biosimulators_gillespy2 package

biosimulators_gillespy2.exec_sed_doc(doc, working_dir, base_out_path, rel_out_path=None, apply_xml_model_changes=True, log=None, indent=0, pretty_print_modified_xml_models=False, log_level=StandardOutputErrorCapturerLevel.c, config=None)

Execute the tasks specified in a SED document and generate the specified outputs

Parameters

• doc (SedDocument or str) – SED document or a path to SED-ML file which defines a SED document

• working_dir (str) – working directory of the SED document (path relative to which models are located)

• base_out_path (str) –

  path to store the outputs

  • CSV: directory in which to save outputs to files {base_out_path}/{rel_out_path}/{report.id}.csv

  • HDF5: directory in which to save a single HDF5 file ({base_out_path}/reports.h5), with reports at keys {rel_out_path}/{report.id} within the HDF5 file

• rel_out_path (str, optional) – path relative to base_out_path to store the outputs

• apply_xml_model_changes (bool, optional) – if True, apply any model changes specified in the SED-ML file before calling task_executer.

• log (SedDocumentLog, optional) – log of the document

• indent (int, optional) – degree to indent status messages

• pretty_print_modified_xml_models (bool, optional) – if True, pretty print modified XML models

• log_level (StandardOutputErrorCapturerLevel, optional) – level at which to log output

• config (Config, optional) – BioSimulators common configuration

• simulator_config (SimulatorConfig, optional) – tellurium configuration

Returns

• ReportResults: results of each report

• SedDocumentLog: log of the document

Return type

tuple

biosimulators_gillespy2.exec_sed_task(task, variables, preprocessed_task=None, log=None, config=None)

Execute a task and save its results

Parameters

• task (Task) – task

• variables (list of Variable) – variables that should be recorded

• preprocessed_task (dict, optional) – preprocessed information about the task, including possible model changes and variables. This can be used to avoid repeatedly executing the same initialization for repeated calls to this method.

• log (TaskLog, optional) – log for the task

• config (Config, optional) – BioSimulators common configuration

Returns

VariableResults: results of variables TaskLog: log

Return type

tuple

Raises

• ValueError – if the task or an aspect of the task is not valid, or the requested output variables could not be recorded

• NotImplementedError – if the task is not of a supported type or involves an unsuported feature

biosimulators_gillespy2.exec_sedml_docs_in_combine_archive(archive_filename, out_dir, config=None)

Execute the SED tasks defined in a COMBINE/OMEX archive and save the outputs

Parameters

• archive_filename (str) – path to COMBINE/OMEX archive

• out_dir (str) –

  path to store the outputs of the archive

  • CSV: directory in which to save outputs to files { out_dir }/{ relative-path-to-SED-ML-file-within-archive }/{ report.id }.csv

  • HDF5: directory in which to save a single HDF5 file ({ out_dir }/reports.h5), with reports at keys { relative-path-to-SED-ML-file-within-archive }/{ report.id } within the HDF5 file

• config (Config, optional) – BioSimulators common configuration

Returns

• SedDocumentResults: results

• CombineArchiveLog: log

Return type

tuple

biosimulators_gillespy2.get_simulator_version()

Get the version of GillesPy2

Returns

version

Return type

str

biosimulators_gillespy2.preprocess_sed_task(task, variables, config=None)

Preprocess a SED task, including its possible model changes and variables. This is useful for avoiding repeatedly initializing tasks on repeated calls of exec_sed_task.

Parameters

• task (Task) – task

• variables (list of Variable) – variables that should be recorded

• config (Config, optional) – BioSimulators common configuration

Returns

preprocessed information about the task

Return type

dict

Submodules

biosimulators_gillespy2.core module

Methods for using GillesPy2 to execute SED tasks in COMBINE archives and save their outputs

Author

Jonathan Karr <karr@mssm.edu>

Author

Bilal Shaikh <bilalshaikh42@gmail.com>

Date

2020-12-09

Copyright

2020, Center for Reproducible Biomedical Modeling

License

MIT

biosimulators_gillespy2.core.exec_sed_doc(doc, working_dir, base_out_path, rel_out_path=None, apply_xml_model_changes=True, log=None, indent=0, pretty_print_modified_xml_models=False, log_level=StandardOutputErrorCapturerLevel.c, config=None)

Execute the tasks specified in a SED document and generate the specified outputs

Parameters

• doc (SedDocument or str) – SED document or a path to SED-ML file which defines a SED document

• working_dir (str) – working directory of the SED document (path relative to which models are located)

• base_out_path (str) –

  path to store the outputs

  • CSV: directory in which to save outputs to files {base_out_path}/{rel_out_path}/{report.id}.csv

  • HDF5: directory in which to save a single HDF5 file ({base_out_path}/reports.h5), with reports at keys {rel_out_path}/{report.id} within the HDF5 file

• rel_out_path (str, optional) – path relative to base_out_path to store the outputs

• apply_xml_model_changes (bool, optional) – if True, apply any model changes specified in the SED-ML file before calling task_executer.

