Class: SimulationExperiment

URI: tvbo:Simulation

 classDiagram
    class SimulationExperiment
    click SimulationExperiment href "./SimulationExperiment.html"
      SimulationExperiment : additional_equations
        
          
    
        
        
        SimulationExperiment --> "*" Equation : additional_equations
        click Equation href "./Equation.html"
    

        
      SimulationExperiment : algorithms
        
          
    
        
        
        SimulationExperiment --> "*" Algorithm : algorithms
        click Algorithm href "./Algorithm.html"
    

        
      SimulationExperiment : connectivity
        
          
    
        
        
        SimulationExperiment --> "0..1" Network : connectivity
        click Network href "./Network.html"
    

        
      SimulationExperiment : continuations
        
          
    
        
        
        SimulationExperiment --> "*" Continuation : continuations
        click Continuation href "./Continuation.html"
    

        
      SimulationExperiment : coupling
        
          
    
        
        
        SimulationExperiment --> "0..1" Coupling : coupling
        click Coupling href "./Coupling.html"
    

        
      SimulationExperiment : dataset
        
          
    
        
        
        SimulationExperiment --> "0..1" Dataset : dataset
        click Dataset href "./Dataset.html"
    

        
      SimulationExperiment : description
        
          
    
        
        
        SimulationExperiment --> "0..1" String : description
        click String href "../http://www.w3.org/2001/XMLSchema#string.html"
    

        
      SimulationExperiment : dynamics
        
          
    
        
        
        SimulationExperiment --> "0..1" Dynamics : dynamics
        click Dynamics href "./Dynamics.html"
    

        
      SimulationExperiment : environment
        
          
    
        
        
        SimulationExperiment --> "0..1" SoftwareEnvironment : environment
        click SoftwareEnvironment href "./SoftwareEnvironment.html"
    

        
      SimulationExperiment : events
        
          
    
        
        
        SimulationExperiment --> "*" Event : events
        click Event href "./Event.html"
    

        
      SimulationExperiment : execution
        
          
    
        
        
        SimulationExperiment --> "0..1" ExecutionConfig : execution
        click ExecutionConfig href "./ExecutionConfig.html"
    

        
      SimulationExperiment : explorations
        
          
    
        
        
        SimulationExperiment --> "*" Exploration : explorations
        click Exploration href "./Exploration.html"
    

        
      SimulationExperiment : field_dynamics
        
          
    
        
        
        SimulationExperiment --> "0..1" PDE : field_dynamics
        click PDE href "./PDE.html"
    

        
      SimulationExperiment : functions
        
          
    
        
        
        SimulationExperiment --> "*" Function : functions
        click Function href "./Function.html"
    

        
      SimulationExperiment : id
        
          
    
        
        
        SimulationExperiment --> "1" Integer : id
        click Integer href "../http://www.w3.org/2001/XMLSchema#integer.html"
    

        
      SimulationExperiment : inferences
        
          
    
        
        
        SimulationExperiment --> "*" Inference : inferences
        click Inference href "./Inference.html"
    

        
      SimulationExperiment : integration
        
          
    
        
        
        SimulationExperiment --> "0..1" Integrator : integration
        click Integrator href "./Integrator.html"
    

        
      SimulationExperiment : label
        
          
    
        
        
        SimulationExperiment --> "0..1" String : label
        click String href "../http://www.w3.org/2001/XMLSchema#string.html"
    

        
      SimulationExperiment : model
        
          
    
        
        
        SimulationExperiment --> "0..1" Dynamics : model
        click Dynamics href "./Dynamics.html"
    

        
      SimulationExperiment : network
        
          
    
        
        
        SimulationExperiment --> "0..1" Network : network
        click Network href "./Network.html"
    

        
      SimulationExperiment : observations
        
          
    
        
        
        SimulationExperiment --> "*" Observation : observations
        click Observation href "./Observation.html"
    

        
      SimulationExperiment : optimizations
        
          
    
        
        
        SimulationExperiment --> "*" Optimization : optimizations
        click Optimization href "./Optimization.html"
    

        
      SimulationExperiment : references
        
          
    
        
        
        SimulationExperiment --> "*" String : references
        click String href "../http://www.w3.org/2001/XMLSchema#string.html"
    

        
      SimulationExperiment : software
        
          
    
        
        
        SimulationExperiment --> "0..1" SoftwareRequirement : software
        click SoftwareRequirement href "./SoftwareRequirement.html"
    

        
      SimulationExperiment : stimulation
        
          
    
        
        
        SimulationExperiment --> "0..1" Stimulus : stimulation
        click Stimulus href "./Stimulus.html"
    

        
      

