brainsimulation

Metadata for model building, simulation and validation.

class fairgraph.brainsimulation.ModelProject(name, owners, authors, description, date_created, private, collab_id=None, alias=None, organization=None, pla_components=None, brain_region=None, species=None, celltype=None, abstraction_level=None, model_of=None, old_uuid=None, parents=None, instances=None, images=None, id=None, instance=None)

Bases: fairgraph.base.KGObject, fairgraph.base.HasAliasMixin

Representation of a neuroscience model or modelling project.

We distinguish a model in an abstract sense (this class), which may have multiple parameterizations and multiple implementations, from a specific version and parameterization of a model - see ModelInstance and ModelScript

Parameters:

• name (str) –
• owners (Person) –
• authors (Person) –
• description (str) –
• date_created (datetime) –
• private (bool) –
• collab_id (str) –
• alias (str) –
• organization (Organization) –
• pla_components (str) –
• brain_region (BrainRegion) –
• species (Species) –
• celltype (CellType) –
• abstraction_level (AbstractionLevel) –
• model_of (ModelScope) –
• old_uuid (str) –
• parents (ModelProject) –
• instances (ModelInstance, MEModel) –
• images (dict) –

class fairgraph.brainsimulation.ModelInstance(name, main_script, version, timestamp=None, brain_region=None, species=None, model_of=None, release=None, part_of=None, description=None, parameters=None, old_uuid=None, alternate_of=None, id=None, instance=None)

Bases: fairgraph.base.KGObject

A specific implementation, code version and parameterization of a model.

See also: ModelProject, MEModel, ModelScript

Parameters:

• name (str) –
• brain_region (BrainRegion) –
• species (Species) –
• model_of (CellType, BrainRegion) –
• main_script (ModelScript) –
• release (str) –
• version (str) –
• timestamp (datetime) –
• part_of (KGObject) –
• description (str) –
• parameters (str) –
• old_uuid (str) –
• alternate_of (KGObject) –

class fairgraph.brainsimulation.MEModel(name, e_model, morphology, main_script, version, timestamp=None, brain_region=None, species=None, model_of=None, release=None, part_of=None, description=None, parameters=None, old_uuid=None, alternate_of=None, id=None, instance=None)

Bases: fairgraph.brainsimulation.ModelInstance

A specific implementation, code version and parameterization of a single neuron model

with a defined morphology (M) and electrical (E) behaviour.

This is a specialized sub-class of ModelInstance.

See also: ModelProject, ModelScript, Morphology, EModel

Parameters:

• name (str) –
• brain_region (BrainRegion) –
• species (Species) –
• model_of (CellType, BrainRegion) –
• main_script (ModelScript) –
• release (str) –
• version (str) –
• timestamp (datetime) –
• part_of (KGObject) –
• description (str) –
• parameters (str) –
• old_uuid (str) –
• alternate_of (KGObject) –
• morphology (Morphology) –
• e_model (EModel) –

class fairgraph.brainsimulation.Morphology(name, cell_type=None, morphology_file=None, distribution=None, id=None, instance=None)

Bases: fairgraph.base.KGObject

The morphology of a single neuron model, typically defined as a set of cylinders or

truncated cones connected in a tree structure.

Parameters:

• name (str) –
• cell_type (CellType) –
• distribution (Distribution) –

class fairgraph.brainsimulation.ModelScript(name, code_location=None, code_format=None, license=None, distribution=None, id=None, instance=None)

Bases: fairgraph.base.KGObject

Code or markup defining all or part of a model.

See also: ModelInstance, MEModel, EModel

Parameters:

• name (str) –
• code_format (str) –
• license (str) –
• distribution (Distribution) –

class fairgraph.brainsimulation.EModel(name, main_script=None, version=None, timestamp=None, brain_region=None, species=None, model_of=None, release=None, part_of=None, description=None, parameters=None, old_uuid=None, id=None, instance=None)

Bases: fairgraph.brainsimulation.ModelInstance

The electrical component of an MEModel

Parameters:

• name (str) –
• brain_region (BrainRegion) –
• species (Species) –
• model_of (CellType, BrainRegion) –
• main_script (ModelScript) –
• release (str) –
• version (str) –
• timestamp (datetime) –
• part_of (KGObject) –
• description (str) –
• parameters (str) –
• old_uuid (str) –

class fairgraph.brainsimulation.ValidationTestDefinition(id=None, instance=None, **properties)

Bases: fairgraph.base.KGObject, fairgraph.base.HasAliasMixin

Definition of a model validation test.

