: Parameter
description: Average number of synapses between populations (stellate to pyramidal)
default value: 108.0
has db xref: GO_0099536
definition: Average number of synapses between populations (stellate to pyramidal).
notation: gamma_2

gamma_2T (ZetterbergJansen parameter)
type: NamedIndividual
type: Parameter
description: Coupling factor from the extrinisic input to the pyramidal population
default value: 1.0
has db xref: CL_0000598
has db xref: GO_0099536
definition: Coupling factor from the extrinisic input to the pyramidal population.
notation: gamma_2T

gamma_3 (ZetterbergJansen parameter)
type: NamedIndividual
type: Parameter
description: Connectivity constant (pyramidal to interneurons)
default value: 33.75
has db xref: CL_0000099
has db xref: CL_0000598
has db xref: GO_0099536
notation: gamma_3

gamma_3T (ZetterbergJansen parameter)
type: NamedIndividual
type: Parameter
description: Coupling factor from the extrinisic input to the inhibitory population
default value: 1.0
has db xref: GO_0099536
definition: Coupling factor from the extrinisic input to the inhibitory population.
notation: gamma_3T

gamma_4 (ZetterbergJansen parameter)
type: NamedIndividual
type: Parameter
description: Connectivity constant (interneurons to pyramidal)
default value: 33.75
has db xref: CL_0000099
has db xref: CL_0000598
notation: gamma_4

gamma_5 (ZetterbergJansen parameter)
type: NamedIndividual
type: Parameter
description: Connectivity constant (interneurons to interneurons)
default value: 15.0
has db xref: CL_0000099
notation: gamma_5

ke (ZetterbergJansen parameter)
type: NamedIndividual
type: Parameter
description: Reciprocal of the time constant of passive membrane and all other spatially distributed delays in the dendritic network [ms^-1]
default value: 0.1
definition: 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: ke

ki (ZetterbergJansen parameter)
type: NamedIndividual
type: Parameter
description: Reciprocal of the time constant of passive membrane and all other spatially distributed delays in the dendritic network [ms^-1]
default value: 0.05
definition: 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: ki

rho_1 (ZetterbergJansen parameter)
type: NamedIndividual
type: Parameter
description: Steepness of the sigmoidal transformation [mV^-1]
default value: 0.56
definition: Steepness of the sigmoidal transformation [mV^-1].
notation: rho_1

rho_2 (ZetterbergJansen parameter)
type: NamedIndividual
type: Parameter
description: Firing threshold (PSP) for which a 50% firing rate is achieved
default value: 6.0
definition: 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: rho_2

v1 (ZetterbergJansen state variable)
type: NamedIndividual
type: StateVariable
notation: v1
lhs: Derivative(v1, t)
rhs: y1

v2 (ZetterbergJansen state variable)
type: NamedIndividual
type: StateVariable
notation: v2
lhs: Derivative(v2, t)
rhs: y2

v3 (ZetterbergJansen state variable)
type: NamedIndividual
type: StateVariable
notation: v3
lhs: Derivative(v3, t)
rhs: y3

v4 (ZetterbergJansen state variable)
type: NamedIndividual
type: StateVariable
notation: v4
lhs: Derivative(v4, t)
rhs: y4

v5 (ZetterbergJansen state variable)
type: NamedIndividual
type: StateVariable
notation: v5
lhs: Derivative(v5, t)
rhs: y5

v6 (ZetterbergJansen state variable)
type: NamedIndividual
type: StateVariable
notation: v6
lhs: Derivative(v6, t)
rhs: y2 - y3

v7 (ZetterbergJansen state variable)
type: NamedIndividual
type: StateVariable
notation: v7
lhs: Derivative(v7, t)
rhs: y4 - y5

y1 (ZetterbergJansen state variable)
type: NamedIndividual
type: StateVariable
notation: y1
lhs: Derivative(y1, t)
rhs: He*ke*(gamma_1*sigma_v23 + gamma_1T*(U + coupled_input)) - ke**2*v1 - 2*ke*y1

y2 (ZetterbergJansen state variable)
type: NamedIndividual
type: StateVariable
notation: y2
lhs: Derivative(y2, t)
rhs: He*ke*(gamma_2*sigma_v1 + gamma_2T*(P + coupled_input)) - ke**2*v2 - 2*ke*y2

y3 (ZetterbergJansen state variable)
type: NamedIndividual
type: StateVariable
notation: y3
lhs: Derivative(y3, t)
rhs: Hi*gamma_4*ki*sigma_v45 - ki**2*v3 - 2*ki*y3

y4 (ZetterbergJansen state variable)
type: NamedIndividual
type: StateVariable
notation: y4
lhs: Derivative(y4, t)
rhs: He*ke*(gamma_3*sigma_v23 + gamma_3T*(Q + coupled_input)) - ke**2*v4 - 2*ke*y4

y5 (ZetterbergJansen state variable)
type: NamedIndividual
type: StateVariable
notation: y5
lhs: Derivative(y5, t)
rhs: Hi*gamma_5*ki*sigma_v45 - ke**2*v5 - 2*ki*y5

space-MNI152_atlas-Yeo17_res-1_dseg
type: NamedIndividual
type: BrainAtlas
alternative label: Yeo17

tpl-FSLMNI152_atlas-Schaefer2018_seg-17Networks_scale-1000_dseg
type: NamedIndividual
type: BrainAtlas
alternative label: Schaefer2018

tpl-FSLMNI152_atlas-Schaefer2018_seg-17Networks_scale-100_dseg
type: NamedIndividual
type: BrainAtlas
alternative label: Schaefer2018

tpl-FSLMNI152_atlas-Schaefer2018_seg-17Networks_scale-200_dseg
type: NamedIndividual
type: BrainAtlas
alternative label: Schaefer2018

tpl-FSLMNI152_atlas-Schaefer2018_seg-17Networks_scale-300_dseg
type: NamedIndividual
type: BrainAtlas
alternative label: Schaefer2018

tpl-FSLMNI152_atlas-Schaefer2018_seg-17Networks_scale-400_dseg
type: NamedIndividual
type: BrainAtlas
alternative label: Schaefer2018

tpl-FSLMNI152_atlas-Schaefer2018_seg-17Networks_scale-500_dseg
type: NamedIndividual
type: BrainAtlas
alternative label: Schaefer2018

tpl-FSLMNI152_atlas-Schaefer2018_seg-17Networks_scale-600_dseg
type: NamedIndividual
type: BrainAtlas
alternative label: Schaefer2018

tpl-FSLMNI152_atlas-Schaefer2018_seg-17Networks_scale-700_dseg
type: NamedIndividual
type: BrainAtlas
alternative label: Schaefer2018

tpl-FSLMNI152_atlas-Schaefer2018_seg-17Networks_scale-800_dseg
type: NamedIndividual
type: BrainAtlas
alternative label: Schaefer2018

tpl-FSLMNI152_atlas-Schaefer2018_seg-17Networks_scale-900_dseg
type: NamedIndividual
type: BrainAtlas
alternative label: Schaefer2018

tpl-FSLMNI152_atlas-Schaefer2018_seg-7Networks_scale-1000_dseg
type: NamedIndividual
type: BrainAtlas
alternative label: Schaefer2018

tpl-FSLMNI152_atlas-Schaefer2018_seg-7Networks_scale-100_dseg
type: NamedIndividual
type: BrainAtlas
alternative label: Schaefer2018

tpl-FSLMNI152_atlas-Schaefer2018_seg-7Networks_scale-200_dseg
type: NamedIndividual
type: BrainAtlas
alternative label: Schaefer2018

tpl-FSLMNI152_atlas-Schaefer2018_seg-7Networks_scale-300_dseg
type: NamedIndividual
type: BrainAtlas
alternative label: Schaefer2018

tpl-FSLMNI152_atlas-Schaefer2018_seg-7Networks_scale-400_dseg
type: NamedIndividual
type: BrainAtlas
alternative label: Schaefer2018

tpl-FSLMNI152_atlas-Schaefer2018_seg-7Networks_scale-500_dseg
type: NamedIndividual
type: BrainAtlas
alternative label: Schaefer2018

tpl-FSLMNI152_atlas-Schaefer2018_seg-7Networks_scale-600_dseg
type: NamedIndividual
type: BrainAtlas
alternative label: Schaefer2018

tpl-FSLMNI152_atlas-Schaefer2018_seg-7Networks_scale-700_dseg
type: NamedIndividual
type: BrainAtlas
alternative label: Schaefer2018

tpl-FSLMNI152_atlas-Schaefer2018_seg-7Networks_scale-800_dseg
type: NamedIndividual
type: BrainAtlas
alternative label: Schaefer2018

tpl-FSLMNI152_atlas-Schaefer2018_seg-7Networks_scale-900_dseg
type: NamedIndividual
type: BrainAtlas
alternative label: Schaefer2018

https://w3id.org/tvbo/atlases/tpl-MNI152NLin2009b_atlas-hcpmmp1_desc-ordered_dseg
type: NamedIndividual
type: BrainAtlas
alternative label: hcpmmp1

https://w3id.org/tvbo/atlases/tpl-MNI152NLin2009c_atlas-DesikanKilliany_desc-ranked_dseg
type: NamedIndividual
type: BrainAtlas
alternative label: DesikanKilliany

https://w3id.org/tvbo/atlases/tpl-MNI152Nlin2009c_atlas-Destrieux_desc-ranked_dseg
type: NamedIndividual
type: BrainAtlas
alternative label: Destrieux

eq_in_a
type: NamedIndividual
type: Continuation
description: 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_full
type: NamedIndividual
type: Continuation
description: 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.

