entity_management.simulation¶

Simulation domain entities.

Classes

`Analysis`(*[, name, status, generated, ...])	Simulation analysis activity.
`AnalysisConfiguration`(*[, name, ...])	Simulation analysis configuration.
`AnalysisReport`(*[, name, description, ...])	Analysis report.
`BluePyEfeConfiguration`(*[, name, ...])	BluePyEfe configuration entity
`BluePyEfeFeatures`(*[, name, description, ...])	BluePyEfe configuration entity
`BluePyOptRun`(*[, name, description, ...])	Release base entity
`CampaignAnalysis`(*[, name, status, ...])	Simulation campaign analysis activity.
`CircuitCellProperties`(*[, name, ...])	Cell properties provides locationd of the MVD3 file with cell properties.
`Configuration`(*[, name, description, ...])	Configuration file
`CoreTraceCollection`(*[, name, description, ...])	Collection of traces
`DetailedCircuit`(*[, name, description, ...])	Detailed circuit.
`DetailedCircuitValidation`(*[, name, status, ...])	Detailed circuit validation activity.
`DetailedCircuitValidationReport`(*[, name, ...])	Detailed circuit validation report.
`EModelGenerationShape`(*[, name, ...])	EModel generation.
`ETypeFeatureProtocol`(*[, name, description, ...])	Trace protocol.
`EdgeCollection`(*[, name, description, ...])	Edge collection represents circuit connectivity(synapses, projections)
`ExperimentalCell`(*, name, channel[, description])	Experimental cell.
`IonChannelMechanismRelease`(*[, name, ...])	Ion channel models release represents a collection of mod files.
`ModelInstance`(*[, name, description, ...])	Abstract model instance.
`ModelRelease`(*[, name, description, ...])	Release base entity
`ModelReleaseIndex`(*[, name, description, ...])	Index files attached to release entities
`ModelScript`(*[, name, description, ...])	Base entity for the scripts attached to the model.
`Morphology`(*[, name, description, ...])	Neuron morphology.
`MorphologyRelease`(*[, name, description, ...])	Morphology release can be located at the external location or constituted from individual `Morphology` entities.
`NodeCollection`(*[, name, description, ...])	Node collection represents circuit nodes(positions, orientations)
`PlotCollection`(*[, name, description, ...])	Collection of plots.
`ReconstructedCellCollection`(*[, name, ...])	Reconstructed cell collection produced by the morphology release.
`Report`(*[, name, description, ...])	Generic report.
`Simulation`(*[, name, description, ...])	Simulation of the campaign entity.
`SimulationCampaign`(*[, name, description, ...])	Simulation campaign entity that was executed.
`SimulationCampaignAnalysis`(*[, name, ...])	Simulation campaign analysis entity.
`SimulationCampaignConfiguration`(*[, name, ...])	Simulation campaign configuration entity.
`SimulationCampaignExecution`(*[, name, ...])	Simulation campagn execution activity.
`SimulationCampaignGeneration`(*[, name, ...])	Simulation campaign generation activity.
`SimulationCampaignReportCollection`(*[, ...])	Simulation campaign.
`SimulationConfiguration`(*[, name, ...])	Simulation configuration in terms of BlueConfig.
`SingleCellSimulationTrace`(*[, name, ...])	Single cell simulation trace file
`SingleCellTraceGeneration`(*[, name, status, ...])	Single cell simulation trace genaration activity
`SpikeReport`(*[, name, description, ...])	Spike report.
`SynapseRelease`(*[, name, description, ...])	Synapse release represents a collection of mod files.
`Target`(*[, name, description, ...])	Location of the text file defining cell targets (i.e. named collections of cell GIDs).
`Threshold`(*[, name, description, ...])	Threshold.
`TraceCollection`(*[, name, description, ...])	Collection of traces
`TraceFeature`(*[, name, description, ...])	Trace feature.
`TraceFeatureExtraction`(*[, name, status, ...])	Trace feature extraction activity.
`VariableReport`(*[, name, description, ...])	Variable report.

class entity_management.simulation.Analysis(*, name=None, status=None, generated=None, startedAtTime=None, endedAtTime=None, wasStartedBy=None, wasInformedBy=None, wasInfluencedBy=None, wasAssociatedWith=None, used=None)¶

Bases: Activity

Simulation analysis activity.

Parameters:: used (Identifiable) – Used variable report/analysis configuration.

class entity_management.simulation.AnalysisConfiguration(*, name=None, description=None, wasAttributedTo=None, wasGeneratedBy=None, wasDerivedFrom=None, dateCreated=None, contribution=None, distribution)¶

Bases: Entity

Simulation analysis configuration.

