Reference·Classes

Class: SimulationStudy

URI: tvbo:SimulationStudy

 classDiagram
    class SimulationStudy
    click SimulationStudy href "./SimulationStudy.html"
      Study <|-- SimulationStudy
        click Study href "./Study.html"
      
      SimulationStudy : analyses
        
          
    
        
        
        SimulationStudy --> "*" Analysis : analyses
        click Analysis href "./Analysis.html"
    

        
      SimulationStudy : archive
        
          
    
        
        
        SimulationStudy --> "0..1" ArchiveConfig : archive
        click ArchiveConfig href "./ArchiveConfig.html"
    

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

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

        
      SimulationStudy : code_source
        
          
    
        
        
        SimulationStudy --> "0..1" CodeSource : code_source
        click CodeSource href "./CodeSource.html"
    

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

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

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

        
      SimulationStudy : figures
        
          
    
        
        
        SimulationStudy --> "*" Figure : figures
        click Figure href "./Figure.html"
    

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

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

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

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

        
      SimulationStudy : requires
        
          
    
        
        
        SimulationStudy --> "*" SoftwarePackage : requires
        click SoftwarePackage href "./SoftwarePackage.html"
    

        
      SimulationStudy : results
        
          
    
        
        
        SimulationStudy --> "*" ResultBinding : results
        click ResultBinding href "./ResultBinding.html"
    

        
      SimulationStudy : sample
        
          
    
        
        
        SimulationStudy --> "0..1" Sample : sample
        click Sample href "./Sample.html"
    

        
      SimulationStudy : simulation_experiments
        
          
    
        
        
        SimulationStudy --> "*" SimulationExperiment : simulation_experiments
        click SimulationExperiment href "./SimulationExperiment.html"
    

        
      SimulationStudy : studies
        
          
    
        
        
        SimulationStudy --> "*" SimulationStudy : studies
        click SimulationStudy href "./SimulationStudy.html"
    

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

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

        
      SimulationStudy : workflow
        
          
    
        
        
        SimulationStudy --> "0..1" WorkflowConfig : workflow
        click WorkflowConfig href "./WorkflowConfig.html"
    

        
      SimulationStudy : year
        
          
    
        
        
        SimulationStudy --> "0..1" Integer : year
        click Integer href "../http://www.w3.org/2001/XMLSchema#integer.html"
    

        
      

Inheritance

• Study
  • SimulationStudy

Class Properties

Property	Value
Class URI	tvbo:SimulationStudy

Slots

Name	Cardinality and Range	Description	Inheritance
label	0..1 xsd:string		direct
derived_from	0..1 xsd:string		direct
model	0..1 Dynamics		direct
references	* xsd:string		direct
key	0..1 xsd:string	Deprecated alias of the inherited citekey; retained for back-compatibilit…	direct
sample	0..1 Sample		direct
workflow	0..1 WorkflowConfig	Study-wide default orchestration for rendering its experiments’ sweeps into d…	direct
simulation_experiments	* SimulationExperiment		direct
analyses	* Analysis	Analyses of this study’s results, each persisted as its own container and so …	direct
figures	* Figure	Declarative Figure specs rendered from this study’s experiment results — clos…	direct
code_source	0..1 CodeSource	Where this study’s callable code lives — the builders and transform/observati…	direct
requires	* SoftwarePackage	Packages this study’s own code needs beyond what tvbo itself installs, keyed …	direct
studies	* SimulationStudy	Other studies this one aggregates, each a SimulationStudy in its own righ…	direct
results	* ResultBinding	The named numbers the prose cites, each keyed by the manuscript token that st…	direct
archive	0..1 ArchiveConfig	How to package the run into a COMBINE/OMEX archive — the single supplementary…	direct
description	0..1 xsd:string		Study
citekey	0..1 xsd:string	BibTeX citation key; the join key into references	Study
type	0..1 xsd:string	Publication type (article, book, inproceedings, …)	Study
title	0..1 xsd:string		Study
authors	* xsd:string	Author display strings (full detail in references	Study
year	0..1 xsd:integer		Study
doi	0..1 xsd:string		Study

