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

        
      SimulationExperiment : derived_observations
        
          
    
        
        
        SimulationExperiment --> "*" DerivedObservation : derived_observations
        click DerivedObservation href "./DerivedObservation.html"
    

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

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

        
      SimulationExperiment : environment
        
          
    
        
        
        SimulationExperiment --> "0..1" SoftwareEnvironment : environment
        click SoftwareEnvironment href "./SoftwareEnvironment.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 : 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 : local_dynamics
        
          
    
        
        
        SimulationExperiment --> "0..1" Dynamics : local_dynamics
        click Dynamics href "./Dynamics.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 : optimization
        
          
    
        
        
        SimulationExperiment --> "*" Optimization : optimization
        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"
    

        
      

Slots

Name	Cardinality and Range	Description	Inheritance
model	0..1 Dynamics		direct
id	1 xsd:integer		direct
description	0..1 xsd:string		direct
additional_equations	* Equation		direct
label	0..1 xsd:string		direct
local_dynamics	0..1 Dynamics	Default dynamics model for all nodes (used when node	direct
dynamics	* Dynamics	Dictionary of dynamics models keyed by name	direct
integration	0..1 Integrator		direct
connectivity	0..1 Network		direct
network	0..1 Network		direct
coupling	0..1 Coupling		direct
observations	* Observation		direct
derived_observations	* DerivedObservation	Observations derived from combining other observations	direct
functions	* Function	Reusable function definitions	direct
stimulation	0..1 Stimulus		direct
field_dynamics	0..1 PDE		direct
optimization	* Optimization	Parameter optimization configurations	direct
explorations	* Exploration	Parameter exploration/grid search specifications	direct
algorithms	* Algorithm	Iterative parameter tuning algorithms (FIC, EIB, etc	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
references	* xsd:string		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
attributes:
  id:
    name: id
    from_schema: https://w3id.org/tvbo
    identifier: true
    domain_of:
    - Node
    - SimulationExperiment
    range: integer
    required: true
  description:
    name: description
    from_schema: https://w3id.org/tvbo
    domain_of:
    - ClinicalScore
    - Equation
    - Stimulus
    - Tractogram
    - Matrix
    - Network
    - File
    - Node
    - Edge
    - Observation
    - Dynamics
    - StateVariable
    - Parameter
    - CouplingInput
    - Argument
    - Function
    - Callable
    - DerivedParameter
    - DerivedVariable
    - RandomStream
    - DataSource
    - OptimizationStage
    - Exploration
    - UpdateRule
    - TuningObjective
    - Algorithm
    - Integrator
    - Coupling
    - RegionMapping
    - SimulationExperiment
    - SimulationStudy
    - TimeSeries
    - SoftwareEnvironment
    - SoftwareRequirement
    - SoftwarePackage
    - 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
    domain_of:
    - ParcellationTerminology
    - Dataset
    - Contact
    - Equation
    - Stimulus
    - Parcellation
    - Tractogram
    - Matrix
    - Network
    - Node
    - Edge
    - Observation
    - Dynamics
    - StateVariable
    - Parameter
    - Function
    - DerivedVariable
    - RandomStream
    - DataSource
    - OptimizationStage
    - Exploration
    - TuningObjective
    - Coupling
    - RegionMapping
    - SimulationExperiment
    - SimulationStudy
    - TimeSeries
    - SoftwareEnvironment
    - NDArray
    - SpatialDomain
    - Mesh
    - SpatialField
    - FieldStateVariable
    - DifferentialOperator
    - BoundaryCondition
    - PDESolver
    - PDE
    range: string
  local_dynamics:
    name: local_dynamics
    description: Default dynamics model for all nodes (used when node.dynamics not
      specified or as fallback)
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - SimulationExperiment
    range: Dynamics
    inlined: true
  dynamics:
    name: dynamics
    description: Dictionary of dynamics models keyed by name. Nodes reference these
      by name.
    from_schema: https://w3id.org/tvbo
    domain_of:
    - Node
    - SimulationExperiment