Parameters:: distribution (DataDownload) – Json representation of the configuration.

class entity_management.simulation.AnalysisReport(*, name=None, description=None, wasAttributedTo=None, wasGeneratedBy=None, wasDerivedFrom=None, dateCreated=None, contribution=None, distribution, image=None)¶

Bases: Entity

Analysis report.

Deprecated since version 1.3.2: Use entity_management.analysis.AnalysisReport instead.

Parameters:

distribution (DataDownload) – Generated report.
image (DataDownload) – Generated report image preview when applicable.

class entity_management.simulation.BluePyEfeConfiguration(*, name=None, description=None, wasAttributedTo=None, wasGeneratedBy=None, wasDerivedFrom=None, dateCreated=None, distribution=None, contribution=None, brainLocation, subject=None, mType, eType, experimentalCell, featureExtractionConfiguration, stimuliToExperimentMap=None)¶

Bases: Entity

BluePyEfe configuration entity

class entity_management.simulation.BluePyEfeFeatures(*, name=None, description=None, wasAttributedTo=None, wasGeneratedBy=None, wasDerivedFrom=None, dateCreated=None, distribution=None, contribution=None, features, hadProtocol, eType, hypampThreshold=None)¶

Bases: Entity

BluePyEfe configuration entity

class entity_management.simulation.BluePyOptRun(*, name=None, description=None, wasAttributedTo=None, wasGeneratedBy=None, wasDerivedFrom=None, dateCreated=None, distribution=None, contribution=None, gitHash, inputMechanisms, bluePyOptParameters=None, bluePyOptProtocol=None, bluePyOptRecipe=None, experimentalFeatures=None, morphology=None)¶

Bases: Entity

Release base entity

class entity_management.simulation.CampaignAnalysis(*, name=None, status=None, startedAtTime=None, endedAtTime=None, wasStartedBy=None, wasInformedBy=None, wasInfluencedBy=None, wasAssociatedWith=None, used=None, generated=None)¶

Bases: Activity

Simulation campaign analysis activity.

Parameters:

used (List[VariableReport]) – Used simulation campaign variable reports.
generated (AnalysisReport) – Generated analysis report.
wasInformedBy (entity_management.simulation.SimulationCampaign) – Links to the simulation campaign which generated simulations used for the analysis.

class entity_management.simulation.CircuitCellProperties(*, name=None, description=None, wasAttributedTo=None, wasGeneratedBy=None, wasDerivedFrom=None, dateCreated=None, contribution=None, distribution)¶

Bases: Entity

Cell properties provides locationd of the MVD3 file with cell properties.

Parameters:: distribution (DataDownload) – Location of the cell placement file.

class entity_management.simulation.Configuration(*, name=None, description=None, wasAttributedTo=None, wasGeneratedBy=None, wasDerivedFrom=None, dateCreated=None, distribution=None, contribution=None)¶

Bases: Entity

Configuration file

class entity_management.simulation.CoreTraceCollection(*, name=None, description=None, wasAttributedTo=None, wasGeneratedBy=None, wasDerivedFrom=None, dateCreated=None, distribution=None, contribution=None, hadMember=None)¶

Bases: Entity

Collection of traces

Parameters:: hadMember (List[Trace]) – List of traces.

class entity_management.simulation.DetailedCircuit(*, name=None, description=None, wasAttributedTo=None, wasGeneratedBy=None, wasDerivedFrom=None, dateCreated=None, distribution=None, contribution=None, modelOf=None, brainLocation=None, subject=None, circuitBase=None, circuitConfigPath=None, circuitType=None, nodeCollection=None, edgeCollection=None, target=None, atlasRelease=None)¶

Bases: ModelInstance

Detailed circuit.

Parameters:

circuitBase (DataDownload) –
Path to the CircuitConfig.

Deprecated since version 1.2.7: Use circuitConfigPath instead.
circuitConfigPath (DataDownload) – Full path to the CircuitConfig including file name.
circuitType (str) –
Circuit type. For example:
- O1 circuit (e.g. circuit with central column + 6 surrounding columns)
- Atlas-based
nodeCollection (NodeCollection) – Node collection.
edgeCollection (EdgeCollection) – Edge collection.
target (Target) – Target.
atlasRelease (AtlasRelease) – AtlasRelease associated with the circuit.

class entity_management.simulation.DetailedCircuitValidation(*, name=None, status=None, used=None, generated=None, startedAtTime=None, endedAtTime=None, wasStartedBy=None, wasInformedBy=None, wasInfluencedBy=None, wasAssociatedWith=None)¶

