classDiagram
class Dynamics
click Dynamics href "./Dynamics.html"
Dynamics : autonomous
Dynamics --> "0..1" Boolean : autonomous
click Boolean href "../http://www.w3.org/2001/XMLSchema#boolean.html"
Dynamics : compile
Dynamics --> "0..1" Boolean : compile
click Boolean href "../http://www.w3.org/2001/XMLSchema#boolean.html"
Dynamics : coupling_inputs
Dynamics --> "*" CouplingInput : coupling_inputs
click CouplingInput href "./CouplingInput.html"
Dynamics : coupling_terms
Dynamics --> "*" Parameter : coupling_terms
click Parameter href "./Parameter.html"
Dynamics : cse
Dynamics --> "0..1" Boolean : cse
click Boolean href "../http://www.w3.org/2001/XMLSchema#boolean.html"
Dynamics : dataLocation
Dynamics --> "0..1" String : dataLocation
click String href "../http://www.w3.org/2001/XMLSchema#string.html"
Dynamics : derived_from_model
Dynamics --> "0..1" Dynamics : derived_from_model
click Dynamics href "./Dynamics.html"
Dynamics : derived_parameters
Dynamics --> "*" DerivedParameter : derived_parameters
click DerivedParameter href "./DerivedParameter.html"
Dynamics : derived_variables
Dynamics --> "*" DerivedVariable : derived_variables
click DerivedVariable href "./DerivedVariable.html"
Dynamics : description
Dynamics --> "0..1" String : description
click String href "../http://www.w3.org/2001/XMLSchema#string.html"
Dynamics : events
Dynamics --> "*" Event : events
click Event href "./Event.html"
Dynamics : functions
Dynamics --> "*" Function : functions
click Function href "./Function.html"
Dynamics : has_reference
Dynamics --> "0..1" String : has_reference
click String href "../http://www.w3.org/2001/XMLSchema#string.html"
Dynamics : iri
Dynamics --> "0..1" Uriorcurie : iri
click Uriorcurie href "../http://www.w3.org/2001/XMLSchema#anyURI.html"
Dynamics : label
Dynamics --> "0..1" String : label
click String href "../http://www.w3.org/2001/XMLSchema#string.html"
Dynamics : local_coupling_term
Dynamics --> "0..1" Parameter : local_coupling_term
click Parameter href "./Parameter.html"
Dynamics : model_type
Dynamics --> "0..1" ModelType : model_type
click ModelType href "../../enums/ModelType.html"
Dynamics : modes
Dynamics --> "*" Dynamics : modes
click Dynamics href "./Dynamics.html"
Dynamics : modified
Dynamics --> "0..1" Boolean : modified
click Boolean href "../http://www.w3.org/2001/XMLSchema#boolean.html"
Dynamics : name
Dynamics --> "1" String : name
click String href "../http://www.w3.org/2001/XMLSchema#string.html"
Dynamics : number_of_modes
Dynamics --> "0..1" Integer : number_of_modes
click Integer href "../http://www.w3.org/2001/XMLSchema#integer.html"
Dynamics : observed
Dynamics --> "*" DerivedVariable : observed
click DerivedVariable href "./DerivedVariable.html"
Dynamics : output
Dynamics --> "*" String : output
click String href "../http://www.w3.org/2001/XMLSchema#string.html"
Dynamics : parameters
Dynamics --> "*" Parameter : parameters
click Parameter href "./Parameter.html"
Dynamics : references
Dynamics --> "*" String : references
click String href "../http://www.w3.org/2001/XMLSchema#string.html"
Dynamics : source
Dynamics --> "0..1" String : source
click String href "../http://www.w3.org/2001/XMLSchema#string.html"
Dynamics : state_variables
Dynamics --> "*" StateVariable : state_variables