MNI152NLin2009b
type: NamedIndividual
type: CommonCoordinateSpace
description: Nonlinear 6th-generation MNI152 average, 2009b release (symmetric variant). Produced by the McConnell Brain Imaging Centre (Fonov et al., 2011).
alternative label: MNI152NLin2009bSym
alternative label: tpl-MNI152NLin2009bSym
anatomical axes orientation: RAS
axes origin: anterior commissure
unit (slot): mm

MNI152NLin2009c
type: NamedIndividual
type: CommonCoordinateSpace
description: Nonlinear 6th-generation MNI152 average, 2009c release (symmetric variant). Produced by the McConnell Brain Imaging Centre (Fonov et al., 2011).
alternative label: MNI152NLin2009cSym
alternative label: tpl-MNI152NLin2009cSym
anatomical axes orientation: RAS
axes origin: anterior commissure
unit (slot): mm

MNI152NLin2009cAsym
type: NamedIndividual
type: CommonCoordinateSpace
description: 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`.
alternative label: MNI152_2009c_asym
alternative label: tpl-MNI152NLin2009cAsym
anatomical axes orientation: RAS
axes origin: anterior commissure
unit (slot): mm

MNI152NLin6Asym
type: NamedIndividual
type: CommonCoordinateSpace
description: 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`.
alternative label: FSLMNI152
alternative label: MNI152
alternative label: MNI152NLin6
anatomical axes orientation: RAS
axes origin: anterior commissure
unit (slot): mm

Difference
type: NamedIndividual
type: Coupling
has parameter: a (Difference parameter)

FastLinearCoupling
type: NamedIndividual
type: Coupling
description: 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: G (FastLinearCoupling parameter)
has parameter: b (FastLinearCoupling parameter)

HyperbolicTangent
type: NamedIndividual
type: Coupling
has parameter: a (HyperbolicTangent parameter)
has parameter: b (HyperbolicTangent parameter)
has parameter: midpoint (HyperbolicTangent parameter)
has parameter: sigma (HyperbolicTangent parameter)

KuramotoCoupling
type: NamedIndividual
type: Coupling
has parameter: N (KuramotoCoupling parameter)
has parameter: a (KuramotoCoupling parameter)

Linear
type: NamedIndividual
type: Coupling
has parameter: a (Linear parameter)
has parameter: b (Linear parameter)

PreSigmoidal
type: NamedIndividual
type: Coupling
has parameter: G (PreSigmoidal parameter)
has parameter: H (PreSigmoidal parameter)
has parameter: P (PreSigmoidal parameter)
has parameter: Q (PreSigmoidal parameter)
has parameter: theta (PreSigmoidal parameter)

Scaling
type: NamedIndividual
type: Coupling
has parameter: a (Scaling parameter)

Sigmoidal
type: NamedIndividual
type: Coupling
has parameter: a (Sigmoidal parameter)
has parameter: cmax (Sigmoidal parameter)
has parameter: cmin (Sigmoidal parameter)
has parameter: midpoint (Sigmoidal parameter)
has parameter: sigma (Sigmoidal parameter)

SigmoidalJansenRit
type: NamedIndividual
type: Coupling
has parameter: a (SigmoidalJansenRit parameter)
has parameter: cmax (SigmoidalJansenRit parameter)
has parameter: cmin (SigmoidalJansenRit parameter)
has parameter: midpoint (SigmoidalJansenRit parameter)
has parameter: r (SigmoidalJansenRit parameter)

a (Difference parameter)
type: NamedIndividual
type: Parameter
default value: 0.1
notation: a

G (FastLinearCoupling parameter)
type: NamedIndividual
type: Parameter
description: Global coupling strength scaling long-range connections
default value: 0.1
notation: G

b (FastLinearCoupling parameter)
type: NamedIndividual
type: Parameter
description: Offset/bias added to coupling signal
default value: 0.0
notation: b

a (HyperbolicTangent parameter)
type: NamedIndividual
type: Parameter
description: Minimum of the sigmoid function
default value: 1.0
notation: a

b (HyperbolicTangent parameter)
type: NamedIndividual
type: Parameter
description: Scaling factor for the variable
default value: 1.0
notation: b

midpoint (HyperbolicTangent parameter)
type: NamedIndividual
type: Parameter
description: Midpoint of the linear portion of the sigmoid
default value: 0.0
notation: midpoint

sigma (HyperbolicTangent parameter)
type: NamedIndividual
type: Parameter
description: Standard deviation of the coupling
default value: 1.0
notation: sigma

N (KuramotoCoupling parameter)
type: NamedIndividual
type: Parameter
description: Number of nodes, i.e., size of network.
default value: 1.0
notation: N

a (KuramotoCoupling parameter)
type: NamedIndividual
type: Parameter
description: Rescales the connection strength.
default value: 1.0
notation: a

a (Linear parameter)
type: NamedIndividual
type: Parameter
description: Linear scaling factor of the coupled (delayed) input.
default value: 0.00390625
notation: a

b (Linear parameter)
type: NamedIndividual
type: Parameter
description: Shifts the base of the connection strength while maintaining the absolute difference between different values.
default value: 0.0
notation: b

G (PreSigmoidal parameter)
type: NamedIndividual
type: Parameter
description: Gain
default value: 60.0
notation: G

H (PreSigmoidal parameter)
type: NamedIndividual
type: Parameter
description: Global Factor
default value: 0.5
notation: H

P (PreSigmoidal parameter)
type: NamedIndividual
type: Parameter
description: Excitation-Inhibition ratio
default value: 1.0
notation: P

Q (PreSigmoidal parameter)
type: NamedIndividual
type: Parameter
description: Average
default value: 1.0
notation: Q

theta (PreSigmoidal parameter)
type: NamedIndividual
type: Parameter
description: Threshold
default value: 0.5
notation: theta

a (Scaling parameter)
type: NamedIndividual
type: Parameter
description: Linear scaling factor of the coupled (delayed) input.
default value: 0.00390625
notation: a

a (Sigmoidal parameter)
type: NamedIndividual
type: Parameter
description: Scaling of sigmoidal
default value: 1.0
notation: a

cmax (Sigmoidal parameter)
type: NamedIndividual
type: Parameter
description: Maximum of the sigmoid function
default value: 1.0
notation: cmax

cmin (Sigmoidal parameter)
type: NamedIndividual
type: Parameter
description: Minimum of sigmoid function
default value: -1.0
notation: cmin

midpoint (Sigmoidal parameter)
type: NamedIndividual
type: Parameter
default value: 0.0
notation: midpoint

sigma (Sigmoidal parameter)
type: NamedIndividual
type: Parameter
default value: 230.0
notation: sigma

a (SigmoidalJansenRit parameter)
type: NamedIndividual
type: Parameter
description: Scaling of the coupling term
default value: 1.0
notation: a

cmax (SigmoidalJansenRit parameter)
type: NamedIndividual
type: Parameter
description: Maximum of the Sigmoid function
default value: 0.005
notation: cmax

cmin (SigmoidalJansenRit parameter)
type: NamedIndividual
type: Parameter
description: minimum of the Sigmoid function
default value: 0.0
notation: cmin

midpoint (SigmoidalJansenRit parameter)
type: NamedIndividual
type: Parameter
description: Midpoint of the linear portion of the sigmoid
default value: 6.0
notation: midpoint

r (SigmoidalJansenRit parameter)
type: NamedIndividual
type: Parameter
description: The steepness of the sigmoidal transformation
default value: 0.56
notation: r

EI Tuning: Functional Connectivity Fitting
type: NamedIndividual
type: SimulationExperiment
description: 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.

JR Peak Frequency Optimization
type: NamedIndividual
type: SimulationExperiment
description: 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).

RWW Functional Connectivity Fitting
type: NamedIndividual
type: SimulationExperiment
description: Fitting functional connectivity using the Reduced Wong-Wang model. Two-stage optimization: global parameters first, then regional heterogeneity. Based on tvboptim RWW.qmd tutorial.

RateML rwongwang ground truth
type: NamedIndividual
type: SimulationExperiment

Multiscale BNM: Decision-Making with E/I Balance Tuning
type: NamedIndividual
type: SimulationExperiment
description: 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).

Dopri5
type: NamedIndividual
type: Integrator

Dopri853
type: NamedIndividual
type: Integrator

Euler
type: NamedIndividual
type: Integrator

Heun
type: NamedIndividual
type: Integrator

Identity
type: NamedIndividual
type: Integrator

RungeKutta4thOrder
type: NamedIndividual
type: Integrator

VODE
type: NamedIndividual
type: Integrator

SmileyNetwork
type: NamedIndividual
type: Network
has parameter: conduction_speed (SmileyNetwork parameter)

acq-EEGBrainstorm65_sensors
type: NamedIndividual
type: Network
description: 65-channel EEG sensor array (Brainstorm default). Positions in mm, Brainstorm coordinate space.
alternative label: EEG Brainstorm 65
has parameter: conduction_speed (acq-EEGBrainstorm65_sensors parameter)

acq-MEGBrainstorm276_sensors
type: NamedIndividual
type: Network
description: 276-channel MEG sensor array (Brainstorm default). Positions and orientations in mm.
alternative label: MEG Brainstorm 276
has parameter: conduction_speed (acq-MEGBrainstorm276_sensors parameter)

acq-SEEG588_sensors
type: NamedIndividual
type: Network
description: 588-contact stereo-EEG array (TVB default). Intracranial depth electrodes. No precomputed projection — gain is computed analytically.
alternative label: SEEG 588 contacts
has parameter: conduction_speed (acq-SEEG588_sensors parameter)

example_3node_network
type: NamedIndividual
type: Network
description: Example network with 3 nodes and two different coupling types (excitatory and inhibitory)
alternative label: Simple 3-Node Network Example
has parameter: G (example_3node_network parameter)
has parameter: conduction_speed (example_3node_network parameter)

sensors_eeg_standard1005_fsaverage_aparc_projection
type: NamedIndividual
type: Network
description: MNE standard_1005 EEG sensors (MNI, mm) with fsaverage aparc projection gain matrix (sensors x regions).
alternative label: EEG standard_1005 fsaverage projection
has parameter: conduction_speed (sensors_eeg_standard1005_fsaverage_aparc_projection parameter)

tpl-FSLMNI152_cohort-HCPYA_rec-Hansen2022_atlas-Schaefer2018_seg-7Networks_scale-100_desc-SCFC_relmat
type: NamedIndividual
type: Network
description: 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.
alternative label: Schaefer2018_100_7Networks_Hansen2022_SCFC
has parameter: conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-Hansen2022_atlas-Schaefer2018_seg-7Networks_scale-100_desc-SCFC_relmat parameter)

tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_scale-1000_desc-SC_relmat
type: NamedIndividual
type: Network
alternative label: Schaefer1000 (dTOR)
has parameter: conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_scale-1000_desc-SC_relmat parameter)

tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-1000_desc-SC_relmat
type: NamedIndividual
type: Network
alternative label: Schaefer2018_1000_17Networks_dTOR
has parameter: conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-1000_desc-SC_relmat parameter)

tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-100_desc-SC_relmat
type: NamedIndividual
type: Network
alternative label: Schaefer2018_100_17Networks_dTOR
has parameter: conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-100_desc-SC_relmat parameter)

tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-200_desc-SC_relmat
type: NamedIndividual
type: Network
alternative label: Schaefer2018_200_17Networks_dTOR
has parameter: conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-200_desc-SC_relmat parameter)

tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-300_desc-SC_relmat
type: NamedIndividual
type: Network
alternative label: Schaefer2018_300_17Networks_dTOR
has parameter: conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-300_desc-SC_relmat parameter)

tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-400_desc-SC_relmat
type: NamedIndividual
type: Network
alternative label: Schaefer2018_400_17Networks_dTOR
has parameter: conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-400_desc-SC_relmat parameter)

tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-500_desc-SC_relmat
type: NamedIndividual
type: Network
alternative label: Schaefer2018_500_17Networks_dTOR
has parameter: conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-500_desc-SC_relmat parameter)

tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-600_desc-SC_relmat
type: NamedIndividual
type: Network
alternative label: Schaefer2018_600_17Networks_dTOR
has parameter: conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-600_desc-SC_relmat parameter)

tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-700_desc-SC_relmat
type: NamedIndividual
type: Network
alternative label: Schaefer2018_700_17Networks_dTOR
has parameter: conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-700_desc-SC_relmat parameter)

tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-800_desc-SC_relmat
type: NamedIndividual
type: Network
alternative label: Schaefer2018_800_17Networks_dTOR
has parameter: conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-800_desc-SC_relmat parameter)

tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-900_desc-SC_relmat
type: NamedIndividual
type: Network
alternative label: Schaefer2018_900_17Networks_dTOR
has parameter: conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-900_desc-SC_relmat parameter)

tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-1000_desc-SC_relmat
type: NamedIndividual
type: Network
alternative label: Schaefer2018_1000_7Networks_dTOR
has parameter: conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-1000_desc-SC_relmat parameter)

tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-100_desc-SC_relmat
type: NamedIndividual
type: Network
alternative label: Schaefer2018_100_7Networks_dTOR
has parameter: conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-100_desc-SC_relmat parameter)

tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-200_desc-SC_relmat
type: NamedIndividual
type: Network
alternative label: Schaefer2018_200_7Networks_dTOR
has parameter: conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-200_desc-SC_relmat parameter)

tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-300_desc-SC_relmat
type: NamedIndividual
type: Network
alternative label: Schaefer2018_300_7Networks_dTOR
has parameter: conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-300_desc-SC_relmat parameter)

tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-400_desc-SC_relmat
type: NamedIndividual
type: Network
alternative label: Schaefer2018_400_7Networks_dTOR
has parameter: conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-400_desc-SC_relmat parameter)

tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-500_desc-SC_relmat
type: NamedIndividual
type: Network
alternative label: Schaefer2018_500_7Networks_dTOR
has parameter: conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-500_desc-SC_relmat parameter)

tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-600_desc-SC_relmat
type: NamedIndividual
type: Network
alternative label: Schaefer2018_600_7Networks_dTOR
has parameter: conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-600_desc-SC_relmat parameter)

tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-700_desc-SC_relmat
type: NamedIndividual
type: Network
alternative label: Schaefer2018_700_7Networks_dTOR
has parameter: conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-700_desc-SC_relmat parameter)

tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-800_desc-SC_relmat
type: NamedIndividual
type: Network
alternative label: Schaefer2018_800_7Networks_dTOR
has parameter: conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-800_desc-SC_relmat parameter)

tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-900_desc-SC_relmat
type: NamedIndividual
type: Network
alternative label: Schaefer2018_900_7Networks_dTOR
has parameter: conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-900_desc-SC_relmat parameter)

tpl-FSLMNI152_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-Schaefer2018_scale-1000_desc-SC_relmat
type: NamedIndividual
type: Network
alternative label: Schaefer1000 (MghUscHcp32)
has parameter: conduction_speed (tpl-FSLMNI152_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-Schaefer2018_scale-1000_desc-SC_relmat parameter)

tpl-FSLMNI152_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-Schaefer2018_seg-17Networks_scale-1000_desc-SC_relmat
type: NamedIndividual
type: Network
alternative label: Schaefer100017Networks (MghUscHcp32)
has parameter: conduction_speed (tpl-FSLMNI152_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-Schaefer2018_seg-17Networks_scale-1000_desc-SC_relmat parameter)

tpl-FSLMNI152_cohort-PPMI85_rec-PPMI85_atlas-Schaefer2018_scale-1000_desc-SC_relmat
type: NamedIndividual
type: Network
alternative label: Schaefer1000 (PPMI85)
has parameter: conduction_speed (tpl-FSLMNI152_cohort-PPMI85_rec-PPMI85_atlas-Schaefer2018_scale-1000_desc-SC_relmat parameter)

tpl-FSLMNI152_cohort-PPMI85_rec-PPMI85_atlas-Schaefer2018_seg-17Networks_scale-1000_desc-SC_relmat
type: NamedIndividual
type: Network
alternative label: Schaefer100017Networks (PPMI85)
has parameter: conduction_speed (tpl-FSLMNI152_cohort-PPMI85_rec-PPMI85_atlas-Schaefer2018_seg-17Networks_scale-1000_desc-SC_relmat parameter)

https://w3id.org/tvbo/networks/tpl-MNI152NLin2009bAsym_cohort-HCPYA_rec-dTOR_atlas-HCPMMP1_desc-SC_relmat
type: NamedIndividual
type: Network
alternative label: hcpmmp1 (dTOR)
has parameter: conduction_speed (tpl-MNI152NLin2009bAsym_cohort-HCPYA_rec-dTOR_atlas-HCPMMP1_desc-SC_relmat parameter)

https://w3id.org/tvbo/networks/tpl-MNI152NLin2009bAsym_cohort-HCPYA_rec-dTOR_atlas-HCPMMP1_seg-ordered_desc-SC_relmat
type: NamedIndividual
type: Network
alternative label: hcpmmp1ordered (dTOR)
has parameter: conduction_speed (tpl-MNI152NLin2009bAsym_cohort-HCPYA_rec-dTOR_atlas-HCPMMP1_seg-ordered_desc-SC_relmat parameter)

https://w3id.org/tvbo/networks/tpl-MNI152NLin2009bAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-HCPMMP1_desc-SC_relmat
type: NamedIndividual
type: Network
alternative label: hcpmmp1 (MghUscHcp32)
has parameter: conduction_speed (tpl-MNI152NLin2009bAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-HCPMMP1_desc-SC_relmat parameter)

https://w3id.org/tvbo/networks/tpl-MNI152NLin2009bAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-HCPMMP1_seg-ordered_desc-SC_relmat
type: NamedIndividual
type: Network
alternative label: hcpmmp1ordered (MghUscHcp32)
has parameter: conduction_speed (tpl-MNI152NLin2009bAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-HCPMMP1_seg-ordered_desc-SC_relmat parameter)

https://w3id.org/tvbo/networks/tpl-MNI152NLin2009bAsym_cohort-PPMI85_rec-PPMI85_atlas-HCPMMP1_desc-SC_relmat
type: NamedIndividual
type: Network
alternative label: hcpmmp1 (PPMI85)
has parameter: conduction_speed (tpl-MNI152NLin2009bAsym_cohort-PPMI85_rec-PPMI85_atlas-HCPMMP1_desc-SC_relmat parameter)

https://w3id.org/tvbo/networks/tpl-MNI152NLin2009bAsym_cohort-PPMI85_rec-PPMI85_atlas-HCPMMP1_seg-ordered_desc-SC_relmat
type: NamedIndividual
type: Network
alternative label: hcpmmp1ordered (PPMI85)
has parameter: conduction_speed (tpl-MNI152NLin2009bAsym_cohort-PPMI85_rec-PPMI85_atlas-HCPMMP1_seg-ordered_desc-SC_relmat parameter)

https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-HCPYA_atlas-Lobar8_desc-surf_relmat
type: NamedIndividual
type: Network
alternative label: Lobar8 surface (fsaverage 164k, 327684 vertices)
has parameter: conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_atlas-Lobar8_desc-surf_relmat parameter)

https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-HCPYA_atlas-Lobar8_hemi-L_desc-surf_relmat
type: NamedIndividual
type: Network
alternative label: Lobar8 LH surface (fsaverage 164k, 163842 vertices)
has parameter: conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_atlas-Lobar8_hemi-L_desc-surf_relmat parameter)

https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-HCPYA_atlas-Lobar8_hemi-R_desc-surf_relmat
type: NamedIndividual
type: Network
alternative label: Lobar8 RH surface (fsaverage 164k, 163842 vertices)
has parameter: conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_atlas-Lobar8_hemi-R_desc-surf_relmat parameter)

https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-DesikanKilliany_desc-SC_relmat
type: NamedIndividual
type: Network
alternative label: DesikanKilliany (dTOR)
has parameter: conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-DesikanKilliany_desc-SC_relmat parameter)

https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Destrieux_desc-SC_relmat
type: NamedIndividual
type: Network
alternative label: Destrieux (dTOR)
has parameter: conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Destrieux_desc-SC_relmat parameter)

https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-HCPex_desc-SC_relmat
type: NamedIndividual
type: Network
alternative label: HCPex (dTOR)
has parameter: conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-HCPex_desc-SC_relmat parameter)

https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Lobar8_desc-SCFC_relmat
type: NamedIndividual
type: Network
alternative label: Lobar8 (dTOR)
has parameter: conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Lobar8_desc-SCFC_relmat parameter)

https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Lobar_desc-SC_relmat
type: NamedIndividual
type: Network
alternative label: Lobar (dTOR)
has parameter: conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Lobar_desc-SC_relmat parameter)

https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Lobar_desc-surf_relmat
type: NamedIndividual
type: Network
alternative label: Lobar surface (fsLR 32k, 64984 vertices)
has parameter: conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Lobar_desc-surf_relmat parameter)

https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Yeo17_desc-SC_relmat
type: NamedIndividual
type: Network
alternative label: Yeo17 (dTOR)
has parameter: conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Yeo17_desc-SC_relmat parameter)

https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-virtualdbs_desc-SC_relmat
type: NamedIndividual
type: Network
alternative label: virtualdbs (dTOR)
has parameter: conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-virtualdbs_desc-SC_relmat parameter)

https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-DesikanKilliany_desc-SC_relmat
type: NamedIndividual
type: Network
alternative label: DesikanKilliany (MghUscHcp32)
has parameter: conduction_speed (tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-DesikanKilliany_desc-SC_relmat parameter)

https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-Destrieux_desc-SC_relmat
type: NamedIndividual
type: Network
alternative label: Destrieux (MghUscHcp32)
has parameter: conduction_speed (tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-Destrieux_desc-SC_relmat parameter)

https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-HOCPA_desc-SC_relmat
type: NamedIndividual
type: Network
alternative label: HOCPA (MghUscHcp32)
has parameter: conduction_speed (tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-HOCPA_desc-SC_relmat parameter)

https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-Yeo17_desc-SC_relmat
type: NamedIndividual
type: Network
alternative label: Yeo17 (MghUscHcp32)
has parameter: conduction_speed (tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-Yeo17_desc-SC_relmat parameter)

https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-virtualdbs_desc-SC_relmat
type: NamedIndividual
type: Network
alternative label: virtualdbs (MghUscHcp32)
has parameter: conduction_speed (tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-virtualdbs_desc-SC_relmat parameter)

https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-PPMI85_rec-PPMI85_atlas-DesikanKilliany_desc-SC_relmat
type: NamedIndividual
type: Network
alternative label: DesikanKilliany (PPMI85)
has parameter: conduction_speed (tpl-MNI152NLin2009cAsym_cohort-PPMI85_rec-PPMI85_atlas-DesikanKilliany_desc-SC_relmat parameter)

https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-PPMI85_rec-PPMI85_atlas-Destrieux_desc-SC_relmat
type: NamedIndividual
type: Network
alternative label: Destrieux (PPMI85)
has parameter: conduction_speed (tpl-MNI152NLin2009cAsym_cohort-PPMI85_rec-PPMI85_atlas-Destrieux_desc-SC_relmat parameter)