Class Properties

Property	Value
Class URI	tvbo:Simulation
Tree Root	Yes

Slots

Name	Cardinality and Range	Description	Inheritance
model	0..1 Dynamics		direct
references	* xsd:string		direct
id	1 xsd:integer		direct
description	0..1 xsd:string		direct
additional_equations	* Equation		direct
label	0..1 xsd:string		direct
dynamics	0..1 Dynamics	Default dynamics model for all nodes	direct
integration	0..1 Integrator		direct
connectivity	0..1 Network		direct
network	0..1 Network		direct
coupling	0..1 Coupling		direct
observations	* Observation	All observations on this experiment, keyed by name	direct
functions	* Function	Reusable function definitions	direct
stimulation	0..1 Stimulus		direct
events	* Event	Events that apply at the experiment level	direct
field_dynamics	0..1 PDE		direct
optimizations	* Optimization	Parameter optimization configurations	direct
explorations	* Exploration	Parameter exploration/grid search specifications	direct
inferences	* Inference	Bayesian inference configurations (posterior over parameters given an observa…	direct
algorithms	* Algorithm	Iterative parameter tuning algorithms (FIC, EIB, etc	direct
continuations	* Continuation	Numerical continuation and bifurcation analysis specifications	direct
environment	0..1 SoftwareEnvironment	Execution environment (collection of requirements)	direct
execution	0..1 ExecutionConfig	Computational execution configuration (parallelization, devices)	direct
software	0..1 SoftwareRequirement	(Deprecated) Single software requirement; prefer ‘environment’ with aggregate…	direct
dataset	0..1 Dataset	Multi-subject dataset for workflow rendering	direct

Usages

used by	used in	type	used
SimulationStudy	simulation_experiments	range	SimulationExperiment
TimeSeries	source_experiment	range	SimulationExperiment