click StateVariable href "./StateVariable.html"
Dynamics : stimulus
Dynamics --> "0..1" Stimulus : stimulus
click Stimulus href "./Stimulus.html"
Dynamics : system_type
Dynamics --> "0..1" SystemType : system_type
click SystemType href "../../enums/SystemType.html"
Class: Dynamics
URI: tvbo:Dynamics
Class Properties
| Property | Value |
|---|---|
| Class URI | tvbo:Dynamics |
Slots
| Name | Cardinality and Range | Description | Inheritance |
|---|---|---|---|
| has_reference | 0..1 xsd:string |
direct | |
| name | 1 xsd:string |
Globally unique identifier for the entity | direct |
| label | 0..1 xsd:string |
direct | |
| iri | 0..1 xsd:anyURI |
Optional stable IRI (or compact URI) for this entity in an external ontology … | direct |
| parameters | * Parameter |
direct | |
| description | 0..1 xsd:string |
direct | |
| source | 0..1 xsd:string |
direct | |
| references | * xsd:string |
direct | |
| dataLocation | 0..1 xsd:string |
Add the location of the data file containing the parcellation terminology | direct |
| derived_parameters | * DerivedParameter |
direct | |
| derived_variables | * DerivedVariable |
direct | |
| coupling_terms | * Parameter |
direct | |
| coupling_inputs | * CouplingInput |
direct | |
| state_variables | * StateVariable |
direct | |
| modified | 0..1 xsd:boolean |
direct | |
| output | * xsd:string |
Output variable names to include in simulation results | direct |
| derived_from_model | 0..1 Dynamics |
direct | |
| number_of_modes | 0..1 xsd:integer |
direct | |
| local_coupling_term | 0..1 Parameter |
direct | |
| functions | * Function |
direct | |
| stimulus | 0..1 Stimulus |
direct | |
| modes | * Dynamics |
direct | |
| model_type | 0..1 ModelType |
Coarse classification of this model (mean_field, neural_mass, phase_oscillato… | direct |
| system_type | 0..1 SystemType |
direct | |
| autonomous | 0..1 xsd:boolean |
Whether the system is autonomous (equations do not depend explicitly on time … | direct |
| observed | * DerivedVariable |
Observable functions computed from states, inputs, and parameters after simul… | direct |
| events | * Event |
Discrete state transitions intrinsic to the dynamical system, such as thresho… | direct |
| cse | 0..1 xsd:boolean |
Code-generation hint (opt-in, backend-independent): eliminate common subexpre… | direct |
| compile | 0..1 xsd:boolean |
Code-generation hint (opt-in, backend-independent): request that the generate… | direct |
Usages
| used by | used in | type | used |
|---|---|---|---|
| Network | dynamics | range | Dynamics |
| Node | dynamics | range | Dynamics |
| Edge | dynamics | range | Dynamics |
| Dynamics | derived_from_model | range | Dynamics |
| Dynamics | modes | range | Dynamics |
| Continuation | dynamics | range | Dynamics |
| SimulationExperiment | model | range | Dynamics |
| SimulationExperiment | dynamics | range | Dynamics |
| SimulationStudy | model | range | Dynamics |
Aliases
- NeuralMassModel
Identifier and Mapping Information
Schema Source
- from schema: https://w3id.org/tvbo
Mappings
| Mapping Type | Mapped Value |
|---|---|
| self | tvbo:Dynamics |
| native | tvbo:Dynamics |
LinkML Source
Direct
name: Dynamics
comments:
- Successor class replacing deprecated NeuralMassModel.