https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-PPMI85_rec-PPMI85_atlas-Yeo17_desc-SC_relmat
type: NamedIndividual
type: Network
alternative label: Yeo17 (PPMI85)
has parameter: conduction_speed (tpl-MNI152NLin2009cAsym_cohort-PPMI85_rec-PPMI85_atlas-Yeo17_desc-SC_relmat parameter)

https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_cohort-PPMI85_rec-PPMI85_atlas-virtualdbs_desc-SC_relmat
type: NamedIndividual
type: Network
alternative label: virtualdbs (PPMI85)
has parameter: conduction_speed (tpl-MNI152NLin2009cAsym_cohort-PPMI85_rec-PPMI85_atlas-virtualdbs_desc-SC_relmat parameter)

https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_rec-avgMatrix_atlas-DesikanKilliany_desc-SCFC_relmat
type: NamedIndividual
type: Network
alternative label: DesikanKilliany (avgMatrix SC+FC)
has parameter: conduction_speed (tpl-MNI152NLin2009cAsym_rec-avgMatrix_atlas-DesikanKilliany_desc-SCFC_relmat parameter)

https://w3id.org/tvbo/networks/tpl-MNI152NLin2009cAsym_rec-avgMatrix_atlas-Lobar8_desc-SCFC_relmat
type: NamedIndividual
type: Network
alternative label: Lobar8 (avgMatrix)
has parameter: conduction_speed (tpl-MNI152NLin2009cAsym_rec-avgMatrix_atlas-Lobar8_desc-SCFC_relmat parameter)

tpl-fsaverage_acq-EEGstandard1005_atlas-DesikanKilliany_desc-projection_sensors
type: NamedIndividual
type: Network
description: MNE standard_1005 EEG sensors (MNI, mm) with fsaverage aparc projection gain matrix (sensors x regions).
alternative label: EEG standard_1005 fsaverage projection
has parameter: conduction_speed (tpl-fsaverage_acq-EEGstandard1005_atlas-DesikanKilliany_desc-projection_sensors parameter)

conduction_speed (SmileyNetwork parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (acq-EEGBrainstorm65_sensors parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (acq-MEGBrainstorm276_sensors parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (acq-SEEG588_sensors parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

G (example_3node_network parameter)
type: NamedIndividual
type: Parameter
default value: 1.0
notation: G

conduction_speed (example_3node_network parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (sensors_eeg_standard1005_fsaverage_aparc_projection parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-Hansen2022_atlas-Schaefer2018_seg-7Networks_scale-100_desc-SCFC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_scale-1000_desc-SC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-1000_desc-SC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-100_desc-SC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-200_desc-SC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-300_desc-SC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-400_desc-SC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-500_desc-SC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-600_desc-SC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-700_desc-SC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-800_desc-SC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-17Networks_scale-900_desc-SC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-1000_desc-SC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-100_desc-SC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-200_desc-SC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-300_desc-SC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-400_desc-SC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-500_desc-SC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-600_desc-SC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-700_desc-SC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-800_desc-SC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-FSLMNI152_cohort-HCPYA_rec-dTOR_atlas-Schaefer2018_seg-7Networks_scale-900_desc-SC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-FSLMNI152_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-Schaefer2018_scale-1000_desc-SC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-FSLMNI152_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-Schaefer2018_seg-17Networks_scale-1000_desc-SC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-FSLMNI152_cohort-PPMI85_rec-PPMI85_atlas-Schaefer2018_scale-1000_desc-SC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-FSLMNI152_cohort-PPMI85_rec-PPMI85_atlas-Schaefer2018_seg-17Networks_scale-1000_desc-SC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-MNI152NLin2009bAsym_cohort-HCPYA_rec-dTOR_atlas-HCPMMP1_desc-SC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-MNI152NLin2009bAsym_cohort-HCPYA_rec-dTOR_atlas-HCPMMP1_seg-ordered_desc-SC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-MNI152NLin2009bAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-HCPMMP1_desc-SC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-MNI152NLin2009bAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-HCPMMP1_seg-ordered_desc-SC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-MNI152NLin2009bAsym_cohort-PPMI85_rec-PPMI85_atlas-HCPMMP1_desc-SC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-MNI152NLin2009bAsym_cohort-PPMI85_rec-PPMI85_atlas-HCPMMP1_seg-ordered_desc-SC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_atlas-Lobar8_desc-surf_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_atlas-Lobar8_hemi-L_desc-surf_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_atlas-Lobar8_hemi-R_desc-surf_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-DesikanKilliany_desc-SC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Destrieux_desc-SC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-HCPex_desc-SC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Lobar8_desc-SCFC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Lobar_desc-SC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Lobar_desc-surf_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-Yeo17_desc-SC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-MNI152NLin2009cAsym_cohort-HCPYA_rec-dTOR_atlas-virtualdbs_desc-SC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-DesikanKilliany_desc-SC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-Destrieux_desc-SC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-HOCPA_desc-SC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-Yeo17_desc-SC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-MNI152NLin2009cAsym_cohort-MghUscHcp32_rec-MghUscHcp32_atlas-virtualdbs_desc-SC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-MNI152NLin2009cAsym_cohort-PPMI85_rec-PPMI85_atlas-DesikanKilliany_desc-SC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-MNI152NLin2009cAsym_cohort-PPMI85_rec-PPMI85_atlas-Destrieux_desc-SC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-MNI152NLin2009cAsym_cohort-PPMI85_rec-PPMI85_atlas-Yeo17_desc-SC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-MNI152NLin2009cAsym_cohort-PPMI85_rec-PPMI85_atlas-virtualdbs_desc-SC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-MNI152NLin2009cAsym_rec-avgMatrix_atlas-DesikanKilliany_desc-SCFC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-MNI152NLin2009cAsym_rec-avgMatrix_atlas-Lobar8_desc-SCFC_relmat parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

conduction_speed (tpl-fsaverage_acq-EEGstandard1005_atlas-DesikanKilliany_desc-projection_sensors parameter)
type: NamedIndividual
type: Parameter
default value: 3.0
notation: conduction_speed
unit (slot): mm_per_ms

FunctionalConnectivity
type: NamedIndividual
type: Observation
description: 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: TR (FC parameter)
has parameter: fisher_z (FC parameter)

AfferentCoupling
type: NamedIndividual
type: Observation
description: 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.

AfferentCouplingTemporalAverage
type: NamedIndividual
type: Observation
description: Temporally averaged afferent coupling input at each node. Combines coupling input recording with temporal averaging.

BOLD_DoubleExponential
type: NamedIndividual
type: Observation
description: BOLD fMRI observation model using a Double Exponential hemodynamic response function.
has parameter: TR (bold_double_exponential parameter)

BOLD_Gamma
type: NamedIndividual
type: Observation
description: BOLD fMRI observation model using a Gamma-shaped hemodynamic response function. Provides a simpler, unimodal HRF shape.
has parameter: TR (bold_gamma parameter)

BOLD_MixtureOfGammas
type: NamedIndividual
type: Observation
description: 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: TR (bold_mixture_of_gammas parameter)

BOLD_RegionROI
type: NamedIndividual
type: Observation
description: 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: hrf_length (bold_region_roi parameter)

BOLD_TVB
type: NamedIndividual
type: Observation
description: 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: TR (bold_tvb parameter)

EEG
type: NamedIndividual
type: Observation
description: 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: conductivity (eeg parameter)
has parameter: reference_electrode (eeg parameter)

GlobalAverage
type: NamedIndividual
type: Observation
description: Spatial mean across all network nodes at each sampling period. Reduces spatial dimension to a single global signal per state variable.

iEEG
type: NamedIndividual
type: Observation
description: 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: conductivity (ieeg parameter)

MEG
type: NamedIndividual
type: Observation
description: 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: permeability (meg parameter)

Raw
type: NamedIndividual
type: Observation
description: Records all state variables at every integration step without any transformation. Identity passthrough of the full simulation state.

SpatialAverage
type: NamedIndividual
type: Observation
description: 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: spatial_mask (spatial_average parameter)

SubSample
type: NamedIndividual
type: Observation
description: Temporal decimation of selected state variables. Records every N-th integration step without any averaging or smoothing.

TemporalAverage
type: NamedIndividual
type: Observation
description: Running temporal mean over a sliding window of configurable length. Returns one averaged sample per period.

TR (FC parameter)
type: NamedIndividual
type: Parameter
description: Repetition time
default value: 720.0
notation: TR
unit (slot): ms

fisher_z (FC parameter)
type: NamedIndividual
type: Parameter
description: Apply Fisher z-transformation to correlations
default value: true
notation: fisher_z

TR (bold_double_exponential parameter)
type: NamedIndividual
type: Parameter
default value: 2000.0
notation: TR
unit (slot): ms

TR (bold_gamma parameter)
type: NamedIndividual
type: Parameter
default value: 2000.0
notation: TR
unit (slot): ms

TR (bold_mixture_of_gammas parameter)
type: NamedIndividual
type: Parameter
default value: 2000.0
notation: TR
unit (slot): ms

hrf_length (bold_region_roi parameter)
type: NamedIndividual
type: Parameter
default value: 20000.0
notation: hrf_length
unit (slot): ms

TR (bold_tvb parameter)
type: NamedIndividual
type: Parameter
description: Repetition time (sampling period)
default value: 720.0
notation: TR
unit (slot): ms

conductivity (eeg parameter)
type: NamedIndividual
type: Parameter
description: Volume conductor conductivity for the single-sphere analytic approximation. Only used when no precomputed gain is available.
default value: 1.0
notation: conductivity
unit (slot): S_per_m

reference_electrode (eeg parameter)
type: NamedIndividual
type: Parameter
description: 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: reference_electrode

conductivity (ieeg parameter)
type: NamedIndividual
type: Parameter
description: Tissue conductivity for the analytic point-dipole approximation. Only used when no precomputed gain is available.
default value: 1.0
notation: conductivity
unit (slot): S_per_m

permeability (meg parameter)
type: NamedIndividual
type: Parameter
description: Magnetic constant (permeability of free space)
default value: 1.256637E-6
notation: permeability
unit (slot): H_per_m

spatial_mask (spatial_average parameter)
type: NamedIndividual
type: Parameter
description: Vector of length N_nodes mapping each node to a region index (0-indexed). Inferred from network topology if not provided.
notation: spatial_mask

AUTO-07p
type: NamedIndividual
type: Software package
description: A software package for continuation and bifurcation problems in ordinary differential equations. The standard tool for numerical continuation in dynamical systems since 1980.
license: BSD-2-Clause
code repository: https://github.com/auto-07p/auto-07p

Arbor
type: NamedIndividual
type: Software package
description: 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: BSD-2-Clause
code repository: https://github.com/arbor-sim/arbor

BSB
type: NamedIndividual
type: Software package
description: Brain Scaffold Builder — a framework for reconstructing and simulating data-driven brain tissue models using morphological and connectivity scaffolds.
license: Apache-2.0
code repository: https://github.com/dbbs-lab/bsb-core

