biosimulators_xpp package

biosimulators_xpp.exec_sed_doc(doc, working_dir, base_out_path, rel_out_path=None, apply_xml_model_changes=False, 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_xpp.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 XPP doesn’t support * Task requires an algorithm that XPP doesn’t support

biosimulators_xpp.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_xpp.get_simulator_version()[source]

Get the installed version of XPP

Returns

version

Return type

str

biosimulators_xpp.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_xpp.core module

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

Author

Jonathan Karr <karr@mssm.edu>

Date

2021-08-06

Copyright

2021, Center for Reproducible Biomedical Modeling

License

MIT

biosimulators_xpp.core.exec_sed_doc(doc, working_dir, base_out_path, rel_out_path=None, apply_xml_model_changes=False, 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_xpp.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 XPP doesn’t support * Task requires an algorithm that XPP doesn’t support

biosimulators_xpp.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_xpp.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_xpp.data_model module

Data model

Author

Jonathan Karr <karr@mssm.edu>

Date

2021-08-07

Copyright

2021, Center for Reproducible Biomedical Modeling

License

MIT

biosimulators_xpp.utils module

Utility methods

Author

Jonathan Karr <karr@mssm.edu>

Date

2021-08-06

Copyright

2021, Center for Reproducible Biomedical Modeling

License

MIT

biosimulators_xpp.utils.apply_model_changes(xpp_model, sed_changes)[source]

Validate the SED variables for a XPP model

Parameters

  • xpp_model (dict) – XPP model

  • sed_changes (list of ModelAttributeChange) – SED model attribute changes

biosimulators_xpp.utils.exec_xpp_simulation(sim_filename, simulation, set_filename=None, overwrite_parameters=True, overwrite_initial_conditions=True, overwrite_method=True)[source]

Execute an XPP simulation, optionally overwriting its default parameters and initial conditions

Parameters

  • sim_filename (str) – path to the XPP file

  • simulation (dict) – simulation parameters, initial conditions, and method to override defaults

  • set_filename (str, optional) – path to XPP set file

  • overwrite_parameters (bool, optional) – whether to overwrite the default parameters

  • overwrite_initial_conditions (bool, optional) – whether to overwrite the default initial conditions

  • overwrite_method (bool, optional) – whether to overwrite the default simulation method and its settings

Returns

simulation results

Return type

pandas.DataFrame

biosimulators_xpp.utils.get_results_of_sed_variables(sed_simulation, xpp_results, sed_variables)[source]

Get the results of a list of SED variables

Parameters

  • sed_simulation (UniformTimeCourseSimulation) – SED simulation

  • xpp_results (pandas.DataFrame) – raw results generated by XPP

  • sed_variables (list of Variable) – SED variables

Returns

results

Return type

VariableResults

biosimulators_xpp.utils.get_simulation_method_kisao_map()[source]

Invert the map from KiSAO ids to simulation methods

Returns

inverted map

Return type

dict

biosimulators_xpp.utils.set_up_simulation(sed_sim, xpp_sim, config=None)[source]

Apply SED simulation settings to the configuration of a XPP simulation

Parameters

  • sed_sim (UniformTimeCourseSimulation) – SED simulation

  • xpp_sim (dict) – XPP simulation

  • config (Config, optional) – configuration

Returns

  • dict: XPP simulation

  • str: KiSAO id of the algorithm to execute

Return type

tuple

biosimulators_xpp.utils.validate_variables(xpp_model, sed_variables)[source]

Validate the SED variables for a XPP model

Parameters

  • xpp_model (dict) – XPP model

  • sed_variables (list of Variable) – SED variables

biosimulators_xpp.utils.write_method_to_xpp_simulation_file(simulation_method, in_filename, out_filename)[source]

Overwrite the simulation method settings in an XPP simulation file

Parameters

  • simulation_method (dict) – dictionary of simulation method settings

  • in_filename (str) – base XPP simulation file

  • out_filename (str) – path to save modified XPP simulation file

biosimulators_xpp.utils.write_xpp_initial_conditions_file(initial_conditions, filename)[source]

Write a set of initial conditions to a XPP initial conditions (.ic) file

Parameters

  • initial_conditions (collections.OrderedDict) – dictionary that maps the id of each parameter to its value

  • filename (str) – path to save the initial conditions

biosimulators_xpp.utils.write_xpp_parameter_file(parameters, filename)[source]

Write a set of parameters to a XPP parameter (.par) file

Parameters

  • parameters (dict) – dictionary that maps the id of each parameter to its value

  • filename (str) – path to save the parameters