Identifier and Mapping Information

Schema Source

• from schema: https://w3id.org/tvbo

Mappings

Mapping Type	Mapped Value
self	tvbo:Simulation
native	tvbo:SimulationExperiment

LinkML Source

Direct

name: SimulationExperiment
from_schema: https://w3id.org/tvbo
slots:
- model
- references
attributes:
  id:
    name: id
    from_schema: https://w3id.org/tvbo
    slot_uri: dcterms:identifier
    identifier: true
    domain_of:
    - Node
    - SimulationExperiment
    range: integer
  description:
    name: description
    from_schema: https://w3id.org/tvbo
    slot_uri: dcterms:description
    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
  additional_equations:
    name: additional_equations
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - SimulationExperiment
    range: Equation
    multivalued: true
  label:
    name: label
    from_schema: https://w3id.org/tvbo
    slot_uri: rdfs:label
    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
  dynamics:
    name: dynamics
    description: Default dynamics model for all nodes. For heterogeneous networks
      with multiple dynamics, use network.dynamics instead.
    from_schema: https://w3id.org/tvbo
    domain_of:
    - Network
    - Node
    - Edge
    - Continuation
    - SimulationExperiment
    range: Dynamics
    inlined: true
  integration:
    name: integration
    from_schema: https://w3id.org/tvbo
    domain_of:
    - Optimization
    - Inference
    - SimulationExperiment
    range: Integrator
    inlined: true
  connectivity:
    name: connectivity
    deprecated: Use 'network' instead. 'connectivity' is kept for backward compatibility
      only and will be removed in a future version.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - SimulationExperiment
    range: Network
    inlined: true
  network:
    name: network
    from_schema: https://w3id.org/tvbo
    domain_of:
    - Subject
    - Session
    - SimulationExperiment
    range: Network
    inlined: true
  coupling:
    name: coupling
    from_schema: https://w3id.org/tvbo
    domain_of:
    - Network
    - Edge
    - SimulationExperiment
    range: Coupling
    inlined: true
  observations:
    name: observations
    description: All observations on this experiment, keyed by name. An Observation
      is considered derived (computed from other observations rather than directly
      from state variables) when any item in its multivalued ``source`` slot names
      another observation in this same dict.
    from_schema: https://w3id.org/tvbo
    domain_of:
    - Algorithm
    - SimulationExperiment
    range: Observation
    multivalued: true
    inlined: true
  functions:
    name: functions
    description: 'Reusable function definitions. Referenced by name in observation
      pipelines. Enables DRY: define compute_fc once, use in both simulated and empirical
      paths.'
    from_schema: https://w3id.org/tvbo
    domain_of:
    - Dynamics
    - Algorithm
    - SimulationExperiment
    - PDE
    range: Function
    multivalued: true
    inlined: true
  stimulation:
    name: stimulation
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - SimulationExperiment
    range: Stimulus
    inlined: true
  events:
    name: events
    description: Events that apply at the experiment level. For component-level events,
      attach them to individual nodes or edges instead.
    from_schema: https://w3id.org/tvbo
    domain_of:
    - Node
    - Edge
    - Dynamics
    - SimulationExperiment
    range: Event
    multivalued: true
    inlined: true
  field_dynamics:
    name: field_dynamics
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - SimulationExperiment
    range: PDE
    inlined: true
  optimizations:
    name: optimizations
    description: Parameter optimization configurations
    from_schema: https://w3id.org/tvbo
    aliases:
    - optimization
    rank: 1000
    domain_of:
    - SimulationExperiment
    range: Optimization
    multivalued: true
    inlined: true
  explorations:
    name: explorations
    description: Parameter exploration/grid search specifications
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - SimulationExperiment
    range: Exploration
    multivalued: true
    inlined: true
  inferences:
    name: inferences
    description: Bayesian inference configurations (posterior over parameters given
      an observation, via MCMC). Keyed by name, like optimizations.
    from_schema: https://w3id.org/tvbo
    aliases:
    - inference
    rank: 1000
    domain_of:
    - SimulationExperiment
    range: Inference
    multivalued: true
    inlined: true
  algorithms:
    name: algorithms
    description: Iterative parameter tuning algorithms (FIC, EIB, etc.)
    from_schema: https://w3id.org/tvbo
    domain_of:
    - Exploration
    - SimulationExperiment
    range: Algorithm
    multivalued: true
    inlined: true
  continuations:
    name: continuations
    description: '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'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - SimulationExperiment
    range: Continuation
    multivalued: true
    inlined: true
  environment:
    name: environment
    description: Execution environment (collection of requirements).
    from_schema: https://w3id.org/tvbo
    domain_of:
    - Observation
    - SimulationExperiment
    - PDESolver
    range: SoftwareEnvironment
    inlined: true
  execution:
    name: execution
    description: Computational execution configuration (parallelization, devices).
    from_schema: https://w3id.org/tvbo
    domain_of:
    - Optimization
    - Exploration
    - Inference
    - Algorithm
    - Continuation
    - SimulationExperiment
    range: ExecutionConfig
    inlined: true
  software:
    name: software
    description: (Deprecated) Single software requirement; prefer 'environment' with
      aggregated requirements.
    from_schema: https://w3id.org/tvbo
    domain_of:
    - Callable
    - Continuation
    - SimulationExperiment
    range: SoftwareRequirement
    inlined: true
  dataset:
    name: dataset
    description: Multi-subject dataset for workflow rendering. When set, render_workflow()
      uses dataset.subjects/sessions to generate per-subject parallel jobs.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - SimulationExperiment
    range: Dataset
    inlined: true
class_uri: tvbo:Simulation
tree_root: true