Bases: Activity

Detailed circuit validation activity.

class entity_management.simulation.DetailedCircuitValidationReport(*, name=None, description=None, wasAttributedTo=None, wasGeneratedBy=None, wasDerivedFrom=None, dateCreated=None, contribution=None, distribution, image=None)¶

Bases: AnalysisReport

Detailed circuit validation report.

class entity_management.simulation.EModelGenerationShape(*, name=None, description=None, wasAttributedTo=None, wasGeneratedBy=None, wasDerivedFrom=None, dateCreated=None, distribution=None, contribution=None, activity)¶

Bases: Entity

EModel generation.

class entity_management.simulation.ETypeFeatureProtocol(*, name=None, description=None, wasAttributedTo=None, wasGeneratedBy=None, wasDerivedFrom=None, dateCreated=None, distribution=None, contribution=None)¶

Bases: Entity

Trace protocol.

class entity_management.simulation.EdgeCollection(*, name=None, description=None, wasAttributedTo=None, wasGeneratedBy=None, wasDerivedFrom=None, dateCreated=None, distribution=None, contribution=None, edgePopulation, synapseRelease)¶

Bases: Entity

Edge collection represents circuit connectivity(synapses, projections)

Parameters:

edgePopulation (core.Entity) – DataDownload providing path to the collection of nrn files or syn2.
synapseRelease (SynapseRelease) – Synapse release used for this edge collection.

class entity_management.simulation.ExperimentalCell(*, name, channel, description=None)¶

Bases: Frozen

Experimental cell.

Parameters:

name (str) – TODO.
channel (int) – TODO.
description (str) – TODO.

class entity_management.simulation.IonChannelMechanismRelease(*, name=None, description=None, wasAttributedTo=None, wasGeneratedBy=None, wasDerivedFrom=None, dateCreated=None, distribution=None, contribution=None, brainLocation=None, subject=None)¶

Bases: ModelRelease

Ion channel models release represents a collection of mod files.

class entity_management.simulation.ModelInstance(*, name=None, description=None, wasAttributedTo=None, wasGeneratedBy=None, wasDerivedFrom=None, dateCreated=None, distribution=None, contribution=None, modelOf=None, brainLocation=None, subject=None)¶

Bases: Entity

Abstract model instance.

Parameters:

modelOf (str) – Specifies the model.
brainLocation (BrainLocation) – Brain location.
subject (Subject) – Species ontology term.

class entity_management.simulation.ModelRelease(*, name=None, description=None, wasAttributedTo=None, wasGeneratedBy=None, wasDerivedFrom=None, dateCreated=None, distribution=None, contribution=None, brainLocation=None, subject=None)¶

Bases: Entity

Release base entity

class entity_management.simulation.ModelReleaseIndex(*, name=None, description=None, wasAttributedTo=None, wasGeneratedBy=None, wasDerivedFrom=None, dateCreated=None, distribution=None, contribution=None)¶

Bases: Entity

Index files attached to release entities

class entity_management.simulation.ModelScript(*, name=None, description=None, wasAttributedTo=None, wasGeneratedBy=None, wasDerivedFrom=None, dateCreated=None, distribution=None, contribution=None)¶

Bases: Entity

Base entity for the scripts attached to the model.

class entity_management.simulation.Morphology(*, name=None, description=None, wasAttributedTo=None, wasGeneratedBy=None, wasDerivedFrom=None, dateCreated=None, contribution=None, modelOf=None, brainLocation=None, subject=None, distribution=None, mType=None, isPartOf=None, view2d=None, view3d=None)¶

Bases: ModelInstance

Neuron morphology. Actual morphology file can be stored as the attachment of this entity or stored at the location provided in the distribution attribute.

Parameters:

distribution (DataDownload) – If morphology is stored at the external location distribution should provide the path to it.
mType (OntologyTerm) – Morphological cell type.
isPartOf (MorphologyRelease) – Release this morphology is part of.
view2d (Identifiable) – Morphology view in 2D.
view3d (Identifiable) – Morphology view in 3D.

class entity_management.simulation.MorphologyRelease(*, name=None, description=None, wasAttributedTo=None, wasGeneratedBy=None, wasDerivedFrom=None, dateCreated=None, contribution=None, brainLocation=None, subject=None, distribution, morphologyIndex=None)¶

Bases: ModelRelease

Morphology release can be located at the external location or constituted from individual Morphology entities.

Deprecated since version 1.0.19: Use ReconstructedCellCollection instead.