    range: Dynamics
    multivalued: true
    inlined: true
    inlined_as_list: false
  integration:
    name: integration
    from_schema: https://w3id.org/tvbo
    domain_of:
    - Optimization
    - SimulationExperiment
    range: Integrator
    inlined: true
  connectivity:
    name: connectivity
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - SimulationExperiment
    range: Network
    inlined: true
  network:
    name: network
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - 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
    from_schema: https://w3id.org/tvbo
    domain_of:
    - Algorithm
    - SimulationExperiment
    range: Observation
    multivalued: true
    inlined: true
  derived_observations:
    name: derived_observations
    description: 'Observations derived from combining other observations. Computed
      after all regular observations are available. Examples: fc_corr (from fc, fc_target),
      rmse, etc.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - SimulationExperiment
    range: DerivedObservation
    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
  field_dynamics:
    name: field_dynamics
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - SimulationExperiment
    range: PDE
    inlined: true
  optimization:
    name: optimization
    description: Parameter optimization configurations
    from_schema: https://w3id.org/tvbo
    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
  algorithms:
    name: algorithms
    description: Iterative parameter tuning algorithms (FIC, EIB, etc.)
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - SimulationExperiment
    range: Algorithm
    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
    - Algorithm
    - 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
    - SimulationExperiment
    range: SoftwareRequirement
    inlined: true
  references:
    name: references
    from_schema: https://w3id.org/tvbo
    domain_of:
    - Dynamics
    - SimulationExperiment
    range: string
    multivalued: 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
    identifier: true
    alias: id
    owner: SimulationExperiment
    domain_of:
    - Node
    - SimulationExperiment
    range: integer
    required: true
  description:
    name: description
    from_schema: https://w3id.org/tvbo
    alias: description
    owner: SimulationExperiment
    domain_of:
    - ClinicalScore
    - Equation
    - Stimulus
    - Tractogram
    - Matrix
    - Network
    - File
    - Node
    - Edge
    - Observation
    - Dynamics
    - StateVariable
    - Parameter
    - CouplingInput
    - Argument
    - Function
    - Callable
    - DerivedParameter
    - DerivedVariable
    - RandomStream
    - DataSource
    - OptimizationStage
    - Exploration
    - UpdateRule
    - TuningObjective
    - Algorithm
    - Integrator
    - Coupling
    - RegionMapping
    - SimulationExperiment
    - SimulationStudy
    - TimeSeries
    - SoftwareEnvironment
    - SoftwareRequirement
    - SoftwarePackage
    - NDArray
    - SpatialDomain
    - Mesh
    - SpatialField
    - FieldStateVariable
    - BoundaryCondition
    - PDESolver
    - PDE
    range: string
  additional_equations:
    name: additional_equations
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: additional_equations
    owner: SimulationExperiment
    domain_of:
    - SimulationExperiment
    range: Equation
    multivalued: true
  label:
    name: label
    from_schema: https://w3id.org/tvbo
    alias: label
    owner: SimulationExperiment
    domain_of:
    - ParcellationTerminology
    - Dataset
    - Contact
    - Equation
    - Stimulus
    - Parcellation
    - Tractogram
    - Matrix
    - Network
    - Node
    - Edge
    - Observation
    - Dynamics
    - StateVariable
    - Parameter
    - Function
    - DerivedVariable
    - RandomStream
    - DataSource
    - OptimizationStage
    - Exploration
    - TuningObjective
    - Coupling
    - RegionMapping
    - SimulationExperiment
    - SimulationStudy
    - TimeSeries
    - SoftwareEnvironment
    - NDArray
    - SpatialDomain
    - Mesh
    - SpatialField
    - FieldStateVariable
    - DifferentialOperator
    - BoundaryCondition
    - PDESolver
    - PDE
    range: string
  local_dynamics:
    name: local_dynamics
    description: Default dynamics model for all nodes (used when node.dynamics not
      specified or as fallback)
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: local_dynamics