from_schema: https://w3id.org/tvbo
aliases:
- NeuralMassModel
slots:
- has_reference
- name
- label
- iri
- parameters
- description
- source
- references
- dataLocation
slot_usage:
name:
name: name
ifabsent: Dynamics
system_type:
name: system_type
ifabsent: continuous
attributes:
derived_parameters:
name: derived_parameters
from_schema: https://w3id.org/tvbo
rank: 1000
domain_of:
- Dynamics
- PDE
range: DerivedParameter
multivalued: true
inlined: true
derived_variables:
name: derived_variables
from_schema: https://w3id.org/tvbo
rank: 1000
domain_of:
- Dynamics
- PDE
range: DerivedVariable
multivalued: true
inlined: true
coupling_terms:
name: coupling_terms
from_schema: https://w3id.org/tvbo
rank: 1000
domain_of:
- Dynamics
range: Parameter
multivalued: true
inlined: true
coupling_inputs:
name: coupling_inputs
from_schema: https://w3id.org/tvbo
rank: 1000
domain_of:
- Dynamics
range: CouplingInput
multivalued: true
inlined: true
state_variables:
name: state_variables
from_schema: https://w3id.org/tvbo
rank: 1000
domain_of:
- Dynamics
- PDE
range: StateVariable
multivalued: true
inlined: true
modified:
name: modified
from_schema: https://w3id.org/tvbo
rank: 1000
domain_of:
- Dynamics
range: boolean
output:
name: output
description: Output variable names to include in simulation results. References
to state_variables or derived_variables by name.
deprecated: 'Use ''record: true'' on the derived variable (or ''record'' on the
state variable) instead. The ''output'' list is retained for backward compatibility.'
from_schema: https://w3id.org/tvbo
domain_of:
- Procedure
- Dynamics
- Function
- FunctionCall
range: string
multivalued: true
derived_from_model:
name: derived_from_model
from_schema: https://w3id.org/tvbo
rank: 1000
domain_of:
- Dynamics
range: Dynamics
number_of_modes:
name: number_of_modes
from_schema: https://w3id.org/tvbo
rank: 1000
ifabsent: integer(1)
domain_of:
- Dynamics
range: integer
local_coupling_term:
name: local_coupling_term
from_schema: https://w3id.org/tvbo
rank: 1000
domain_of:
- Dynamics
range: Parameter
functions:
name: functions
from_schema: https://w3id.org/tvbo
rank: 1000
domain_of:
- Dynamics
- Algorithm
- SimulationExperiment
- PDE
range: Function
multivalued: true
inlined: true
stimulus:
name: stimulus
from_schema: https://w3id.org/tvbo
rank: 1000
domain_of:
- Dynamics
range: Stimulus
inlined: true
modes:
name: modes
from_schema: https://w3id.org/tvbo
aliases:
- components
rank: 1000
domain_of:
- Dynamics
range: Dynamics
multivalued: true
inlined: true
model_type:
name: model_type
description: Coarse classification of this model (mean_field, neural_mass, phase_oscillator,
phenomenological, spiking, generic, field). Used for filtering in Dynamics.list_db(model_type=...).
from_schema: https://w3id.org/tvbo
rank: 1000
domain_of:
- Dynamics
range: ModelType
system_type:
name: system_type
from_schema: https://w3id.org/tvbo
rank: 1000
domain_of:
- Dynamics
range: SystemType
autonomous:
name: autonomous
description: 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).
from_schema: https://w3id.org/tvbo
rank: 1000
ifabsent: 'true'
domain_of:
- Dynamics
range: boolean
observed:
name: observed
description: 'Observable functions computed from states, inputs, and parameters
after simulation. Unlike derived_variables (which are intermediate algebraic
expressions used within the ODE), observed variables are post-hoc quantities
recoverable from the solution. Maps to obsf/obssym in ND.jl EdgeModel/VertexModel.
Example: absolute force magnitude computed from force components.'
from_schema: https://w3id.org/tvbo
rank: 1000
domain_of:
- Dynamics
- Coupling
range: DerivedVariable
multivalued: true
inlined: true
events:
name: events
description: Discrete state transitions intrinsic to the dynamical system, such
as threshold-triggered resets in spiking neuron models. Unlike experiment-level
events (stimulation, perturbation), these define the model's own discontinuous
behavior.
from_schema: https://w3id.org/tvbo
domain_of:
- Node
- Edge
- Dynamics
- SimulationExperiment
range: Event
multivalued: true
inlined: true
cse:
name: cse
description: 'Code-generation hint (opt-in, backend-independent): eliminate common
subexpressions. When true, the generator evaluates each repeated subexpression
— including repeated calls to model-defined functions — once and reuses the
result instead of re-emitting it at every occurrence. Purely a performance hint:
results are numerically identical. A backend whose compiler already performs
this elimination may honour it as a no-op. Off by default (expressions are emitted
in flat form).'
