Class: Dynamics

URI: tvbo:Dynamics

 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 : coupling_inputs
        
          
    
        
        
        Dynamics --> "*" CouplingInput : coupling_inputs
        click CouplingInput href "./CouplingInput.html"
    

        
      Dynamics : coupling_terms
        
          
    
        
        
        Dynamics --> "*" Parameter : coupling_terms
        click Parameter href "./Parameter.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" String : iri
        click String href "../http://www.w3.org/2001/XMLSchema#string.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 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		direct
label	0..1 xsd:string		direct
iri	0..1 xsd:string		direct
parameters	* Parameter		direct
description	0..1 xsd:string		direct
source	0..1 xsd:string		direct
references	* xsd:string		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

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

Comments

• Successor class replacing deprecated 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
slot_usage:
  name:
    name: name
    ifabsent: Generic2dOscillator
  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.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - 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
class_uri: tvbo:Dynamics

Induced

name: Dynamics
comments:
- Successor class replacing deprecated NeuralMassModel.
from_schema: https://w3id.org/tvbo
aliases:
- NeuralMassModel
slot_usage:
  name:
    name: name
    ifabsent: Generic2dOscillator
  system_type:
    name: system_type
    ifabsent: continuous
attributes:
  derived_parameters:
    name: derived_parameters
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: derived_parameters
    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
    alias: derived_variables
    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
    alias: coupling_terms
    owner: Dynamics
    domain_of:
    - Dynamics
    range: Parameter
    multivalued: true
    inlined: true
  coupling_inputs:
    name: coupling_inputs
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: coupling_inputs
    owner: Dynamics
    domain_of:
    - Dynamics
    range: CouplingInput
    multivalued: true
    inlined: true
  state_variables:
    name: state_variables
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: state_variables
    owner: Dynamics
    domain_of:
    - Dynamics
    - PDE
    range: StateVariable
    multivalued: true
    inlined: true
  modified:
    name: modified
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: modified
    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.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: output
    owner: Dynamics
    domain_of:
    - Dynamics
    - Function
    - FunctionCall
    range: string
    multivalued: true
  derived_from_model:
    name: derived_from_model
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: derived_from_model
    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)
    alias: number_of_modes
    owner: Dynamics
    domain_of:
    - Dynamics
    range: integer
  local_coupling_term:
    name: local_coupling_term
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: local_coupling_term
    owner: Dynamics
    domain_of:
    - Dynamics
    range: Parameter
  functions:
    name: functions
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: functions
    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
    alias: stimulus
    owner: Dynamics
    domain_of:
    - Dynamics
    range: Stimulus
    inlined: true
  modes:
    name: modes
    from_schema: https://w3id.org/tvbo
    aliases:
    - components
    rank: 1000
    alias: modes
    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
    alias: model_type
    owner: Dynamics
    domain_of:
    - Dynamics
    range: ModelType
  system_type:
    name: system_type
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: continuous
    alias: system_type
    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'
    alias: autonomous
    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
    alias: observed
    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
    alias: events
    owner: Dynamics
    domain_of:
    - Node
    - Edge
    - Dynamics
    - SimulationExperiment
    range: Event
    multivalued: true
    inlined: true
  has_reference:
    name: has_reference
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: has_reference
    owner: Dynamics
    domain_of:
    - Dynamics
    range: string
  name:
    name: name
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: Generic2dOscillator
    key: true
    alias: name
    owner: Dynamics
    domain_of:
    - BrainAtlas
    - CommonCoordinateSpace
    - ParcellationEntity
    - DBSProtocol
    - ClinicalScale
    - ClinicalScore
    - Event
    - Tractogram
    - GraphGenerator
    - File
    - StateValue
    - Observation
    - Dynamics
    - StateVariable
    - Distribution
    - Parameter
    - CouplingInput
    - Argument
    - Function
    - FunctionCall
    - Callable
    - DerivedParameter
    - DerivedVariable
    - DataSource
    - OptimizationStage
    - Exploration
    - UpdateRule
    - Algorithm
    - Option
    - BranchSwitch
    - Continuation
    - Coupling
    - SoftwareEnvironment
    - SoftwareRequirement
    - SoftwarePackage
    range: string
    required: true
  label:
    name: label
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: label
    owner: Dynamics
    domain_of:
    - ParcellationTerminology
    - Dataset
    - Contact
    - Equation
    - Stimulus
    - Event
    - Parcellation
    - Tractogram
    - Matrix
    - Network
    - Node
    - Edge
    - Observation
    - Dynamics
    - StateVariable
    - Parameter
    - Function
    - FunctionCall
    - DerivedVariable
    - RandomStream
    - DataSource
    - OptimizationStage
    - Exploration
    - TuningObjective
    - Continuation
    - Coupling
    - RegionMapping
    - SimulationExperiment
    - SimulationStudy
    - TimeSeries
    - SoftwareEnvironment
    - NDArray
    - SpatialDomain
    - Mesh
    - SpatialField
    - FieldStateVariable
    - DifferentialOperator
    - BoundaryCondition
    - PDESolver
    - PDE
    range: string
  iri:
    name: iri
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: iri
    owner: Dynamics
    domain_of:
    - Dynamics
    - Function
    - Coupling
    range: string
  parameters:
    name: parameters
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: parameters
    owner: Dynamics
    domain_of:
    - Equation
    - Stimulus
    - Event
    - TemporalApplicableEquation
    - Network
    - GraphGenerator
    - Node
    - Edge
    - Observation
    - 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
    alias: description
    owner: Dynamics
    domain_of:
    - ClinicalScore
    - Equation
    - Stimulus
    - Event
    - Tractogram
    - Matrix
    - Network
    - GraphGenerator
    - File
    - Node
    - Edge
    - Observation
    - Dynamics
    - StateVariable
    - Parameter
    - CouplingInput
    - Argument
    - Function
    - FunctionCall
    - Callable
    - DerivedParameter
    - DerivedVariable
    - RandomStream
    - DataSource
    - OptimizationStage
    - Exploration
    - UpdateRule
    - TuningObjective
    - Algorithm
    - BranchSwitch
    - Continuation
    - Integrator
    - Coupling
    - RegionMapping
    - SimulationExperiment
    - SimulationStudy
    - TimeSeries
    - SoftwareEnvironment
    - SoftwareRequirement
    - SoftwarePackage
    - NDArray
    - SpatialDomain
    - Mesh
    - SpatialField
    - FieldStateVariable
    - BoundaryCondition
    - PDESolver
    - PDE
    range: string
  source:
    name: source
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: source
    owner: Dynamics
    domain_of:
    - Edge
    - Observation
    - Dynamics
    range: string
  references:
    name: references
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: references
    owner: Dynamics
    domain_of:
    - Provenance
    - Dynamics
    - SimulationExperiment
    range: string
    multivalued: true
class_uri: tvbo:Dynamics