BifurcationKit.jl
type: NamedIndividual
type: Software package
description: 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: MIT
code repository: https://github.com/bifurcationkit/BifurcationKit.jl

BluePyOpt
type: NamedIndividual
type: Software package
description: Blue Brain Python Optimisation Library — a framework for data-driven model parameter optimisation using multi-objective evolutionary algorithms on NEURON models.
license: LGPL-3.0-only
code repository: https://github.com/BlueBrain/BluePyOpt

BrainBrowser
type: NamedIndividual
type: Software package
description: A set of JavaScript visualization tools for rendering brain surfaces, volumes, and connectivity data in the browser using WebGL.
license: MIT
code repository: https://github.com/aces/brainbrowser

BrainPy
type: NamedIndividual
type: Software package
description: 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: Apache-2.0
code repository: https://github.com/brainpy/BrainPy

BrainSimII
type: NamedIndividual
type: Software package
description: A neural simulator exploring AGI-inspired approaches to brain simulation, with a focus on large-scale spiking neuron models and real-time interaction.
license: MIT
code repository: https://github.com/FutureAIGuru/BrainSimII

Brainstorm
type: NamedIndividual
type: Software package
description: A collaborative, open-source application for MEG/EEG/sEEG/ECoG/fNIRS data analysis, visualization, and source localization.
license: GPL-3.0-only
code repository: https://github.com/brainstorm-tools/brainstorm3

Brian2
type: NamedIndividual
type: Software package
description: A simulator for spiking neural networks. Equations are specified in standard mathematical notation, and Brian2 automatically generates efficient C++ code for numerical integration.
license: CeCILL-2.1
code repository: https://github.com/brian-team/brian2

CARLsim
type: NamedIndividual
type: Software package
description: An efficient, easy-to-use, GPU-accelerated library for simulating large-scale spiking neural network models with conductance-based synapses, STDP, and neuromodulation.
license: MIT
code repository: https://github.com/UCI-CARL/CARLsim6

CoreNEURON
type: NamedIndividual
type: Software package
description: Optimized compute engine for the NEURON simulator. Provides efficient execution of NEURON models on CPUs and GPUs using NMODL code generation.
license: BSD-3-Clause
code repository: https://github.com/BlueBrain/CoreNeuron

CxSystem2
type: NamedIndividual
type: Software package
description: A simulation framework for cortical microcircuit models with support for data-driven customization and modular circuit specification. Uses Brian2 as its simulation backend.
license: MIT
code repository: https://github.com/VisualNeuroscience-UH/CxSystem2

DifferentialEquations.jl
type: NamedIndividual
type: Software package
description: 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: MIT
code repository: https://github.com/SciML/DifferentialEquations.jl

EEGLAB
type: NamedIndividual
type: Software package
description: 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: BSD-2-Clause
code repository: https://github.com/sccn/eeglab

Elephant
type: NamedIndividual
type: Software package
description: Electrophysiology Analysis Toolkit — a Python library for the analysis of electrophysiological data, including spike-train statistics, spectral analysis, and unitary event analysis.
license: BSD-3-Clause
code repository: https://github.com/NeuralEnsemble/elephant

FastDMF
type: NamedIndividual
type: Software package
description: 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: MIT
code repository: https://github.com/Picardian14/FastDMF

FieldTrip
type: NamedIndividual
type: Software package
description: A MATLAB toolbox for MEG, EEG, iEEG and NIRS analysis, including preprocessing, source reconstruction, statistical testing, and connectivity analysis.
license: GPL-3.0-only
code repository: https://github.com/fieldtrip/fieldtrip

GENESIS
type: NamedIndividual
type: Software package
description: GEneral NEural SImulation System — one of the earliest simulators for biologically realistic modeling of neural systems, from sub-cellular components to large networks.
license: GPL-2.0-only
code repository: https://github.com/genesis-sim/genesis-2.4

GeNN
type: NamedIndividual
type: Software package
description: GPU Enhanced Neuronal Networks — a framework for GPU-accelerated spiking neural network simulations using NVIDIA CUDA. Generates optimized GPU kernels from model descriptions.
license: GPL-2.0-only
code repository: https://github.com/genn-team/genn

HNN-core
type: NamedIndividual
type: Software package
description: 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: BSD-3-Clause
code repository: https://github.com/jonescompneurolab/hnn-core

LEMS
type: NamedIndividual
type: Software package
description: 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: MIT
code repository: https://github.com/LEMS/jLEMS

LFPy
type: NamedIndividual
type: Software package
description: 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: GPL-3.0-only
code repository: https://github.com/LFPy/LFPy

MCell
type: NamedIndividual
type: Software package
description: Monte Carlo Cell — a program for realistic simulation of cellular signaling using spatially realistic 3D models of sub-cellular reaction-diffusion dynamics.
license: GPL-2.0-only
code repository: https://github.com/mcellteam/mcell

MNE-Python
type: NamedIndividual
type: Software package
description: Open-source Python package for exploring, visualizing, and analyzing human neurophysiological data: MEG, EEG, sEEG, ECoG, NIRS, and more.
license: BSD-3-Clause
code repository: https://github.com/mne-tools/mne-python

MOOSE
type: NamedIndividual
type: Software package
description: Multiscale Object-Oriented Simulation Environment. Supports models from sub-cellular signaling to large networks, including reaction-diffusion, electrical, and chemical compartmental models.
license: GPL-3.0-only
code repository: https://github.com/BhallaLab/moose-core

MatCont
type: NamedIndividual
type: Software package
description: A MATLAB continuation toolbox for interactive bifurcation analysis of dynamical systems. Computes equilibria, limit cycles, and bifurcation curves with graphical user interface.
license: GPL-3.0-only
code repository: https://sourceforge.net/projects/matcont/

ModelDB
type: NamedIndividual
type: Software package
description: A curated database of published computational neuroscience models. Provides source code and metadata for thousands of models linked to peer-reviewed publications.

NEST
type: NamedIndividual
type: Software package
description: 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: GPL-2.0-or-later
code repository: https://github.com/nest/nest-simulator

NEURON
type: NamedIndividual
type: Software package
description: 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: BSD-3-Clause
code repository: https://github.com/neuronsimulator/nrn

NWB
type: NamedIndividual
type: Software package
description: Neurodata Without Borders — a data standard for neurophysiology providing a common format for storing diverse cellular and systems neuroscience data in HDF5 files.
license: BSD-3-Clause
code repository: https://github.com/NeurodataWithoutBorders/pynwb

Nengo
type: NamedIndividual
type: Software package
description: 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: MIT
code repository: https://github.com/nengo/nengo

Neo
type: NamedIndividual
type: Software package
description: 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: BSD-3-Clause
code repository: https://github.com/NeuralEnsemble/python-neo

NetPyNE
type: NamedIndividual
type: Software package
description: 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: MIT
code repository: https://github.com/Neurosim-lab/netpyne

NetworkDynamics.jl
type: NamedIndividual
type: Software package
description: 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: MIT
code repository: https://github.com/PIK-ICoNe/NetworkDynamics.jl

NeuroML
type: NamedIndividual
type: Software package
description: 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: LGPL-3.0-only
code repository: https://github.com/NeuroML/NeuroML2

Neuroblox.jl
type: NamedIndividual
type: Software package
description: 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: MIT
code repository: https://github.com/Neuroblox/Neuroblox.jl

Neurofitter
type: NamedIndividual
type: Software package
description: A parameter optimization tool for neuroscience models. Uses evolutionary algorithms to fit model parameters to experimental electrophysiology data.
license: GPL-2.0-only
code repository: https://github.com/ModelDBRepository/64261

NineML
type: NamedIndividual
type: Software package
description: A language for describing the dynamics and connectivity of spiking neuronal network models. Designed by the INCF to enable simulator-independent model exchange.
license: BSD-2-Clause
code repository: https://github.com/INCF/nineml-spec

Open Source Brain
type: NamedIndividual
type: Software package
description: A platform for sharing and collaboratively developing computational neuroscience models in standardized formats, primarily NeuroML.
license: LGPL-3.0-only
code repository: https://github.com/OpenSourceBrain

OpenWorm
type: NamedIndividual
type: Software package
description: An open science project to build a comprehensive computational model of the C. elegans nematode, including its 302-neuron nervous system.
license: MIT
code repository: https://github.com/openworm/OpenWorm

PSICS
type: NamedIndividual
type: Software package
description: Parallel Stochastic Ion Channel Simulator — a fast simulator for stochastic ion channel models in morphologically detailed neurons using efficient population-based algorithms.
license: MPL-2.0
code repository: https://github.com/BorgwardtLab/PSICS

PyNN
type: NamedIndividual
type: Software package
description: 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: CeCILL-2.0
code repository: https://github.com/NeuralEnsemble/PyNN

PyRates
type: NamedIndividual
type: Software package
description: A Python framework for rate-based and neural mass network simulations. Provides symbolic equation parsing, automatic code generation, and parameter continuation support.
license: BSD-3-Clause
code repository: https://github.com/pyrates-neuroscience/PyRates

PyRhO
type: NamedIndividual
type: Software package
description: A Python module for fitting, simulating, and analyzing optogenetic rhodopsin photocurrent models. Integrates with NEURON and Brian2.
license: BSD-3-Clause
code repository: https://github.com/ProjectPyRhO/PyRhO

SONATA
type: NamedIndividual
type: Software package
description: 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: BSD-3-Clause
code repository: https://github.com/AllenInstitute/sonata

SPM
type: NamedIndividual
type: Software package
description: 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: GPL-2.0-or-later
code repository: https://github.com/spm/spm

STEPS
type: NamedIndividual
type: Software package
description: STochastic Engine for Pathway Simulation — a stochastic reaction-diffusion simulator for modeling biochemical signaling pathways in realistic 3D cellular morphologies.
license: GPL-3.0-only
code repository: https://github.com/CNS-OIST/STEPS

Snudda
type: NamedIndividual
type: Software package
description: 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: GPL-3.0-only
code repository: https://github.com/Hjorthmedansen/Snudda

SpikeInterface
type: NamedIndividual
type: Software package
description: A unified framework for spike sorting, providing a common interface to many spike sorting algorithms, preprocessing tools, and quality metrics.
license: MIT
code repository: https://github.com/SpikeInterface/spikeinterface

SpineCreator
type: NamedIndividual
type: Software package
description: A graphical tool for building neural network models using SpineML component-based descriptions, with export to multiple simulation engines.
license: GPL-3.0-only
code repository: https://github.com/SpineML/SpineCreator

SpineML
type: NamedIndividual
type: Software package
description: A declarative XML-based language for describing spiking neural network models using a component-based approach. Designed for simulator independence.
license: BSD-3-Clause
code repository: https://github.com/SpineML