from_schema: https://w3id.org/tvbo
rank: 1000
ifabsent: 'False'
domain_of:
- Dynamics
range: boolean
compile:
name: compile
description: 'Code-generation hint (opt-in, backend-independent): request that
the generated dynamics be compiled to machine code rather than interpreted,
where the target backend supports it. Purely a performance hint with no effect
on results; a backend that is inherently compiled (or cannot compile) honours
it as a no-op. Off by default. Independent of, and composable with, ``cse``.'
from_schema: https://w3id.org/tvbo
rank: 1000
ifabsent: 'False'
domain_of:
- Dynamics
range: boolean
class_uri: tvbo:DynamicsInduced
name: Dynamics
comments:
- Successor class replacing deprecated NeuralMassModel.
from_schema: https://w3id.org/tvbo
aliases:
- NeuralMassModel
slot_usage:
name:
name: name
ifabsent: Dynamics
system_type:
name: system_type
ifabsent: continuous
attributes:
derived_parameters:
name: derived_parameters
from_schema: https://w3id.org/tvbo
rank: 1000
owner: Dynamics
domain_of:
- Dynamics
- PDE
range: DerivedParameter
multivalued: true
inlined: true
derived_variables:
name: derived_variables
from_schema: https://w3id.org/tvbo
rank: 1000
owner: Dynamics
domain_of:
- Dynamics
- PDE
range: DerivedVariable
multivalued: true
inlined: true
coupling_terms:
name: coupling_terms
from_schema: https://w3id.org/tvbo
rank: 1000
owner: Dynamics
domain_of:
- Dynamics
range: Parameter
multivalued: true
inlined: true
coupling_inputs:
name: coupling_inputs
from_schema: https://w3id.org/tvbo
rank: 1000
owner: Dynamics
domain_of:
- Dynamics
range: CouplingInput
multivalued: true
inlined: true
state_variables:
name: state_variables
from_schema: https://w3id.org/tvbo
rank: 1000
owner: Dynamics
domain_of:
- Dynamics
- PDE
range: StateVariable
multivalued: true
inlined: true
modified:
name: modified
from_schema: https://w3id.org/tvbo
rank: 1000
owner: Dynamics
domain_of:
- Dynamics
range: boolean
output:
name: output
description: Output variable names to include in simulation results. References
to state_variables or derived_variables by name.
deprecated: 'Use ''record: true'' on the derived variable (or ''record'' on the
state variable) instead. The ''output'' list is retained for backward compatibility.'
from_schema: https://w3id.org/tvbo
owner: Dynamics
domain_of:
- Procedure
- Dynamics
- Function
- FunctionCall
range: string
multivalued: true
derived_from_model:
name: derived_from_model
from_schema: https://w3id.org/tvbo
rank: 1000
owner: Dynamics
domain_of:
- Dynamics
range: Dynamics
number_of_modes:
name: number_of_modes
from_schema: https://w3id.org/tvbo
rank: 1000
ifabsent: integer(1)
owner: Dynamics
domain_of:
- Dynamics
range: integer
local_coupling_term:
name: local_coupling_term
from_schema: https://w3id.org/tvbo
rank: 1000
owner: Dynamics
domain_of:
- Dynamics
range: Parameter
functions:
name: functions
from_schema: https://w3id.org/tvbo
rank: 1000
owner: Dynamics
domain_of:
- Dynamics
- Algorithm
- SimulationExperiment
- PDE
range: Function
multivalued: true
inlined: true
stimulus:
name: stimulus
from_schema: https://w3id.org/tvbo
rank: 1000
owner: Dynamics
domain_of:
- Dynamics
range: Stimulus
inlined: true
modes:
name: modes
from_schema: https://w3id.org/tvbo
aliases:
- components
rank: 1000
owner: Dynamics
domain_of:
- Dynamics
range: Dynamics
multivalued: true
inlined: true
model_type:
name: model_type
description: Coarse classification of this model (mean_field, neural_mass, phase_oscillator,
phenomenological, spiking, generic, field). Used for filtering in Dynamics.list_db(model_type=...).