See also: ValidationScript, ValidationActivity, ValidationResult

Parameters:

• name (str) –
• authors (Person) –
• description (str) –
• date_created (date, datetime) –
• alias (str) –
• brain_region (BrainRegion) –
• species (Species) –
• celltype (CellType) –
• test_type (str) –
• age (Age) –
• reference_data (KGObject) –
• data_type (str) –
• recording_modality (str) –
• score_type (str) –
• status (str) –
• old_uuid (str) –

class fairgraph.brainsimulation.ValidationScript(id=None, instance=None, **properties)

Bases: fairgraph.base.KGObject

Code implementing a particular model validation test.

See also: ValidationTestDefinition, ValidationActivity,

ValidationResult

Parameters:

• name (str) –
• date_created (date, datetime) –
• repository (IRI) –
• version (str) –
• description (str) –
• parameters (str) –
• test_class (str) –
• test_definition (ValidationTestDefinition) –
• old_uuid (str) –

class fairgraph.brainsimulation.ValidationResult(id=None, instance=None, **properties)

Bases: fairgraph.base.KGObject

The results of running a model validation test.

Including a numerical score, and optional additional data.

See also: ValidationTestDefinition, ValidationScript, ValidationActivity.

Parameters:

• name (str) –
• generated_by (ValidationActivity) –
• description (str) –
• score (float, int) –
• normalized_score (float, int) –
• passed (bool) –
• timestamp (date, datetime) –
• additional_data (KGObject) –
• old_uuid (str) –
• collab_id (str) –
• hash (str) –

class fairgraph.brainsimulation.ValidationActivity(id=None, instance=None, **properties)

Bases: fairgraph.base.KGObject

Record of the validation of a model against experimental data.

Links a ModelInstance, a ValidationTestDefinition and a reference data set to a ValidationResult.

Parameters:

• model_instance (ModelInstance, MEModel) –
• test_script (ValidationScript) –
• reference_data (Collection) –
• timestamp (datetime) –
• result (ValidationResult) –
• started_by (Person) –
• end_timestamp (datetime) –

class fairgraph.brainsimulation.Simulation(id=None, instance=None, **properties)

Bases: fairgraph.base.KGObject

Parameters:

• name (str) –
• description (str) –
• identifier (str) –
• model_instance (ModelInstance, MEModel) –
• config (SimulationConfiguration) –
• timestamp (datetime) –
• result (SimulationOutput) –
• started_by (Person) –
• end_timestamp (datetime) –
• computing_environment (ComputingEnvironment) –
• status (str) –
• resource_usage (float) –
• tags (str) –
• job_id (str) –

class fairgraph.brainsimulation.SimulationConfiguration(name, config_file=None, description=None, identifier=None, id=None, instance=None)

Bases: fairgraph.base.KGObject

Parameters:

• name (str) –
• identifier (str) –
• description (str) –
• config_file (Distribution, str) –

save(client)

docstring

class fairgraph.brainsimulation.SimulationOutput(name, identifier=None, result_file=None, generated_by=None, derived_from=None, data_type=None, variable=None, target=None, description=None, timestamp=None, brain_region=None, species=None, celltype=None, id=None, instance=None)

Bases: fairgraph.base.KGObject

Parameters:

• name (str) –
• description (str) –
• identifier (str) –
• result_file (Distribution, str) –
• generated_by (Simulation) –
• derived_from (KGObject) –
• target (str) –
• data_type (str) –
• timestamp (datetime) –
• brain_region (BrainRegion) –
• species (Species) –
• celltype (CellType) –

save(client)

docstring

fairgraph.brainsimulation.list_kg_classes()

List all KG classes defined in this module

fairgraph.brainsimulation.use_namespace(namespace)

Set the namespace for all classes in this module.