biosimulators_tellurium package#

class biosimulators_tellurium.PlottingEngine(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]#

Bases: str, Enum

Engine that tellurium uses for plottting

matplotlib = 'matplotlib'[source]#

plotly = 'plotly'[source]#

class biosimulators_tellurium.PreprocesssedTask(road_runners: dict, solvers: dict, model_change_target_tellurium_id_maps: dict, algorithm_kisao_ids: dict, variable_target_tellurium_observable_maps: dict)[source]#

Bases: object

Processed information about a SED task

road_runners[source]#

Road Runner instances with model, per task

Type:: roadrunner.RoadRunner

solver[source]#

solver, per task

Type:: roadrunner.Integrator or roadrunner.SteadyStateSolver

model_change_target_tellurium_id_map[source]#

dictionaries that map the targets of changes to their corresponding tellurium identifiers (tuples of their type and index within their type), per task

Type:: dict

algorithm_kisao_id[source]#

dictionaries of KiSAO id of algorithm to execute, per task

Type:: str

variable_target_tellurium_observable_maps[source]#

dictionary of dictionaries that map tuples of variable targets and symbols to their corresponding tellurium observable identifiers, per task

Type:: dict

algorithm_kisao_ids: dict[source]#

model_change_target_tellurium_id_maps: dict[source]#

road_runners: dict[source]#

solvers: dict[source]#

variable_target_tellurium_observable_maps: dict[source]#

class biosimulators_tellurium.SedmlInterpreter(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]#

Bases: str, Enum

Code that interprets SED-ML

biosimulators = 'biosimulators'[source]#

tellurium = 'tellurium'[source]#

biosimulators_tellurium.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, simulator_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_tellurium.exec_sed_task(task, variables, preprocessed_task=None, log=None, config=None, simulator_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 (PreprocessedTask, 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
simulator_config (SimulatorConfig, optional) – tellurium 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_tellurium.exec_sedml_docs_in_combine_archive(archive_filename, out_dir, config=None, simulator_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
simulator_config (SimulatorConfig, optional) – tellurium configuration

Returns:

SedDocumentResults: results
CombineArchiveLog: log

Return type:

tuple

biosimulators_tellurium.get_simulator_version()[source]#

Get the version of tellurium

Returns:: version
Return type:: str

biosimulators_tellurium.preprocess_sed_task(task, variables, config=None, simulator_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
simulator_config (SimulatorConfig, optional) – tellurium configuration

Returns:

preprocessed information about the task

Return type:

PreprocessedTask

Submodules#

biosimulators_tellurium.config module#

Configuration

Author:: Jonathan Karr <karr@mssm.edu>
Date:: 2021-01-04
Copyright:: 2021, Center for Reproducible Biomedical Modeling
License:: MIT

class biosimulators_tellurium.config.Config[source]#

Bases: object

Configuration

sedml_interpreter[source]#

SED-ML interpreter

Type:: SedmlInterpreter

plotting_engine[source]#

plotting engine

Type:: PlottingEngine

biosimulators_tellurium.core module#

Methods for using tellurium to execute SED tasks in COMBINE/OMEX archives and save their outputs

Author:: Jonathan Karr <karr@mssm.edu>
Date:: 2021-01-04
Copyright:: 2020-2021, Center for Reproducible Biomedical Modeling
License:: MIT

biosimulators_tellurium.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, simulator_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_tellurium.core.exec_sed_task(task, variables, preprocessed_task=None, log=None, config=None, simulator_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 (PreprocessedTask, 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
simulator_config (SimulatorConfig, optional) – tellurium 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_tellurium.core.exec_sedml_docs_in_combine_archive(archive_filename, out_dir, config=None, simulator_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
simulator_config (SimulatorConfig, optional) – tellurium configuration

Returns:

SedDocumentResults: results
CombineArchiveLog: log

Return type:

tuple

biosimulators_tellurium.core.preprocess_sed_task(task, variables, config=None, simulator_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
simulator_config (SimulatorConfig, optional) – tellurium configuration

Returns:

preprocessed information about the task

Return type:

PreprocessedTask

biosimulators_tellurium.data_model module#

Data model for using tellurium to execute SED-ML documents

Author:: Jonathan Karr <karr@mssm.edu>
Date:: 2021-08-23
License:: MIT

class biosimulators_tellurium.data_model.PlottingEngine(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]#

Bases: str, Enum

Engine that tellurium uses for plottting

matplotlib = 'matplotlib'[source]#

plotly = 'plotly'[source]#

class biosimulators_tellurium.data_model.PreprocesssedTask(road_runners: dict, solvers: dict, model_change_target_tellurium_id_maps: dict, algorithm_kisao_ids: dict, variable_target_tellurium_observable_maps: dict)[source]#

Bases: object

Processed information about a SED task

road_runners[source]#

Road Runner instances with model, per task

Type:: roadrunner.RoadRunner

solver[source]#

solver, per task

Type:: roadrunner.Integrator or roadrunner.SteadyStateSolver

model_change_target_tellurium_id_map[source]#

dictionaries that map the targets of changes to their corresponding tellurium identifiers (tuples of their type and index within their type), per task

Type:: dict

algorithm_kisao_id[source]#

dictionaries of KiSAO id of algorithm to execute, per task

Type:: str

variable_target_tellurium_observable_maps[source]#

dictionary of dictionaries that map tuples of variable targets and symbols to their corresponding tellurium observable identifiers, per task

Type:: dict

algorithm_kisao_ids: dict[source]#

model_change_target_tellurium_id_maps: dict[source]#

road_runners: dict[source]#

solvers: dict[source]#

variable_target_tellurium_observable_maps: dict[source]#

class biosimulators_tellurium.data_model.SedmlInterpreter(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]#

Bases: str, Enum

Code that interprets SED-ML

biosimulators = 'biosimulators'[source]#

tellurium = 'tellurium'[source]#