TVB
type: NamedIndividual
type: Software package
description: The Virtual Brain — a neuroinformatics platform for full-brain network simulation using neural mass and mean-field models on individual connectome data.
license: GPL-3.0-or-later
code repository: https://github.com/the-virtual-brain/tvb-root

TVB-O
type: NamedIndividual
type: Software package
description: 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: EUPL-1.2
code repository: https://github.com/virtual-twin/tvbo

TVB-Optim
type: NamedIndividual
type: Software package
description: Differentiable whole-brain simulation and optimization framework using JAX. Supports gradient-based fitting of neural mass models to empirical neuroimaging data.
license: EUPL-1.2
code repository: https://github.com/virtual-twin/tvboptim

jNeuroML
type: NamedIndividual
type: Software package
description: Java-based toolchain for NeuroML/LEMS model validation, simulation, and export to multiple simulator backends including NEURON, NEST, and Brian2.
license: LGPL-3.0-only
code repository: https://github.com/NeuroML/jNeuroML

jaxley
type: NamedIndividual
type: Software package
description: 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: Apache-2.0
code repository: https://github.com/jaxleyverse/jaxley

neuroConstruct
type: NamedIndividual
type: Software package
description: A graphical tool for constructing and simulating biologically realistic 3D neuronal networks with morphologically detailed cells. Exports to NEURON, GENESIS, and NeuroML.
license: GPL-2.0-only
code repository: https://github.com/NeuralEnsemble/neuroConstruct

neurolib
type: NamedIndividual
type: Software package
description: A simulation framework for whole-brain neural mass models with built-in exploration, optimization, and fMRI/EEG forward-model support on empirical connectomes.
license: MIT
code repository: https://github.com/neurolib-dev/neurolib

pyNeuroML
type: NamedIndividual
type: Software package
description: Python API and command-line tools for NeuroML/LEMS model creation, validation, visualization, and simulation via jNeuroML and direct simulator backends.
license: LGPL-3.0-only
code repository: https://github.com/NeuroML/pyNeuroML

pynn_genn
type: NamedIndividual
type: Software package
description: PyNN interface for the GeNN GPU simulator, enabling PyNN models to run on NVIDIA GPUs via the GeNN backend.
license: GPL-2.0-only
code repository: https://github.com/genn-team/pynn_genn

sPyNNaker
type: NamedIndividual
type: Software package
description: 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: GPL-3.0-only
code repository: https://github.com/SpiNNakerManchester/sPyNNaker

Theoretical Neuroscience: Computational and Mathematical Modeling of Neural Systems
type: NamedIndividual
type: Book
issued: 2005
author: Abbott, L. F.
author: Dayan, Peter
publisher: MIT Press
label: Abbott2005

Ergodic Problems of Classical Mechanics
type: NamedIndividual
type: Book
issued: 1968
author: Arnol'd, V. I.
author: Avez, A.
publisher: W. A. Benjamin
label: Arnold1968

Ergodic Problems of Classical Mechanics
type: NamedIndividual
type: Book
issued: 1968
author: Arnol'd, V. I.
author: Avez, A.
publisher: W. A. Benjamin
label: Arnold1968a

K Ion Exchange model reference
type: NamedIndividual
type: Scholarly article
issued: 2021
author: Bandyopadhyay, S.
author: others
is part of: Preprint
label: Bandyopadhyay2021

Chaotic Dynamics in a Quartic Nuclear Collective Hamiltonian
type: NamedIndividual
type: Scholarly article
issued: 1998
author: Baran, V.
author: Raduta, A. A.
is part of: International Journal of Modern Physics E
pagination: 527--551
volume number: 7
label: Baran1998

A hyperchaotic attractor coined from chaotic L"u system
type: NamedIndividual
type: Scholarly article
issued: 2008
author: Bo-Cheng, B.
author: Zhong, L.
is part of: Chinese Physics Letters
issue number: 7
pagination: 2396
volume number: 25
label: Bo-Cheng2008

A hyperchaotic attractor coined from chaotic L"u system
type: NamedIndividual
type: Scholarly article
issued: 2008
author: Bo-Cheng, B.
author: Zhong, L.
is part of: Chinese Physics Letters
issue number: 7
pagination: 2396
volume number: 25
label: BoCheng2008

Next generation neural mass models
type: NamedIndividual
type: Scholarly article
issued: 2020
author: Byrne, A.
author: Coombes, S.
is part of: Journal of Mathematical Neuroscience
label: Byrne2020

Role of local network oscillations in resting-state functional connectivity
type: NamedIndividual
type: Scholarly article
issued: 2011
author: Cabral, Joana
author: others
is part of: NeuroImage
label: Cabral2011

A new finance chaotic attractor
type: NamedIndividual
type: Scholarly article
issued: 2007
author: Cai, G.
author: Huang, J.
is part of: International Journal of Nonlinear Science
issue number: 3
pagination: 213--220
volume number: 3
label: Cai2007

Reference for network mean-field neural mass model
type: NamedIndividual
type: Creative work
author: Cakan, C.
author: Obermayer, K.
label: Cakan

Bursting types and stable domains of Rulkov neuron network with mean field coupling
type: NamedIndividual
type: Scholarly article
issued: 2013
author: Cao, H.
author: Wu, Y.
is part of: International Journal of Bifurcation and Chaos
pagination: 1330041
volume number: 23
label: Cao2013

Generating hyperchaotic L"u attractor via state feedback control
type: NamedIndividual
type: Scholarly article
issued: 2006
author: Chen, A.
author: L"u, J.
author: Lu, J.
author: Yu, S.
is part of: Physica A: Statistical Mechanics and its Applications
pagination: 103--110
volume number: 364
label: Chen2006

Research concerning the theory of nonlinear resonance
type: NamedIndividual
type: Report
issued: 1969
author: Chirikov, Boris V.
issue number: Preprint 267
label: Chirikov1969

The Genesis of Chua's Circuit
type: NamedIndividual
type: Scholarly article
issued: 1992
author: Chua, Leon O.
is part of: Archiv f"ur Elektronik und "Ubertragungstechnik
pagination: 250--257
volume number: 46
label: Chua1992

Chua circuit
type: NamedIndividual
type: Scholarly article
issued: 2007
author: Chua, Leon O.
is part of: Scholarpedia
issue number: 10
pagination: 1488
volume number: 2
label: Chua2007

The brain resting state: dynamics and models
type: NamedIndividual
type: Scholarly article
issued: 2020
author: Courtiol, Julie
author: others
is part of: Journal of Neuroscience Methods
label: Courtiol2020

Abrupt Phase-Space Contraction in a Magnetotransport System
type: NamedIndividual
type: Scholarly article
issued: 2019
author: Datseris, George
author: et al.
is part of: New Journal of Physics
issue number: 5
pagination: 053036
volume number: 21
label: Datseris2019

Resting-State Functional Connectivity Emerges from Structurally and Dynamically Shaped Slow Linear Fluctuations
type: NamedIndividual
type: Scholarly article
issued: 2013
author: Corbetta, M.
author: Deco, G.
author: Hagmann, P.
author: Mantini, D.
author: Ponce-Alvarez, A.
author: Romani, G. L.
is part of: Journal of Neuroscience
issue number: 27
pagination: 11239--11252
publisher: Society for Neuroscience
volume number: 33
label: Deco2013

How local excitation--inhibition ratio impacts the whole brain dynamics
type: NamedIndividual
type: Scholarly article
issued: 2014
author: Deco, Gustavo
author: others
is part of: Journal of Neuroscience
label: Deco2014

The dynamics of resting fluctuations in the brain: metastability and its dynamical cortical core
type: NamedIndividual
type: Scholarly article
issued: 2017
author: Deco, Gustavo
author: Kringelbach, Morten L.
author: others
is part of: Scientific Reports
pagination: 3095
volume number: 7
label: Deco2017

K Ion Exchange model extensions
type: NamedIndividual
type: Scholarly article
issued: 2023
author: Depannemaecker, Damien
author: others
is part of: Preprint
label: Depannemaecker2023

Erzwungene Schwingungen bei ver"anderlicher Eigenfrequenz und ihre technische Bedeutung
type: NamedIndividual
type: Book
issued: 1918
author: Duffing, Georg
publisher: Vieweg+Teubner
label: Duffing1918

A reduced model of coupled neural masses with complex dynamics
type: NamedIndividual
type: Scholarly article
issued: 2019
author: Dumont, Gr\'egoire
author: Gutkin, Boris
is part of: eNeuro
label: Dumont2019

Nuclear Theory: Nuclear Models Collective and Single-Particle Phenomena
type: NamedIndividual
type: Book
issued: 1975
author: Eisenberg, Judah M.
author: Greiner, Walter
publisher: North-Holland
label: Eisenberg1975

Mathematical Foundations of Neuroscience
type: NamedIndividual
type: Book
issued: 2010
author: Ermentrout, G. Bard
author: Terman, David H.
publisher: Springer
label: Ermentrout2010

Quantitative Universality for a Class of Nonlinear Transformations
type: NamedIndividual
type: Scholarly article
issued: 1978
author: Feigenbaum, Mitchell J.
is part of: Journal of Statistical Physics
pagination: 25--52
volume number: 19
label: Feigenbaum1978

Impulses and physiological states in theoretical models of nerve membrane
type: NamedIndividual
type: Scholarly article
issued: 1961
author: FitzHugh, Richard
is part of: Biophysical Journal
label: FitzHugh1961

FitzHugh--Nagumo model
type: NamedIndividual
type: Creative work
label: FitzHughNagumo

Multistability, phase diagrams, and intransitivity in the Lorenz-84 low-order atmospheric circulation model
type: NamedIndividual
type: Scholarly article
issued: 2008
author: Freire, Jos\'e G.
author: others
is part of: Chaos
pagination: 033121
volume number: 18
label: Freire2008

Optimal time scale for spike-time reliability: theory, simulations, and experiments
type: NamedIndividual
type: Scholarly article
issued: 2008
author: Ermentrout, G. Bard
author: Gal\'an, R. F.
author: Urban, N. N.
is part of: Journal of Neurophysiology
label: Galan2008

A mean-field description of bursting dynamics in neural populations
type: NamedIndividual
type: Scholarly article
issued: 2020
author: Gast, Richard
author: Kn\"osche, T. R.
author: Schmidt, Helmut
is part of: PLOS Computational Biology
label: Gast2020

A New Deterministic Model of Chaotic Reversals
type: NamedIndividual
type: Scholarly article
issued: 2012
author: Gissinger, Christophe
is part of: The European Physical Journal B
issue number: 4
pagination: 137
volume number: 85
label: Gissinger2012

Final state sensitivity: An obstruction to predictability
type: NamedIndividual
type: Scholarly article
issued: 1983
author: Grebogi, Celso
author: McDonald, S. W.
author: Ott, Edward
author: Yorke, James A.
is part of: Physics Letters A
issue number: 9
pagination: 373--375
volume number: 99
label: Grebogi1983