Usages

used by	used in	type	used
SimulationStudy	studies	range	SimulationStudy

Identifier and Mapping Information

Schema Source

• from schema: https://w3id.org/tvbo

Mappings

Mapping Type	Mapped Value
self	tvbo:SimulationStudy
native	tvbo:SimulationStudy

LinkML Source

Direct

name: SimulationStudy
from_schema: https://w3id.org/tvbo
is_a: Study
slots:
- label
- derived_from
- model
- references
attributes:
  key:
    name: key
    description: Deprecated alias of the inherited ``citekey``; retained for back-compatibility
      with existing tooling.
    from_schema: https://w3id.org/tvbo
    domain_of:
    - DataSource
    - SimulationStudy
    - ResultBinding
    range: string
  sample:
    name: sample
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - SimulationStudy
    range: Sample
  workflow:
    name: workflow
    description: Study-wide default orchestration for rendering its experiments' sweeps
      into distributed workflows (Slurm/Snakemake/Nextflow). Individual experiments
      refine it via ``workflow_overrides``.
    from_schema: https://w3id.org/tvbo
    domain_of:
    - DistributionConfig
    - SimulationExperiment
    - SimulationStudy
    range: WorkflowConfig
    inlined: true
  simulation_experiments:
    name: simulation_experiments
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: experiments
    domain_of:
    - SimulationStudy
    range: SimulationExperiment
    multivalued: true
    inlined_as_list: true
  analyses:
    name: analyses
    description: 'Analyses of this study''s results, each persisted as its own container
      and so bindable by a figure or a later analysis exactly like a run. These take
      the ``Analysis`` form that invokes a ``callable`` over ``arguments`` (the ``type``/``target``/``wrt``
      form analyses a solve and belongs on an ``Observation`` instead), and each needs
      a unique ``name`` — it keys the container. An argument''s ``used:`` DataRef
      both records what was consumed and orders the run: ``tvbo run`` executes the
      analyses around the experiments — one an experiment consumes first, one consuming
      an experiment after — and then renders the figures.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - SimulationStudy
    range: Analysis
    multivalued: true
    inlined_as_list: true
  figures:
    name: figures
    description: Declarative Figure specs rendered from this study's experiment results
      — closes the replication loop (a study is its experiments plus the figures that
      read them).
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - SimulationStudy
    range: Figure
    multivalued: true
    inlined_as_list: true
  code_source:
    name: code_source
    description: 'Where this study''s callable code lives — the builders and transform/observation
      callables it references by bare ``module:`` name. Decouples the specification
      from its code: a local directory (relative to the recipe YAML or absolute) or
      a git repository fetched and cached at load time. When absent, the conventional
      ``<recipe-dir>/code/`` is used.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - SimulationStudy
    range: CodeSource
    inlined: true
  requires:
    name: requires
    description: Packages this study's own code needs beyond what tvbo itself installs,
      keyed by package name and carrying the version it was reproduced against. A
      replication that matches a paper's method often has to use the paper's tool
      — a spectral parameterisation, a specific solver — and a study whose report
      imports one that nothing declares runs only on the machine that happens to have
      it. This states what is required; ``prov-<label>_soft`` records what actually
      ran, so the two can be compared rather than assumed equal.
    from_schema: https://w3id.org/tvbo
    domain_of:
    - UpdateRule
    - SimulationStudy
    range: SoftwarePackage
    multivalued: true
    inlined: true
  studies:
    name: studies
    description: 'Other studies this one aggregates, each a ``SimulationStudy`` in
      its own right — so a study-of-studies is the same class as the studies it holds,
      and nesting recurses to any depth without a wrapper class standing between a
      study and the studies it holds. A whole manuscript is then one runnable specification
      whose sub-studies are runnable specifications. Written as ``!include <path>``
      so each sub-study keeps its own recipe file and therefore its own directory:
      its ``code_source``, its results root and its relative references all resolve
      against where it lives, not against whoever included it. ``tvbo run`` walks
      the nested studies depth first, then runs the owning study''s own experiments,
      analyses and figures — the paper-native content belonging to no sub-study. Legitimized
      by COMBINE/OMEX, SED-ML and the ISA ``Investigation`` top-level container it
      parallels.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - SimulationStudy
    range: SimulationStudy
    multivalued: true
    inlined: true
    inlined_as_list: true
  results:
    name: results
    description: The named numbers the prose cites, each keyed by the manuscript token
      that stands in for it (``key``) and bound either to a computed value (``used:``
      a DataRef into this study's or a nested study's analysis) or to an authored
      constant quoted from prior work (``value`` + ``source``). ``tvbo run`` collects
      these into a results manifest the document reads, so no reported figure is transcribed
      by hand and a stale or missing key fails the build rather than printing a wrong
      number.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - SimulationStudy
    range: ResultBinding
    multivalued: true
    inlined: true
    inlined_as_list: true
  archive:
    name: archive
    description: How to package the run into a COMBINE/OMEX archive — the single supplementary
      artifact from which every figure, number and caption regenerates. Unset means
      no archive is emitted.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - SimulationStudy
    range: ArchiveConfig
    inlined: true
class_uri: tvbo:SimulationStudy