Parameters:

distribution (DataDownload) – Data download url should point to the v1 folder with morphologies in H5v1 format.
morphologyIndex (ModelReleaseIndex) – Morphology index is a compact representation of the morphology properties (MType, region ids) for the performance purposes. This attribute should provide a path to locate this file(such as neurondb.dat).

class entity_management.simulation.NodeCollection(*, name=None, description=None, wasAttributedTo=None, wasGeneratedBy=None, wasDerivedFrom=None, dateCreated=None, distribution=None, contribution=None, circuitCellProperties)¶

Bases: Entity

Node collection represents circuit nodes(positions, orientations)

Parameters:: circuitCellProperties (CircuitCellProperties) – Cell properties which are used in this node collection.

class entity_management.simulation.PlotCollection(*, name=None, description=None, wasAttributedTo=None, wasGeneratedBy=None, wasDerivedFrom=None, dateCreated=None, contribution=None, distribution=None)¶

Bases: MultiDistributionEntity

Collection of plots.

class entity_management.simulation.ReconstructedCellCollection(*, name=None, description=None, wasAttributedTo=None, wasGeneratedBy=None, wasDerivedFrom=None, dateCreated=None, distribution=None, contribution=None, brainLocation=None, subject=None, morphologyIndex=None)¶

Bases: ModelRelease

Reconstructed cell collection produced by the morphology release.

Parameters:

distribution (DataDownload) – Data download url should point to the v1 folder with morphologies in H5v1 format.
morphologyIndex (ModelReleaseIndex) – Morphology index is a compact representation of the morphology properties (MType, region ids) for the performance purposes. This attribute should provide a path to locate this file(such as neurondb.dat).

class entity_management.simulation.Report(*, name=None, description=None, wasAttributedTo=None, wasGeneratedBy=None, wasDerivedFrom=None, dateCreated=None, distribution=None, contribution=None)¶

Bases: Entity

Generic report.

class entity_management.simulation.Simulation(*, name=None, description=None, wasAttributedTo=None, wasGeneratedBy=None, wasDerivedFrom=None, dateCreated=None, distribution=None, contribution=None, parameter, startedAtTime=None, endedAtTime=None, status=None, log_url=None, config_file=None)¶

Bases: Entity

Simulation of the campaign entity.

Parameters:

parameter (dict) – Dictionary of specific coords within the campaign.
startedAtTime (datetime) – Start time.
endedAtTime (datetime) – End time.
status (str) – Status of the simulation.
log_url (str) – URL at which log file can be viewed.
() (config_file) – Full path to the simulation configuration file.

class entity_management.simulation.SimulationCampaign(*, name=None, description=None, wasAttributedTo=None, wasGeneratedBy=None, wasDerivedFrom=None, dateCreated=None, distribution=None, contribution=None, simulations, parameter={})¶

Bases: Entity

Simulation campaign entity that was executed.

Parameters:

simulations (DataDownload) – serialized simulations xarray.
parameter (dict) – Parameters corresponding to the specific simulation.

class entity_management.simulation.SimulationCampaignAnalysis(*, name=None, status=None, used=None, startedAtTime=None, endedAtTime=None, wasStartedBy=None, wasInformedBy=None, wasInfluencedBy=None, wasAssociatedWith=None, used_config, used_rev, generated=None)¶

Bases: BbpWorkflowActivity

Simulation campaign analysis entity.

class entity_management.simulation.SimulationCampaignConfiguration(*, name=None, description=None, wasAttributedTo=None, wasGeneratedBy=None, wasDerivedFrom=None, dateCreated=None, distribution=None, contribution=None, configuration, template, target=None)¶

Bases: Entity

Simulation campaign configuration entity.

Parameters:

configuration (DataDownload) – Dictionary of the parameters for the simulation campaign stored in a json file.
template (DataDownload) – BlueConfig template file.
target (DataDownload) – Optional user target file to include with the simulations.

class entity_management.simulation.SimulationCampaignExecution(*, name=None, status=None, used=None, startedAtTime=None, endedAtTime=None, wasStartedBy=None, wasInformedBy=None, wasInfluencedBy=None, wasAssociatedWith=None, used_config, used_rev, generated=None)¶

Bases: BbpWorkflowActivity

Simulation campagn execution activity.

class entity_management.simulation.SimulationCampaignGeneration(*, name=None, status=None, startedAtTime=None, endedAtTime=None, wasStartedBy=None, wasInformedBy=None, wasInfluencedBy=None, wasAssociatedWith=None, used=None, generated=None, used_config=None, used_rev=None)¶

Bases: BbpWorkflowActivity

Simulation campaign generation activity.

