biosimulators_bionetgen package¶

biosimulators_bionetgen.get_simulator_version()[source]¶

Get the version of BioNetGen

Returns: version
Return type: str

Submodules¶

biosimulators_bionetgen.config module¶

Configuration for BioSimulators-BioNetGen

Author: Jonathan Karr <karr@mssm.edu>
Date: 2021-01-05
Copyright: 2020-2021, Center for Reproducible Biomedical Modeling
License: MIT

class biosimulators_bionetgen.config.Config[source]¶

Bases: object

Configuration

bionetgen_path[source]¶

path to BioNetGen executable

Type: str

biosimulators_bionetgen.core module¶

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

Author: Jonathan Karr <karr@mssm.edu>
Author: Ali Sinan Saglam <als251@pitt.edu>
Date: 2021-01-05
Copyright: 2020-2021, Center for Reproducible Biomedical Modeling
License: MIT

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

Execute a task and save its results

Parameters

task (Task) – SED 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_bionetgen.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_bionetgen.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_bionetgen.data_model module¶

Data structures for representing BNGL models

Author: Jonathan Karr <karr@mssm.edu>
Date: 2021-01-05
Copyright: 2020-2021, Center for Reproducible Biomedical Modeling
License: MIT

class biosimulators_bionetgen.data_model.Model[source]¶

Bases: collections.OrderedDict

A BNGL model: a collection of model blocks

is_equal(other)[source]¶

Determine whether two models are semantically equivalent

Parameters: other (Model) – second model
Returns: whether the models are semantically equivalent
Return type: bool

class biosimulators_bionetgen.data_model.ModelBlock(iterable=(), /)[source]¶

Bases: list

A “block” or section of a model such as parameters or ‘molecule types’

is_equal(other)[source]¶

Determine whether two model blocks are semantically equivalent

Parameters: other (ModelBlock) – second model block
Returns: whether the model blocks are semantically equivalent
Return type: bool

class biosimulators_bionetgen.data_model.Task(model=None, actions=None)[source]¶

Bases: object

A BNGL task

Attributes: model (Model): model actions (list of str): actions such as simulations

is_equal(other)[source]¶

Determine whether two model blocks are semantically equivalent

Parameters: other (ModelBlock) – second model block
Returns: whether the model blocks are semantically equivalent
Return type: bool

biosimulators_bionetgen.io module¶

Methods for reading BNGL models

Author: Jonathan Karr <karr@mssm.edu>
Date: 2021-01-05
Copyright: 2020-2021, Center for Reproducible Biomedical Modeling
License: MIT

biosimulators_bionetgen.io.read_simulation_results(filename)[source]¶

Read the predicted time courses of the observables of a simulation

Parameters: filename (str) – path to simulation results in BioNetGen’s gdat format
Returns: predicted time courses of the observables
Return type: pandas.DataFrame

biosimulators_bionetgen.io.read_task(filename)[source]¶

Read a BNGL task from a file.

Parameters: filename (str) – path to the task
Returns: task
Return type: Task
Raises: ValueError – if the file is invalid

biosimulators_bionetgen.io.write_task(task, filename)[source]¶

Write a BNGL task to a file

Parameters

task (Task) – task
filename (str) – path to save the model

biosimulators_bionetgen.utils module¶

Utilities for working with BioNetGen

Author: Jonathan Karr <karr@mssm.edu>
Date: 2021-01-05
Copyright: 2020-2021, Center for Reproducible Biomedical Modeling
License: MIT

biosimulators_bionetgen.utils.add_model_attribute_change_to_task(task, change, preprocessed_change=None)[source]¶

Encode SED model attribute changes into a BioNetGen task

Compartment sizes: targets should follow the pattern compartments.<compartment_id>.size
Function expressions: targets should follow the pattern functions.<function_id>.expression
Initial species counts: targets should follow the pattern species.<species_id>.count
Parameter values: targets should follow the pattern parameters.<parameter_id>.value

Parameters

task (Task) – BioNetGen task
change (ModelAttributeChange) – model attribute change
preprocessed_change (dict) – preprocessed information about the change

Raises

ValueError – if a target of a change is not valid

biosimulators_bionetgen.utils.add_variables_to_model(model, variables)[source]¶

Encode SED variables into observables in a BioNetGen task

Parameters

model (Model) – model
variables (list of Variable) – desired variables

Raises

NotImplementedError – if BioNetGen doesn’t support the symbol or target of a variable

biosimulators_bionetgen.utils.create_actions_for_simulation(simulation, config=None)[source]¶

Create BioNetGen actions for a SED simulation

Parameters

simulation (UniformTimeCourseSimulation) – SED simulation
config (Config, optional) – configuration

Raises

NotImplementedError – if BioNetGen doesn’t support the request algorithm or algorithm parameters

Returns

list of str: actions for SED simulation
str: KiSAO id of the algorithm that will be executed

Return type

tuple

biosimulators_bionetgen.utils.exec_bionetgen_task(task, verbose=True)[source]¶

Execute a task and return the predicted values of the observables

Parameters

task (Task) – task
verbose (bool, optional) – whether to display diagnostic information

Returns

predicted values of the observables

Return type

pandas.DataFrame

Raises

Exception – if the task fails

biosimulators_bionetgen.utils.get_variables_results_from_observable_results(observable_results, variables)[source]¶

Get the predicted values of the desired variables

Parameters

observable_results (pandas.DataFrame) – predicted values of the observables of a simulation
variables (list of Variable) – desired variables

Returns

predicted values of the desired variables

Return type

VariableResults

Raises

NotImplementedError – if an unsupported symbol is requested
ValueError – if an undefined target is requested

biosimulators_bionetgen.utils.preprocess_model_attribute_change(task, change)[source]¶

Process a model change

Compartment sizes: targets should follow the pattern compartments.<compartment_id>.size
Function expressions: targets should follow the pattern functions.<function_id>.expression
Initial species counts: targets should follow the pattern species.<species_id>.count
Parameter values: targets should follow the pattern parameters.<parameter_id>.value

Parameters

task (Task) – BioNetGen task
change (ModelAttributeChange) – model attribute change

Returns

processed information about the model change

Return type

dict

Raises

ValueError – if a target of a change is not valid

biosimulators_bionetgen.warnings module¶

Warnings

Author: Jonathan Karr <karr@mssm.edu>
Date: 2021-01-05
License: MIT

exception biosimulators_bionetgen.warnings.BioNetGenWarning[source]¶

Bases: UserWarning

Base class for warnings

exception biosimulators_bionetgen.warnings.IgnoredBnglFileContentWarning[source]¶

Bases: biosimulators_bionetgen.warnings.BioNetGenWarning

Warning for content of a BNGL file that is ignored