A Method for Determining a Stochastic Transition
type: NamedIndividual
type: Scholarly article
issued: 1979
author: Greene, J. M.
is part of: Journal of Mathematical Physics
pagination: 1183--1201
volume number: 20
label: Greene1979

Nonlinear Oscillations, Dynamical Systems, and Bifurcations of Vector Fields
type: NamedIndividual
type: Book
issued: 1983
author: Guckenheimer, John
author: Holmes, Philip
publisher: Springer
volume number: 42
label: Guckenheimer1983

Nonlinear Oscillations, Dynamical Systems, and Bifurcations of Vector Fields
type: NamedIndividual
type: Book
issued: 1983
author: Guckenheimer, John
author: Holmes, Philip
publisher: Springer
volume number: 42
label: GuckenheimerHolmes1983

Alias for GuckenheimerHolmes1983
type: NamedIndividual
type: Scholarly article
label: GuckenheimerHolmes1983Alias

An algebraically simple chaotic system
type: NamedIndividual
type: Creative work
issued: 2000
author: Halvorsen, E.
label: Halvorsen2000

The Applicability of the Third Integral of Motion: Some Numerical Experiments
type: NamedIndividual
type: Scholarly article
issued: 1964
author: Heiles, Carl
author: Henon, Michel
is part of: The Astronomical Journal
pagination: 73--79
volume number: 69
label: Henon1964

A Two-Dimensional Mapping with a Strange Attractor
type: NamedIndividual
type: Scholarly article
issued: 1976
author: H\'enon, Michel
is part of: Communications in Mathematical Physics
pagination: 69--77
volume number: 50
label: Henon1976

The Applicability of the Third Integral of Motion: Some Numerical Experiments
type: NamedIndividual
type: Scholarly article
issued: 1964
author: H\'enon, Michel
author: Heiles, Carl
is part of: The Astronomical Journal
pagination: 73--79
volume number: 69
label: HenonHeiles1964

A model of neuronal bursting using three coupled first order differential equations
type: NamedIndividual
type: Scholarly article
issued: 1984
author: Hindmarsh, J. L.
author: Rose, R. M.
is part of: Proceedings of the Royal Society of London. Series B, Biological Sciences
pagination: 87--102
volume number: 221
label: Hindmarsh1984

A model of neuronal bursting using three coupled first order differential equations
type: NamedIndividual
type: Scholarly article
issued: 1984
author: Hindmarsh, J. L.
author: Rose, R. M.
is part of: Proceedings of the Royal Society of London. Series B, Biological Sciences
pagination: 87--102
volume number: 221
label: HindmarshRose1984

A Quantitative Description of Membrane Current and Its Application to Conduction and Excitation in Nerve
type: NamedIndividual
type: Scholarly article
issued: 1952
author: Hodgkin, A. L.
author: Huxley, A. F.
is part of: The Journal of Physiology
issue number: 4
pagination: 500--544
volume number: 117
label: Hodgkin1952

A Quantitative Description of Membrane Current and Its Application to Conduction and Excitation in Nerve
type: NamedIndividual
type: Scholarly article
issued: 1952
author: Hodgkin, A. L.
author: Huxley, A. F.
is part of: The Journal of Physiology
issue number: 4
pagination: 500--544
volume number: 117
label: HodgkinHuxley1952

Remark on ``Some Simple Chaotic Flows''
type: NamedIndividual
type: Scholarly article
issued: 1995
author: Hoover, William G.
is part of: Physical Review E
pagination: 759--760
volume number: 51
label: Hoover1995

Neural networks and physical systems with emergent collective computational abilities
type: NamedIndividual
type: Scholarly article
issued: 1982
author: Hopfield, John J.
is part of: Proceedings of the National Academy of Sciences
label: Hopfield1982

Neurons with graded response have collective computational properties like those of two-state neurons
type: NamedIndividual
type: Scholarly article
issued: 1984
author: Hopfield, John J.
is part of: Proceedings of the National Academy of Sciences
label: Hopfield1984

Predator-prey model
type: NamedIndividual
type: Scholarly article
issued: 2006
author: Hoppensteadt, Frank
is part of: Scholarpedia
issue number: 10
pagination: 1563
volume number: 1
label: Hoppensteadt2006

Fundamental Unpredictability in Multispecies Competition
type: NamedIndividual
type: Scholarly article
issued: 2001
author: Huisman, Johan
author: Weissing, Franz J.
is part of: The American Naturalist
issue number: 5
volume number: 157
label: Huisman2001

Construction of dynamical non-linear components based on Lorenz system and symmetric group of permutations
type: NamedIndividual
type: Scholarly article
issued: 2015
author: Gondal, M. A.
author: Hussain, A.
author: Hussain, I.
is part of: 3D Research
pagination: 1--6
volume number: 6
label: Hussain2015

Dynamical Systems in Neuroscience: The Geometry of Excitability and Bursting
type: NamedIndividual
type: Book
issued: 2007
author: Izhikevich, Eugene M.
publisher: MIT Press
label: IzhikevichBook

Electroencephalogram and visual evoked potential generation in a mathematical model of coupled cortical columns
type: NamedIndividual
type: Scholarly article
issued: 1993
author: Jansen, Ben H.
author: Rit, Vincent G.
is part of: Biological Cybernetics
label: Jansen1993

Parameter exploration of a realistic neural mass model of visual cortex
type: NamedIndividual
type: Scholarly article
issued: 1995
author: Jansen, Ben H.
author: Rit, Vincent G.
is part of: Biological Cybernetics
label: Jansen1995

On the nature of seizure dynamics
type: NamedIndividual
type: Scholarly article
issued: 2014
author: Jirsa, Viktor
author: others
is part of: Brain
label: Jirsa2014

Van der Pol Oscillator
type: NamedIndividual
type: Scholarly article
issued: 2007
author: Kanamaru, Takashi
is part of: Scholarpedia
issue number: 1
pagination: 2202
volume number: 2
label: Kanamaru2007

On a Robust Method to Detect Intermittency
type: NamedIndividual
type: Scholarly article
issued: 1988
author: Grassberger, Peter
author: Kantz, Holger
is part of: Journal of Physics A: Mathematical and General
pagination: 127--133
volume number: 21
label: KantzGrassberger1988

Self-entrainment of a Population of Coupled Nonlinear Oscillators
type: NamedIndividual
type: Scholarly article
issued: 1975
author: Kuramoto, Yoshiki
is part of: International Symposium on Mathematical Problems in Theoretical Physics
volume number: 39
label: Kuramoto1975

On the problem of turbulence
type: NamedIndividual
type: Scholarly article
issued: 1944
author: Landau, L. D.
is part of: Doklady Akademii Nauk SSSR
issue number: 8
pagination: 339--349
volume number: 44
label: Landau1944

Hyperchaos
type: NamedIndividual
type: Scholarly article
issued: 2007
author: Letellier, Christophe
author: R"ossler, Otto E.
is part of: Scholarpedia
issue number: 8
pagination: 1936
volume number: 2
label: Letellier2007

A novel four-wing strange attractor born in bistability
type: NamedIndividual
type: Scholarly article
issued: 2015
author: Li, Chunbiao
author: et al.
is part of: IEICE Electronics Express
issue number: 4
volume number: 12
label: Li2015

Deterministic Nonperiodic Flow
type: NamedIndividual
type: Scholarly article
issued: 1963
author: Lorenz, Edward N.
is part of: Journal of the Atmospheric Sciences
pagination: 130--141
volume number: 20
label: Lorenz1963

Predictability: A Problem Partly Solved
type: NamedIndividual
type: Scholarly article
issued: 1996
author: Lorenz, Edward N.
is part of: Proc. Seminar on Predictability
label: Lorenz1996

Intermittency, self-similarity and 1/f spectrum in dissipative dynamical systems
type: NamedIndividual
type: Scholarly article
issued: 1980
author: Manneville, Paul
is part of: Journal de Physique
issue number: 11
pagination: 1235--1243
volume number: 41
label: Manneville1980

Intermittency and the Lorenz Model
type: NamedIndividual
type: Scholarly article
issued: 1980
author: Manneville, P.
author: Pomeau, Y.
is part of: Communications in Mathematical Physics
volume number: 74
label: MannevillePomeau1980

Simple mathematical models with very complicated dynamics
type: NamedIndividual
type: Scholarly article
issued: 1976
author: May, Robert M.
is part of: Nature
pagination: 459--467
volume number: 261
label: May1976

Long-range correlations in intermittent maps
type: NamedIndividual
type: Scholarly article
issued: 2019
author: Meyer, R.
author: et al.
is part of: New Journal of Physics
volume number: 20
label: Meyer2019

Chaoticity Evolution in a Quartic Collective Hamiltonian
type: NamedIndividual
type: Scholarly article
issued: 2018
author: Baran, V.
author: Micluta-Campeanu, S.
author: Nicolin, A. I.
author: Raportaru, M. C.
is part of: Romanian Reports in Physics
pagination: 105
volume number: 70
label: Micluta-Campeanu2018

Chaoticity Evolution in a Quartic Collective Hamiltonian
type: NamedIndividual
type: Scholarly article
issued: 2018
author: Micluta-Campeanu, S.
author: Raduta, A.
author: others
is part of: Romanian Journal of Physics
pagination: 105
volume number: 70
label: MiclutaCampeanu2018

Dragon-king-like extreme events in coupled bursting neurons
type: NamedIndividual
type: Scholarly article
issued: 2018
author: Dana, S. K.
author: Kapitaniak, T.
author: Mishra, A.
author: Pal, P.
author: Saha, S.
author: Vigneshwaran, M.
is part of: Physical Review E
issue number: 6
pagination: 062311
volume number: 97
label: Mirshra2018

Dragon-king-like extreme events in coupled bursting neurons
type: NamedIndividual
type: Scholarly article
issued: 2018
author: Dana, S. K.
author: Kapitaniak, T.
author: Mishra, A.
author: Pal, P.
author: Saha, S.
author: Vigneshwaran, M.
is part of: Physical Review E
issue number: 6
pagination: 062311
volume number: 97
label: Mishra2018

Dragon-king-like extreme events in coupled bursting neurons
type: NamedIndividual
type: Scholarly article
issued: 2018
author: Dana, S. K.
author: Kapitaniak, T.
author: Mishra, A.
author: Pal, P.
author: Saha, S.
author: Vigneshwaran, M.
is part of: Physical Review E
issue number: 6
pagination: 062311
volume number: 97
label: Mishra2018a

Macroscopic description for networks of spiking neurons
type: NamedIndividual
type: Scholarly article
issued: 2015
author: Montbri\'o, Ernest
author: Paz\'o, Diego
author: Roxin, Alex
is part of: Physical Review X
label: Montbrio2015

Voltage oscillations in the barnacle giant muscle fiber
type: NamedIndividual
type: Scholarly article
issued: 1981
author: Lecar, H.
author: Morris, C.
is part of: Biophysical Journal
label: MorrisLecar1981