from_schema: https://w3id.org/tvbo
rank: 1000
owner: Dynamics
domain_of:
- Dynamics
range: ModelType
system_type:
name: system_type
from_schema: https://w3id.org/tvbo
rank: 1000
ifabsent: continuous
owner: Dynamics
domain_of:
- Dynamics
range: SystemType
autonomous:
name: autonomous
description: 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).
from_schema: https://w3id.org/tvbo
rank: 1000
ifabsent: 'true'
owner: Dynamics
domain_of:
- Dynamics
range: boolean
observed:
name: observed
description: 'Observable functions computed from states, inputs, and parameters
after simulation. Unlike derived_variables (which are intermediate algebraic
expressions used within the ODE), observed variables are post-hoc quantities
recoverable from the solution. Maps to obsf/obssym in ND.jl EdgeModel/VertexModel.
Example: absolute force magnitude computed from force components.'
from_schema: https://w3id.org/tvbo
rank: 1000
owner: Dynamics
domain_of:
- Dynamics
- Coupling
range: DerivedVariable
multivalued: true
inlined: true
events:
name: events
description: Discrete state transitions intrinsic to the dynamical system, such
as threshold-triggered resets in spiking neuron models. Unlike experiment-level
events (stimulation, perturbation), these define the model's own discontinuous
behavior.
from_schema: https://w3id.org/tvbo
owner: Dynamics
domain_of:
- Node
- Edge
- Dynamics
- SimulationExperiment
range: Event
multivalued: true
inlined: true
cse:
name: cse
description: 'Code-generation hint (opt-in, backend-independent): eliminate common
subexpressions. When true, the generator evaluates each repeated subexpression
— including repeated calls to model-defined functions — once and reuses the
result instead of re-emitting it at every occurrence. Purely a performance hint:
results are numerically identical. A backend whose compiler already performs
this elimination may honour it as a no-op. Off by default (expressions are emitted
in flat form).'
from_schema: https://w3id.org/tvbo
rank: 1000
ifabsent: 'False'
owner: Dynamics
domain_of:
- Dynamics
range: boolean
compile:
name: compile
description: 'Code-generation hint (opt-in, backend-independent): request that
the generated dynamics be compiled to machine code rather than interpreted,
where the target backend supports it. Purely a performance hint with no effect
on results; a backend that is inherently compiled (or cannot compile) honours
it as a no-op. Off by default. Independent of, and composable with, ``cse``.'
from_schema: https://w3id.org/tvbo
rank: 1000
ifabsent: 'False'
owner: Dynamics
domain_of:
- Dynamics
range: boolean
has_reference:
name: has_reference
from_schema: https://w3id.org/tvbo
rank: 1000
slot_uri: dcterms:references
owner: Dynamics
domain_of:
- Dynamics
range: string
name:
name: name
description: Globally unique identifier for the entity.