    owner: SimulationExperiment
    domain_of:
    - SimulationExperiment
    range: Dynamics
    inlined: true
  dynamics:
    name: dynamics
    description: Dictionary of dynamics models keyed by name. Nodes reference these
      by name.
    from_schema: https://w3id.org/tvbo
    alias: dynamics
    owner: SimulationExperiment
    domain_of:
    - Node
    - SimulationExperiment
    range: Dynamics
    multivalued: true
    inlined: true
    inlined_as_list: false
  integration:
    name: integration
    from_schema: https://w3id.org/tvbo
    alias: integration
    owner: SimulationExperiment
    domain_of:
    - Optimization
    - SimulationExperiment
    range: Integrator
    inlined: true
  connectivity:
    name: connectivity
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: connectivity
    owner: SimulationExperiment
    domain_of:
    - SimulationExperiment
    range: Network
    inlined: true
  network:
    name: network
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: network
    owner: SimulationExperiment
    domain_of:
    - SimulationExperiment
    range: Network
    inlined: true
  coupling:
    name: coupling
    from_schema: https://w3id.org/tvbo
    alias: coupling
    owner: SimulationExperiment
    domain_of:
    - Network
    - Edge
    - SimulationExperiment
    range: Coupling
    inlined: true
  observations:
    name: observations
    from_schema: https://w3id.org/tvbo
    alias: observations
    owner: SimulationExperiment
    domain_of:
    - Algorithm
    - SimulationExperiment
    range: Observation
    multivalued: true
    inlined: true
  derived_observations:
    name: derived_observations
    description: 'Observations derived from combining other observations. Computed
      after all regular observations are available. Examples: fc_corr (from fc, fc_target),
      rmse, etc.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: derived_observations
    owner: SimulationExperiment
    domain_of:
    - SimulationExperiment
    range: DerivedObservation
    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
    alias: functions
    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
    alias: stimulation
    owner: SimulationExperiment
    domain_of:
    - SimulationExperiment
    range: Stimulus
    inlined: true
  field_dynamics:
    name: field_dynamics
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: field_dynamics
    owner: SimulationExperiment
    domain_of:
    - SimulationExperiment
    range: PDE
    inlined: true
  optimization:
    name: optimization
    description: Parameter optimization configurations
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: optimization
    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
    alias: explorations
    owner: SimulationExperiment
    domain_of:
    - SimulationExperiment
    range: Exploration
    multivalued: true
    inlined: true
  algorithms:
    name: algorithms
    description: Iterative parameter tuning algorithms (FIC, EIB, etc.)
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: algorithms
    owner: SimulationExperiment
    domain_of:
    - SimulationExperiment
    range: Algorithm
    multivalued: true
    inlined: true
  environment:
    name: environment
    description: Execution environment (collection of requirements).
    from_schema: https://w3id.org/tvbo
    alias: environment
    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
    alias: execution
    owner: SimulationExperiment
    domain_of:
    - Optimization
    - Exploration
    - Algorithm
    - SimulationExperiment
    range: ExecutionConfig
    inlined: true
  software:
    name: software
    description: (Deprecated) Single software requirement; prefer 'environment' with
      aggregated requirements.
    from_schema: https://w3id.org/tvbo
    alias: software
    owner: SimulationExperiment
    domain_of:
    - Callable
    - SimulationExperiment
    range: SoftwareRequirement
    inlined: true
  references:
    name: references
    from_schema: https://w3id.org/tvbo
    alias: references
    owner: SimulationExperiment
    domain_of:
    - Dynamics
    - SimulationExperiment
    range: string
    multivalued: true
  model:
    name: model
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: model
    owner: SimulationExperiment
    domain_of:
    - Electrode
    - SimulationExperiment
    - SimulationStudy
    range: Dynamics
class_uri: tvbo:Simulation
tree_root: true