An active pulse transmission line simulating nerve axon
type: NamedIndividual
type: Scholarly article
issued: 1962
author: Arimoto, S.
author: Nagumo, J.
author: Yoshizawa, S.
is part of: Proceedings of the IRE
label: Nagumo1962

Chaos in Dynamical Systems
type: NamedIndividual
type: Book
issued: 2010
author: Ott, Edward
publisher: Cambridge University Press
label: Ott2002

Chaos in Dynamical Systems
type: NamedIndividual
type: Book
issued: 2010
author: Ott, Edward
publisher: Cambridge University Press
label: Ott2010

The transition to chaotic attractors with riddled basins
type: NamedIndividual
type: Creative work
author: Alexander, J. C.
author: Kan, I.
author: Ott, Edward
author: Sommerer, J. C.
author: Yorke, James A.
label: OttRiddled2014

A new hyperchaotic system from the L"u system and its control
type: NamedIndividual
type: Scholarly article
issued: 2011
author: Liu, Y.
author: Pang, S.
is part of: Journal of Computational and Applied Mathematics
issue number: 8
pagination: 2775--2789
volume number: 235
label: Pang2011

A neural mass model of seizure initiation and propagation
type: NamedIndividual
type: Scholarly article
issued: 2014
author: Proix, Timoth\'ee
author: others
is part of: Brain
label: Proix2014

Individual structural connectivity defines propagation networks in partial epilepsy
type: NamedIndividual
type: Scholarly article
issued: 2017
author: Proix, Timoth\'ee
author: others
is part of: Brain
label: Proix2017

On a new hyperchaotic system
type: NamedIndividual
type: Scholarly article
issued: 2008
author: Chen, G.
author: Qi, G.
author: van Wyk, B. J.
author: van Wyk, M. A.
is part of: Physics Letters A
issue number: 2
pagination: 124--136
volume number: 372
label: Qi2008

An Equation for Continuous Chaos
type: NamedIndividual
type: Scholarly article
issued: 1976
author: R"ossler, Otto E.
is part of: Physics Letters A
issue number: 5
pagination: 397--398
volume number: 57
label: R_ossler1976

Oscillations of a System of Disks
type: NamedIndividual
type: Scholarly article
issued: 1958
author: Rikitake, Tsuneji
is part of: Proceedings of the Cambridge Philosophical Society
pagination: 89--105
volume number: 54
label: Rikitake1958

An Equation for Continuous Chaos
type: NamedIndividual
type: Scholarly article
issued: 1976
author: Roessler, Otto E.
is part of: Physics Letters A
issue number: 5
pagination: 397--398
volume number: 57
label: Roessler1976

An equation for hyperchaos
type: NamedIndividual
type: Scholarly article
issued: 1979
author: R"ossler, Otto E.
is part of: Physics Letters A
issue number: 2--3
pagination: 155--157
volume number: 71
label: Roessler1979

Alias for Rossler1979
type: NamedIndividual
type: Scholarly article
label: Roessler1979Alias

An Equation for Continuous Chaos
type: NamedIndividual
type: Scholarly article
issued: 1976
author: R"ossler, Otto E.
is part of: Physics Letters A
issue number: 5
pagination: 397--398
volume number: 57
label: Rossler1976

An equation for hyperchaos
type: NamedIndividual
type: Scholarly article
issued: 1979
author: R"ossler, O. E.
is part of: Physics Letters A
issue number: 2--3
pagination: 155--157
volume number: 71
label: Rossler1979

Strange Attractors
type: NamedIndividual
type: Scholarly article
issued: 1980
author: Ruelle, David
is part of: The Mathematical Intelligencer
issue number: 3
pagination: 126--137
volume number: 2
label: Ruelle1980

Regularization of Synchronized Chaotic Bursts
type: NamedIndividual
type: Scholarly article
issued: 2001
author: Abarbanel, Henry D. I.
author: Rulkov, Nikolai F.
author: Sushchik, M. M.
author: Tsimring, L. S.
is part of: Physical Review Letters
pagination: 183
volume number: 86
label: Rulkov2001

Modeling of spiking-bursting neural behavior using two-dimensional map
type: NamedIndividual
type: Scholarly article
issued: 2002
author: Rulkov, Nikolai F.
is part of: Physical Review E
pagination: 041922
volume number: 65
label: Rulkov2002

Chaotic Modelling and Simulation: Analysis of Chaotic Models, Attractors and Forms
type: NamedIndividual
type: Book
issued: 2008
author: Skiadas, Christos H.
publisher: CRC Press
label: Skiadas2008

Elegant Chaos: Algebraically Simple Chaotic Flows
type: NamedIndividual
type: Book
issued: 2010
author: Sprott, J. C.
publisher: World Scientific
label: Sprott2010

Simplest Chaotic Flows with Involutional Symmetries
type: NamedIndividual
type: Scholarly article
issued: 2014
author: Sprott, J. C.
is part of: International Journal of Bifurcation and Chaos
pagination: 1450009
volume number: 24
label: Sprott2014

Physics Letters A
type: NamedIndividual
type: Scholarly article
issued: 2014
author: Sprott, J. C.
is part of: Physics Letters A
volume number: 378
label: Sprott2014b

Do We Need More Chaos Examples?
type: NamedIndividual
type: Scholarly article
issued: 2020
author: Sprott, J. C.
is part of: Chaos Theory and Applications
issue number: 2
pagination: 1--3
volume number: 2
label: Sprott2020

Classifying and quantifying basins of attraction
type: NamedIndividual
type: Scholarly article
issued: 2015
author: Sprott, J. C.
author: Xiong, A.
is part of: Chaos: An Interdisciplinary Journal of Nonlinear Science
issue number: 8
pagination: 083101
volume number: 25
label: SprottXiong2015

Hyperchaotic dynamics in a R"ossler-like system
type: NamedIndividual
type: Creative work
issued: 2012
author: Stankevich, N. V.
label: Stankevich2012

Thermohaline convection with two stable regimes of flow
type: NamedIndividual
type: Scholarly article
issued: 1961
author: Stommel, Henry
is part of: Tellus
issue number: 2
volume number: 13
label: Stommel1961

From Kuramoto to Crawford: exploring the onset of synchronization in populations of coupled oscillators
type: NamedIndividual
type: Scholarly article
issued: 2000
author: Strogatz, Steven H.
is part of: Physica D
label: Strogatz2000

Nonlinear Dynamics and Chaos: With Applications to Physics, Biology, Chemistry, and Engineering
type: NamedIndividual
type: Book
issued: 2015
author: Strogatz, Steven H.
publisher: Westview Press
label: Strogatz2015

Deterministic chaos seen in terms of feedback circuits: Analysis, synthesis, \& biological applications
type: NamedIndividual
type: Scholarly article
issued: 1999
author: Thomas, Ren\'e
is part of: International Journal of Bifurcation and Chaos
issue number: 10
pagination: 1889--1905
volume number: 9
label: Thomas1999

Swinging Atwood's Machine
type: NamedIndividual
type: Scholarly article
issued: 1984
author: Abbott, Tyler A.
author: Griffiths, David J.
author: Tufillaro, Nicholas B.
is part of: American Journal of Physics
issue number: 10
pagination: 895--903
volume number: 52
label: Tufillaro1984

An Experimental Approach to Nonlinear Dynamics and Chaos
type: NamedIndividual
type: Book
issued: 1992
author: Abbott, Tyler
author: Reilly, James
author: Tufillaro, Nicholas B.
publisher: Addison-Wesley
label: Tufillaro1992

Randomly Transitional Phenomena in the System Governed by Duffing's Equation
type: NamedIndividual
type: Scholarly article
issued: 1961
author: Ueda, Yoshisuke
is part of: Journal of Statistical Physics
label: Ueda1961

Ulam coupled map on a ring
type: NamedIndividual
type: Creative work
issued: 1960
author: Ulam, Stanislaw
label: Ulam1960s

Biophysical ingredients for a robust model of cortical dynamics
type: NamedIndividual
type: Scholarly article
issued: 2019
author: di Volo, Matteo
author: others
is part of: PLOS Computational Biology
label: Volo2019

Alias for di Volo et al. 2019
type: NamedIndividual
type: Scholarly article
label: Volo2019a

A hyperchaos generated from Lorenz system
type: NamedIndividual
type: Scholarly article
issued: 2008
author: Wang, M.
author: Wang, X.
is part of: Physica A: Statistical Mechanics and its Applications
issue number: 14
pagination: 3751--3758
volume number: 387
label: Wang2008

A 3-D four-wing attractor and its analysis
type: NamedIndividual
type: Scholarly article
issued: 2009
author: Qi, G.
author: Sun, Y.
author: Wang, Z.
author: van Wyk, B. J.
author: van Wyk, M. A.
is part of: Brazilian Journal of Physics
pagination: 547--553
volume number: 39
label: Wang2009

Lotka-Volterra Equations
type: NamedIndividual
type: Creative work
author: Weisstein, Eric W.
label: Weisstein

Excitatory and inhibitory interactions in localized populations of model neurons
type: NamedIndividual
type: Scholarly article
issued: 1972
author: Cowan, Jack D.
author: Wilson, Hugh R.
is part of: Biophysical Journal
label: Wilson1972

A mathematical theory of the functional dynamics of cortical and thalamic nervous tissue
type: NamedIndividual
type: Scholarly article
issued: 1973
author: Cowan, Jack D.
author: Wilson, Hugh R.
is part of: Biological Cybernetics
label: Wilson1973

A Recurrent Network Mechanism of Time Integration in Perceptual Decisions
type: NamedIndividual
type: Scholarly article
issued: 2006
author: Wang, Xiao-Jing
author: Wong, Kong-Fatt
is part of: The Journal of Neuroscience
issue number: 4
pagination: 1314--1328
publisher: Society for Neuroscience
volume number: 26
label: Wong2006

The simplest case of a strange attractor
type: NamedIndividual
type: Scholarly article
issued: 1978
author: Chernikov, A. A.
author: Sagdeev, R. Z.
author: Usikov, D. A.
author: Zaslavskii, G. M.
is part of: Physics Letters A
issue number: 3
pagination: 145--147
volume number: 69
label: Zaslavskii1978

A mean-field model of conductance-based networks of adaptive exponential integrate-and-fire neurons
type: NamedIndividual
type: Scholarly article
issued: 2018
author: Destexhe, Alain
author: Zerlaut, Yann
is part of: Neural Computation
label: Zerlaut2018

A model for the interrelationship between EEG and evoked potentials
type: NamedIndividual
type: Scholarly article
issued: 1978
author: Jansen, B. H.
author: Zetterberg, L. H.
is part of: Biological Cybernetics
label: Zetterberg1978

On relaxation-oscillations
type: NamedIndividual
type: Scholarly article
issued: 1926
author: van der Pol, B.
is part of: The London, Edinburgh, and Dublin Philosophical Magazine and Journal of Science
issue number: 11
pagination: 978--992
volume number: 2
label: vanderpol1926

Chapter

Thesis

Restriction
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Restriction
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Restriction
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