biosimulators_amici package#

biosimulators_amici.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_amici.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

biosimulators_amici.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:

log

Return type:

CombineArchiveLog

biosimulators_amici.get_simulator_version()[source]#

Get the version of AMICI

Returns:

version

Return type:

str

biosimulators_amici.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_amici.core module#

Methods for executing SED tasks in COMBINE archives and saving their outputs

Author:

Jonathan Karr <karr@mssm.edu>

Date:

2020-12-16

Copyright:

2020, BioSimulators Team

License:

MIT

biosimulators_amici.core.cleanup_model(model_name, model_dir)[source]#

Cleanup model created with import_model_from_sbml

Parameters:

  • model_name (str) – name of the Python module for model

  • model_dir (str) – directory which contains the files for the model

biosimulators_amici.core.config_task(task, model, config=None)[source]#

Configure an AMICI model for a SED task

Parameters:

  • task (Task) – task

  • model (amici.amici.ModelPtr) – AMICI model

  • config (Config) – configuration

Returns:

  • amici.amici.SolverPtr: solver

  • str: KiSAO id of the solver

  • dict: dictionary of arguments for the solver

Return type:

tuple

Raises:

  • NotImplementedError – the task involves and unsupported algorithm or parameter

  • ValueError – the task involves an invalid value of a parameter

biosimulators_amici.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_amici.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

biosimulators_amici.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:

log

Return type:

CombineArchiveLog

biosimulators_amici.core.exec_task(model, solver)[source]#

Execute a SED task for an AMICI model and return its results

Parameters:

  • model (amici.amici.ModelPtr) – AMICI model

  • solver (amici.amici.SolverPtr) – solver

Returns:

simulation results

Return type:

amici.numpy.ReturnDataView

biosimulators_amici.core.extract_variables_from_results(variables, variable_observable_map, results)[source]#

Extract data generator variables from results

Parameters:

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

  • variable_observable_map (dict) – dictionary that maps the targets and symbols of variables to AMICI observables

  • results (amici.numpy.ReturnDataView) – simulation results

Returns:

results of variables

Return type:

VariableResults

biosimulators_amici.core.import_model_from_sbml(filename, variables)[source]#

Generate an AMICI model from a SBML file

Parameters:

  • filename (str) – path to SBML file

  • variables (list of str) – ids of SBML objects to observe

Returns:

  • amici.amici.ModelPtr: AMICI model

  • libsbml.Model: SBML model

  • str: name of the Python module for model

  • str: directory which contains the files for the model

Return type:

tuple

biosimulators_amici.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_amici.core.validate_model_changes(model, changes, change_sbml_id_map)[source]#

Validate model changes

Parameters:

  • model (amici.amici.ModelPtr) – AMICI model

  • changes (list of ModelAttributeChange) – model changes

  • change_sbml_id_map (dict of str to str) – dictionary that maps each XPath to the value of the attribute of the object in the XML file that matches the XPath

Returns:

dictionary that maps the targets of changes to AMICI setters

Return type:

dict

Raises:

ValueError – if a change could not be applied

biosimulators_amici.core.validate_task(task, variables, config=None)[source]#

Validate that AMICI can support a SED task

Parameters:

  • task (Task) – task

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

  • config (Config, optional) – BioSimulators common configuration

Returns:

  • dict of str to str: dictionary that maps the XPath of each target of each

    model change to the SBML id of the associated model object

  • dict of str to str: dictionary that maps the XPath of each variable target

    to the SBML id of the associated model object

Return type:

tuple

biosimulators_amici.core.validate_variables(model, variables, variable_target_sbml_id_map)[source]#

Validate variables

Parameters:

  • model (amici.amici.ModelPtr) – AMICI model

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

  • variable_target_sbml_id_map (dict of str to str) – dictionary that maps each XPath to the value of the attribute of the object in the XML file that matches the XPath

Returns:

dictionary that maps the targets and symbols of variables to AMICI observables

Return type:

dict

Raises:

  • NotImplementedError – if a symbol could not be recorded

  • ValueError – if a target could not be recorded

biosimulators_amici.data_model module#

Mappings from KiSAO terms to methods and arguments

Author:

Jonathan Karr <karr@mssm.edu>

Date:

2020-12-16

Copyright:

2020, BioSimulators Team

License:

MIT