Induced

name: SimulationExperiment
from_schema: https://w3id.org/tvbo
attributes:
  id:
    name: id
    from_schema: https://w3id.org/tvbo
    slot_uri: dcterms:identifier
    identifier: true
    owner: SimulationExperiment
    domain_of:
    - Node
    - SimulationExperiment
    range: integer
    required: true
  description:
    name: description
    from_schema: https://w3id.org/tvbo
    slot_uri: dcterms:description
    owner: SimulationExperiment
    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
  additional_equations:
    name: additional_equations
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: SimulationExperiment
    domain_of:
    - SimulationExperiment
    range: Equation
    multivalued: true
  label:
    name: label
    from_schema: https://w3id.org/tvbo
    slot_uri: rdfs:label
    owner: SimulationExperiment
    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
  dynamics:
    name: dynamics
    description: Default dynamics model for all nodes. For heterogeneous networks
      with multiple dynamics, use network.dynamics instead.
    from_schema: https://w3id.org/tvbo
    owner: SimulationExperiment
    domain_of:
    - Network
    - Node
    - Edge
    - Continuation
    - SimulationExperiment
    range: Dynamics
    inlined: true
  integration:
    name: integration
    from_schema: https://w3id.org/tvbo
    owner: SimulationExperiment
    domain_of:
    - Optimization
    - Inference
    - SimulationExperiment
    range: Integrator
    inlined: true
  connectivity:
    name: connectivity
    deprecated: Use 'network' instead. 'connectivity' is kept for backward compatibility
      only and will be removed in a future version.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: SimulationExperiment
    domain_of:
    - SimulationExperiment
    range: Network
    inlined: true
  network:
    name: network
    from_schema: https://w3id.org/tvbo
    owner: SimulationExperiment
    domain_of:
    - Subject
    - Session
    - SimulationExperiment
    range: Network
    inlined: true
  coupling:
    name: coupling
    from_schema: https://w3id.org/tvbo
    owner: SimulationExperiment
    domain_of:
    - Network
    - Edge
    - SimulationExperiment
    range: Coupling
    inlined: true
  observations:
    name: observations
    description: All observations on this experiment, keyed by name. An Observation
      is considered derived (computed from other observations rather than directly
      from state variables) when any item in its multivalued ``source`` slot names
      another observation in this same dict.
    from_schema: https://w3id.org/tvbo
    owner: SimulationExperiment
    domain_of:
    - Algorithm
    - SimulationExperiment
    range: Observation
    multivalued: true
    inlined: true
  functions:
    name: functions
    description: 'Reusable function definitions. Referenced by name in observation
      pipelines. Enables DRY: define compute_fc once, use in both simulated and empirical
      paths.'
    from_schema: https://w3id.org/tvbo
    owner: SimulationExperiment
    domain_of:
    - Dynamics
    - Algorithm
    - SimulationExperiment
    - PDE
    range: Function
    multivalued: true
    inlined: true
  stimulation:
    name: stimulation
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: SimulationExperiment
    domain_of:
    - SimulationExperiment
    range: Stimulus
    inlined: true
  events:
    name: events
    description: Events that apply at the experiment level. For component-level events,
      attach them to individual nodes or edges instead.
    from_schema: https://w3id.org/tvbo
    owner: SimulationExperiment
    domain_of:
    - Node
    - Edge
    - Dynamics
    - SimulationExperiment
    range: Event
    multivalued: true
    inlined: true
  field_dynamics:
    name: field_dynamics
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: SimulationExperiment
    domain_of:
    - SimulationExperiment
    range: PDE
    inlined: true
  optimizations:
    name: optimizations
    description: Parameter optimization configurations
    from_schema: https://w3id.org/tvbo
    aliases:
    - optimization
    rank: 1000
    owner: SimulationExperiment
    domain_of:
    - SimulationExperiment
    range: Optimization
    multivalued: true
    inlined: true
  explorations:
    name: explorations
    description: Parameter exploration/grid search specifications
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: SimulationExperiment
    domain_of:
    - SimulationExperiment
    range: Exploration
    multivalued: true
    inlined: true
  inferences:
    name: inferences
    description: Bayesian inference configurations (posterior over parameters given
      an observation, via MCMC). Keyed by name, like optimizations.
    from_schema: https://w3id.org/tvbo
    aliases:
    - inference
    rank: 1000
    owner: SimulationExperiment
    domain_of:
    - SimulationExperiment
    range: Inference
    multivalued: true
    inlined: true
  algorithms:
    name: algorithms
    description: Iterative parameter tuning algorithms (FIC, EIB, etc.)
    from_schema: https://w3id.org/tvbo
    owner: SimulationExperiment
    domain_of:
    - Exploration
    - SimulationExperiment
    range: Algorithm
    multivalued: true
    inlined: true
  continuations:
    name: continuations
    description: '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'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: SimulationExperiment
    domain_of:
    - SimulationExperiment
    range: Continuation
    multivalued: true
    inlined: true
  environment:
    name: environment
    description: Execution environment (collection of requirements).
    from_schema: https://w3id.org/tvbo
    owner: SimulationExperiment
    domain_of:
    - Observation
    - SimulationExperiment
    - PDESolver
    range: SoftwareEnvironment
    inlined: true
  execution:
    name: execution
    description: Computational execution configuration (parallelization, devices).
    from_schema: https://w3id.org/tvbo
    owner: SimulationExperiment
    domain_of:
    - Optimization
    - Exploration
    - Inference
    - Algorithm
    - Continuation
    - SimulationExperiment
    range: ExecutionConfig
    inlined: true
  software:
    name: software
    description: (Deprecated) Single software requirement; prefer 'environment' with
      aggregated requirements.
    from_schema: https://w3id.org/tvbo
    owner: SimulationExperiment
    domain_of:
    - Callable
    - Continuation
    - SimulationExperiment
    range: SoftwareRequirement
    inlined: true
  dataset:
    name: dataset
    description: Multi-subject dataset for workflow rendering. When set, render_workflow()
      uses dataset.subjects/sessions to generate per-subject parallel jobs.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: SimulationExperiment
    domain_of:
    - SimulationExperiment
    range: Dataset
    inlined: true
  model:
    name: model
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: SimulationExperiment
    domain_of:
    - Electrode
    - SimulationExperiment
    - SimulationStudy
    range: Dynamics
  references:
    name: references
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: dcterms:references
    owner: SimulationExperiment
    domain_of:
    - Provenance
    - Dynamics
    - SimulationExperiment
    - SimulationStudy
    range: string
    multivalued: true
class_uri: tvbo:Simulation
tree_root: true