Induced

name: SimulationStudy
from_schema: https://w3id.org/tvbo
is_a: Study
attributes:
  key:
    name: key
    description: Deprecated alias of the inherited ``citekey``; retained for back-compatibility
      with existing tooling.
    from_schema: https://w3id.org/tvbo
    owner: SimulationStudy
    domain_of:
    - DataSource
    - SimulationStudy
    - ResultBinding
    range: string
  sample:
    name: sample
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: SimulationStudy
    domain_of:
    - SimulationStudy
    range: Sample
  workflow:
    name: workflow
    description: Study-wide default orchestration for rendering its experiments' sweeps
      into distributed workflows (Slurm/Snakemake/Nextflow). Individual experiments
      refine it via ``workflow_overrides``.
    from_schema: https://w3id.org/tvbo
    owner: SimulationStudy
    domain_of:
    - DistributionConfig
    - SimulationExperiment
    - SimulationStudy
    range: WorkflowConfig
    inlined: true
  simulation_experiments:
    name: simulation_experiments
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: experiments
    owner: SimulationStudy
    domain_of:
    - SimulationStudy
    range: SimulationExperiment
    multivalued: true
    inlined: true
    inlined_as_list: true
  analyses:
    name: analyses
    description: 'Analyses of this study''s results, each persisted as its own container
      and so bindable by a figure or a later analysis exactly like a run. These take
      the ``Analysis`` form that invokes a ``callable`` over ``arguments`` (the ``type``/``target``/``wrt``
      form analyses a solve and belongs on an ``Observation`` instead), and each needs
      a unique ``name`` — it keys the container. An argument''s ``used:`` DataRef
      both records what was consumed and orders the run: ``tvbo run`` executes the
      analyses around the experiments — one an experiment consumes first, one consuming
      an experiment after — and then renders the figures.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: SimulationStudy
    domain_of:
    - SimulationStudy
    range: Analysis
    multivalued: true
    inlined: true
    inlined_as_list: true
  figures:
    name: figures
    description: Declarative Figure specs rendered from this study's experiment results
      — closes the replication loop (a study is its experiments plus the figures that
      read them).
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: SimulationStudy
    domain_of:
    - SimulationStudy
    range: Figure
    multivalued: true
    inlined: true
    inlined_as_list: true
  code_source:
    name: code_source
    description: 'Where this study''s callable code lives — the builders and transform/observation
      callables it references by bare ``module:`` name. Decouples the specification
      from its code: a local directory (relative to the recipe YAML or absolute) or
      a git repository fetched and cached at load time. When absent, the conventional
      ``<recipe-dir>/code/`` is used.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: SimulationStudy
    domain_of:
    - SimulationStudy
    range: CodeSource
    inlined: true
  requires:
    name: requires
    description: Packages this study's own code needs beyond what tvbo itself installs,
      keyed by package name and carrying the version it was reproduced against. A
      replication that matches a paper's method often has to use the paper's tool
      — a spectral parameterisation, a specific solver — and a study whose report
      imports one that nothing declares runs only on the machine that happens to have
      it. This states what is required; ``prov-<label>_soft`` records what actually
      ran, so the two can be compared rather than assumed equal.
    from_schema: https://w3id.org/tvbo
    owner: SimulationStudy
    domain_of:
    - UpdateRule
    - SimulationStudy
    range: SoftwarePackage
    multivalued: true
    inlined: true
  studies:
    name: studies
    description: 'Other studies this one aggregates, each a ``SimulationStudy`` in
      its own right — so a study-of-studies is the same class as the studies it holds,
      and nesting recurses to any depth without a wrapper class standing between a
      study and the studies it holds. A whole manuscript is then one runnable specification
      whose sub-studies are runnable specifications. Written as ``!include <path>``
      so each sub-study keeps its own recipe file and therefore its own directory:
      its ``code_source``, its results root and its relative references all resolve
      against where it lives, not against whoever included it. ``tvbo run`` walks
      the nested studies depth first, then runs the owning study''s own experiments,
      analyses and figures — the paper-native content belonging to no sub-study. Legitimized