Parameters:

used (DetailedCircuit) – Detailed circuit used for the simulation campaign.
generated (SimulationCampaignConfiguration) – Configuration of the simulation campaign that is produced as a result of running this activity.

classmethod used(detailed_circuit, **kwargs)¶

List all sim campaign generation activities which used the specified detailed circuit.

Parameters:: detailed_circuit – Detailed circuit that was used in the simulation campaign.
Returns:: Iterator through the found resources.

class entity_management.simulation.SimulationCampaignReportCollection(*, name=None, description=None, wasAttributedTo=None, wasGeneratedBy=None, wasDerivedFrom=None, dateCreated=None, distribution=None, contribution=None, hadMember=None)¶

Bases: Entity

Simulation campaign.

Groups multiple simulations when same circuit is tested under different conditions.

Parameters:: hadMember (List[Report]) – Collection of simulation reports(spikes, soma voltage report).

class entity_management.simulation.SimulationConfiguration(*, name=None, description=None, wasAttributedTo=None, wasGeneratedBy=None, wasDerivedFrom=None, dateCreated=None, distribution=None, contribution=None, circuit=None)¶

Bases: Entity

Simulation configuration in terms of BlueConfig.

Parameters:: circuit (DetailedCircuit) – reference to the detailed circuit.

class entity_management.simulation.SingleCellSimulationTrace(*, name=None, description=None, wasAttributedTo=None, wasGeneratedBy=None, wasDerivedFrom=None, dateCreated=None, distribution=None, contribution=None)¶

Bases: Entity

Single cell simulation trace file

class entity_management.simulation.SingleCellTraceGeneration(*, name=None, status=None, used=None, generated=None, startedAtTime=None, endedAtTime=None, wasStartedBy=None, wasInformedBy=None, wasInfluencedBy=None, wasAssociatedWith=None, description=None)¶

Bases: Activity

Single cell simulation trace genaration activity

class entity_management.simulation.SpikeReport(*, name=None, description=None, wasAttributedTo=None, wasGeneratedBy=None, wasDerivedFrom=None, dateCreated=None, contribution=None, distribution)¶

Bases: Report

Spike report.

Parameters:: distribution (DataDownload) – Spike report file out.dat.

class entity_management.simulation.SynapseRelease(*, name=None, description=None, wasAttributedTo=None, wasGeneratedBy=None, wasDerivedFrom=None, dateCreated=None, contribution=None, brainLocation=None, subject=None, distribution)¶

Bases: ModelRelease

Synapse release represents a collection of mod files.

Parameters:: distribution (DataDownload) – Location of the synapse release/mod files.

class entity_management.simulation.Target(*, name=None, description=None, wasAttributedTo=None, wasGeneratedBy=None, wasDerivedFrom=None, dateCreated=None, contribution=None, distribution)¶

Bases: Entity

Location of the text file defining cell targets (i.e. named collections of cell GIDs)

Parameters:: distribution (DataDownload) – Location of the target file.

class entity_management.simulation.Threshold(*, name=None, description=None, wasAttributedTo=None, wasGeneratedBy=None, wasDerivedFrom=None, dateCreated=None, distribution=None, contribution=None)¶

Bases: Entity

Threshold.

class entity_management.simulation.TraceCollection(*, name=None, description=None, wasAttributedTo=None, wasGeneratedBy=None, wasDerivedFrom=None, dateCreated=None, distribution=None, contribution=None, hadMember=None)¶

Bases: Entity

Collection of traces

Parameters:: hadMember (List[Trace]) – List of traces.

class entity_management.simulation.TraceFeature(*, name=None, description=None, wasAttributedTo=None, wasGeneratedBy=None, wasDerivedFrom=None, dateCreated=None, distribution=None, contribution=None)¶

Bases: Entity

Trace feature.

class entity_management.simulation.TraceFeatureExtraction(*, name=None, status=None, startedAtTime=None, endedAtTime=None, wasStartedBy=None, wasInformedBy=None, wasInfluencedBy=None, wasAssociatedWith=None, used, generated=None)¶

Bases: Activity

Trace feature extraction activity.

Parameters:

used (List[Union[CoreTraceCollection, BluePyEfeConfiguration]]) – Used resources.
generated (BluePyEfeFeatures) – Extracted features.

class entity_management.simulation.VariableReport(*, name=None, description=None, wasAttributedTo=None, wasGeneratedBy=None, wasDerivedFrom=None, dateCreated=None, distribution=None, contribution=None, variable, target)¶

Bases: Report

Variable report.

Parameters:

variable (str) – Variable shape(voltage, curent).
target (str) – The variable report target (compartment, soma, summation, extra cellular recording).