biosimulators_ginsim package

biosimulators_ginsim.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)[source]

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_ginsim.exec_sed_task(task, variables, preprocessed_task=None, log=None, config=None)[source]

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

NotImplementedError –

  • Task requires a time course that GINsim doesn’t support * Task requires an algorithm that GINsim doesn’t support

biosimulators_ginsim.exec_sedml_docs_in_combine_archive(archive_filename, out_dir, config=None)[source]

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_ginsim.get_simulator_version()[source]

Get the version of GINsim

Returns

version

Return type

str

biosimulators_ginsim.preprocess_sed_task(task, variables, config=None)[source]

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_ginsim.core module

BioSimulators-compliant command-line interface to the GINsim simulation program.

Author

Jonathan Karr <karr@mssm.edu>

Date

2021-07-07

Copyright

2021, Center for Reproducible Biomedical Modeling

License

MIT

biosimulators_ginsim.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)[source]

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_ginsim.core.exec_sed_task(task, variables, preprocessed_task=None, log=None, config=None)[source]

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

NotImplementedError –

  • Task requires a time course that GINsim doesn’t support * Task requires an algorithm that GINsim doesn’t support

biosimulators_ginsim.core.exec_sedml_docs_in_combine_archive(archive_filename, out_dir, config=None)[source]

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_ginsim.core.preprocess_sed_task(task, variables, config=None)[source]

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_ginsim.data_model module

Data model

Author

Jonathan Karr <karr@mssm.edu>

Date

2021-07-07

Copyright

2021, Center for Reproducible Biomedical Modeling

License

MIT

class biosimulators_ginsim.data_model.UpdatePolicy(value)[source]

Bases: str, enum.Enum

Update policy

asynchronous = 'asynchronous'[source]
complete = 'complete'[source]
sequential = 'sequential'[source]
synchronous = 'synchronous'[source]

biosimulators_ginsim.utils module

Utility methods

Author

Jonathan Karr <karr@mssm.edu>

Date

2021-07-07

Copyright

2021, Center for Reproducible Biomedical Modeling

License

MIT

biosimulators_ginsim.utils.exec_simulation(method_name, model, args=None)[source]

Execute a task

Parameters

  • method_name (str) – name of the biolqm simulation/analysis method

  • model (py4j.java_gateway.JavaObject) – model

  • args (list of str, optional) – argument to method

Returns

result of method for model and args

Return type

list of dict

biosimulators_ginsim.utils.get_variable_results(variables, model_language, target_xpath_ids, simulation, raw_results)[source]

Get the result of each SED-ML variable

Parameters

  • variables (list of Variable) – variables

  • model_language (str) – model language

  • target_xpath_ids (dict) – dictionary that maps XPaths to the SBML qualitative ids of the corresponding objects

  • simulation (Simulation) – simulation

  • raw_results (list of dict) – predicted simulatioin states

Returns

result of each SED-ML variable

Return type

VariableResults

biosimulators_ginsim.utils.get_variable_target_xpath_ids(variables, model_etree)[source]

Get the SBML-qual id for each XML XPath target of a SED-ML variable

Parameters

  • variables (list of Variable) – variables of data generators

  • model_etree (lxml.etree._ElementTree) – element tree for model

Returns

dictionary that maps each variable target to the id of the

corresponding qualitative species

Return type

dict

biosimulators_ginsim.utils.read_model(filename, language)[source]

Read a model

Parameters

language (ModelLanguage) – language

Returns

model

Return type

py4j.java_gateway.JavaObject

biosimulators_ginsim.utils.set_up_simulation(simulation, config=None)[source]

Set up an analysis

Parameters

  • simulation (Simulation) – analysis

  • config (Config, optional) – configuration

Returns

  • str: KiSAO of algorithm to execute

  • str: name of the biolqm simulation/analysis method

  • types.LambdaType of Simulation -> list of str: arguments for simulation method

Return type

tuple

biosimulators_ginsim.utils.validate_simulation(simulation)[source]

Validate a simulation

Parameters

simulation (Simulation) – simulation

Returns

  • nested list of str: nested list of errors (e.g., required ids missing or ids not unique)

  • nested list of str: nested list of errors (e.g., required ids missing or ids not unique)

Return type

tuple

biosimulators_ginsim.utils.validate_time_course(simulation)[source]

Validate a time course

Parameters

simulation (UniformTimeCourseSimulation) – simulation

Returns

  • nested list of str: nested list of errors (e.g., required ids missing or ids not unique)

  • nested list of str: nested list of errors (e.g., required ids missing or ids not unique)

Return type

tuple

biosimulators_ginsim.utils.validate_variables(variables, model, model_language, target_xpath_ids, simulation)[source]

Get the result of each SED-ML variable

Parameters

  • variables (list of Variable) – variables

  • model (py4j.java_gateway.JavaObject) – bioLQM model

  • model_language (str) – model language

  • target_xpath_ids (dict) – dictionary that maps XPaths to the SBML qualitative ids of the corresponding objects

  • simulation (Simulation) – analysis