      by COMBINE/OMEX, SED-ML and the ISA ``Investigation`` top-level container it
      parallels.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: SimulationStudy
    domain_of:
    - SimulationStudy
    range: SimulationStudy
    multivalued: true
    inlined: true
    inlined_as_list: true
  results:
    name: results
    description: The named numbers the prose cites, each keyed by the manuscript token
      that stands in for it (``key``) and bound either to a computed value (``used:``
      a DataRef into this study's or a nested study's analysis) or to an authored
      constant quoted from prior work (``value`` + ``source``). ``tvbo run`` collects
      these into a results manifest the document reads, so no reported figure is transcribed
      by hand and a stale or missing key fails the build rather than printing a wrong
      number.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: SimulationStudy
    domain_of:
    - SimulationStudy
    range: ResultBinding
    multivalued: true
    inlined: true
    inlined_as_list: true
  archive:
    name: archive
    description: How to package the run into a COMBINE/OMEX archive — the single supplementary
      artifact from which every figure, number and caption regenerates. Unset means
      no archive is emitted.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: SimulationStudy
    domain_of:
    - SimulationStudy
    range: ArchiveConfig
    inlined: true
  label:
    name: label
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: rdfs:label
    owner: SimulationStudy
    domain_of:
    - ParcellationTerminology
    - Subject
    - Session
    - Dataset
    - Contact
    - SoftwareEnvironment
    - Figure
    - Panel
    - Inset
    - Layer
    - Colorbar
    - Rule
    - 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
  derived_from:
    name: derived_from
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: prov:wasDerivedFrom
    owner: SimulationStudy
    domain_of:
    - Provenance
    - SimulationStudy
    range: string
  model:
    name: model
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: SimulationStudy
    domain_of:
    - Electrode
    - SimulationExperiment
    - SimulationStudy
    range: Dynamics
  references:
    name: references
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: dcterms:references
    owner: SimulationStudy
    domain_of:
    - Provenance
    - Observation
    - Dynamics
    - SimulationExperiment
    - SimulationStudy
    range: string
    multivalued: true
  description:
    name: description
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: dcterms:description
    owner: SimulationStudy
    domain_of:
    - CommonCoordinateSpace
    - Dataset
    - StudyLayout
    - StudyTemplate
    - StudyDirectory
    - StudyFile
    - ClinicalScore
    - SoftwarePackage
    - SoftwareRequirement
    - SoftwareEnvironment
    - Figure
    - Panel
    - Equation
    - Stimulus
    - Event
    - Tractogram
    - Matrix
    - ResultEntity
    - Activity
    - 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
    - ResultBinding
    - TimeSeries
    - NDArray
    - SpatialDomain
    - Mesh
    - SpatialField
    - FieldStateVariable
    - BoundaryCondition
    - PDESolver
    - PDE
    - Reducer
    range: string
  citekey:
    name: citekey
    description: BibTeX citation key; the join key into references.bib for full bibliographic
      detail. A study is identified by its key/citekey and described by its title
      — no ``name`` needed.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: SimulationStudy
    domain_of:
    - Study
    range: string
  type:
    name: type
    description: Publication type (article, book, inproceedings, …).
    from_schema: https://w3id.org/tvbo
    owner: SimulationStudy
    domain_of:
    - Activity
    - GraphGenerator
    - ProcedureStep
    - File
    - Analysis
    - Aggregation
    - TuningObjective
    - Algorithm
    - Study
    range: string
  title:
    name: title
    from_schema: https://w3id.org/tvbo
    slot_uri: dcterms:title
    owner: SimulationStudy
    domain_of:
    - Panel
    - Inset
    - Legend
    - Study
    range: string
  authors:
    name: authors
    description: Author display strings (full detail in references.bib).
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: SimulationStudy
    domain_of:
    - Study
    range: string
    multivalued: true
  year:
    name: year
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: dcterms:issued
    owner: SimulationStudy
    domain_of:
    - Study
    range: integer
  doi:
    name: doi
    from_schema: https://w3id.org/tvbo
    slot_uri: bibo:doi
    owner: SimulationStudy
    domain_of:
    - SoftwarePackage
    - Study
    range: string
class_uri: tvbo:SimulationStudy