from_schema: https://w3id.org/tvbo/common
slot_uri: schema:name
ifabsent: Dynamics
identifier: true
owner: Dynamics
domain_of:
- BrainAtlas
- CommonCoordinateSpace
- ParcellationEntity
- DBSProtocol
- ClinicalScale
- ClinicalScore
- SoftwarePackage
- SoftwareRequirement
- SoftwareEnvironment
- Event
- Tractogram
- MeasureSpec
- NamedArray
- GraphGenerator
- Binding
- ProcedureStep
- File
- StateValue
- Observation
- Dynamics
- StateVariable
- Distribution
- Parameter
- CouplingInput
- Argument
- Function
- FunctionCall
- Callable
- DerivedParameter
- DerivedVariable
- DataSource
- OptimizationStage
- Exploration
- Inference
- Prior
- Likelihood
- UpdateRule
- Algorithm
- Option
- BranchSwitch
- Continuation
- Coupling
range: string
required: true
label:
name: label
from_schema: https://w3id.org/tvbo
rank: 1000
slot_uri: rdfs:label
owner: Dynamics
domain_of:
- ParcellationTerminology
- Subject
- Session
- Dataset
- Contact
- SoftwareEnvironment
- Equation
- Stimulus
- Event
- Parcellation
- Tractogram
- Matrix
- Phenotype
- Network
- Node
- Edge
- Observation
- Dynamics
- StateVariable
- Parameter
- Function
- FunctionCall
- DerivedVariable
- RandomStream
- DataSource
- OptimizationStage
- Exploration
- ExplorationAxis
- FreeParameter
- Inference
- AlgorithmStage
- TuningObjective
- Continuation
- Coupling
- RegionMapping
- SimulationExperiment
- SimulationStudy
- TimeSeries
- NDArray
- SpatialDomain
- Mesh
- SpatialField
- FieldStateVariable
- DifferentialOperator
- BoundaryCondition
- PDESolver
- PDE
range: string
iri:
name: iri
description: 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).
from_schema: https://w3id.org/tvbo
rank: 1000
slot_uri: dcterms:identifier
owner: Dynamics
domain_of:
- Parcellation
- Tractogram
- ReferenceFingerprint
- GraphGenerator
- Reference
- Dynamics
- Function
- Coupling
range: uriorcurie
parameters:
name: parameters
from_schema: https://w3id.org/tvbo
rank: 1000
owner: Dynamics
domain_of:
- Equation
- Stimulus
- Event
- TemporalApplicableEquation
- Network
- GraphGenerator
- Node
- Edge
- Observation
- Analysis
- Dynamics
- Distribution
- Noise
- Exploration
- Discretization
- BranchSwitch
- Integrator
- Coupling
- PDE
range: Parameter
multivalued: true
inlined: true
description:
name: description
from_schema: https://w3id.org/tvbo
rank: 1000
slot_uri: dcterms:description
owner: Dynamics
domain_of:
- Dataset
- ClinicalScore
- SoftwarePackage
- SoftwareRequirement
- SoftwareEnvironment
- Equation
- Stimulus
- Event
- Tractogram
- Matrix
- Phenotype
- MeasureSpec
- NamedArray
- Network
- GraphGenerator
- ProcedureStep
- File
- Node
- Edge
- Observation
- Dynamics
- StateVariable
- Parameter
- CouplingInput
- Argument
- Function
- FunctionCall
- Callable
- DerivedParameter
- DerivedVariable
- RandomStream
- DataSource
- OptimizationStage
- Exploration
- ExplorationAxis
- FreeParameter
- Inference
- Prior
- Likelihood
- UpdateRule
- AlgorithmStage
- TuningObjective
- Algorithm
- BranchSwitch
- Continuation
- Integrator
- Coupling
- RegionMapping
- SimulationExperiment
- Study
- TimeSeries
- NDArray
- SpatialDomain
- Mesh
- SpatialField
- FieldStateVariable
- BoundaryCondition
- PDESolver
- PDE
range: string
source:
name: source
from_schema: https://w3id.org/tvbo
rank: 1000
slot_uri: dcterms:source
owner: Dynamics
domain_of:
- Edge
- Observation
- Dynamics
- Parameter
- CouplingInput
- Likelihood
range: string
references:
name: references
from_schema: https://w3id.org/tvbo
rank: 1000
slot_uri: dcterms:references
owner: Dynamics
domain_of:
- Provenance
- Dynamics
- SimulationExperiment
- SimulationStudy
range: string
multivalued: true
dataLocation:
name: dataLocation
description: Add the location of the data file containing the parcellation terminology.
from_schema: https://openminds.ebrains.eu/sands/BrainAtlas
owner: Dynamics
domain_of:
- ParcellationTerminology
- SoftwareRequirement
- SoftwareEnvironment
- Stimulus
- Event
- Matrix
- Dynamics
- RandomStream
- RegionMapping
- TimeSeries
- NDArray
- Mesh
range: string
class_uri: tvbo:Dynamics
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