• log (SedDocumentLog, optional) – log of the document

• indent (int, optional) – degree to indent status messages

• pretty_print_modified_xml_models (bool, optional) – if True, pretty print modified XML models

• log_level (StandardOutputErrorCapturerLevel, optional) – level at which to log output

• config (Config, optional) – BioSimulators common configuration

• simulator_config (SimulatorConfig, optional) – tellurium configuration

Returns

• ReportResults: results of each report

• SedDocumentLog: log of the document

Return type

tuple

biosimulators_gillespy2.core.exec_sed_task(task, variables, preprocessed_task=None, log=None, config=None)

Execute a task and save its results

Parameters

• task (Task) – task

• variables (list of Variable) – variables that should be recorded

• preprocessed_task (dict, optional) – preprocessed information about the task, including possible model changes and variables. This can be used to avoid repeatedly executing the same initialization for repeated calls to this method.

• log (TaskLog, optional) – log for the task

• config (Config, optional) – BioSimulators common configuration

Returns

VariableResults: results of variables TaskLog: log

Return type

tuple

Raises

• ValueError – if the task or an aspect of the task is not valid, or the requested output variables could not be recorded

• NotImplementedError – if the task is not of a supported type or involves an unsuported feature

biosimulators_gillespy2.core.exec_sedml_docs_in_combine_archive(archive_filename, out_dir, config=None)

Execute the SED tasks defined in a COMBINE/OMEX archive and save the outputs

Parameters

• archive_filename (str) – path to COMBINE/OMEX archive

• out_dir (str) –

  path to store the outputs of the archive

  • CSV: directory in which to save outputs to files { out_dir }/{ relative-path-to-SED-ML-file-within-archive }/{ report.id }.csv

  • HDF5: directory in which to save a single HDF5 file ({ out_dir }/reports.h5), with reports at keys { relative-path-to-SED-ML-file-within-archive }/{ report.id } within the HDF5 file

• config (Config, optional) – BioSimulators common configuration

Returns

• SedDocumentResults: results

• CombineArchiveLog: log

Return type

tuple

biosimulators_gillespy2.core.preprocess_sed_task(task, variables, config=None)

Preprocess a SED task, including its possible model changes and variables. This is useful for avoiding repeatedly initializing tasks on repeated calls of exec_sed_task.

Parameters

• task (Task) – task

• variables (list of Variable) – variables that should be recorded

• config (Config, optional) – BioSimulators common configuration

Returns

preprocessed information about the task

Return type

dict

biosimulators_gillespy2.data_model module

Data model for GillesPy2 algorithms and their parameters

Author

Jonathan Karr <karr@mssm.edu>

Date

2020-12-09

Copyright

2020, Center for Reproducible Biomedical Modeling

License

MIT

class biosimulators_gillespy2.data_model.Algorithm(name, solver, parameters=None, **solver_args)

Bases: object

Simulation algorithm

name

name

Type

str

solver

solver

Type

type

solver_args

solver arguments

Type

dict

parameters

dictionary that maps KiSAO ids to AlgorithmParameters

Type

dict

class biosimulators_gillespy2.data_model.AlgorithmParameter(name, key, data_type, default)

Bases: object

Simulation algorithm parameter

name

name

Type

str

key

key

Type

str

data_type

data type

Type

type

default

defualt value

Type

object

set_value(solver_args, str_value)

Apply the value of a parameter to a data structure of solver arguments

Parameters

• solver_args (dict) – solver arguments

• str_value (string) – string representation of parameter value

Raises

• ValueError – if str_value is not a valid string representation of the data type of the parameter

• NotImplementedError – if str_value is not a valid value of an enumerated parameter

class biosimulators_gillespy2.data_model.HybridTauIntegrationMethod(value)

Bases: str, enum.Enum

Hybrid tau integration method

BDF = 'KISAO_0000288'

LSODA = 'KISAO_0000088'

RK23 = 'KISAO_0000537'

RK45 = 'KISAO_0000032'

Radau = 'KISAO_0000304'

class biosimulators_gillespy2.data_model.VodeMethod(value)

Bases: str, enum.Enum

VODE method

adams = 'KISAO_0000289'

bdf = 'KISAO_0000288'