biosimulators_utils.model_lang.rba package

Submodules

biosimulators_utils.model_lang.rba.utils module

Utilities for working with RBA models

Author

Jonathan Karr <karr@mssm.edu>

Date

2021-08-28

Copyright

2021, Center for Reproducible Biomedical Modeling

License

MIT

biosimulators_utils.model_lang.rba.utils.get_parameters_variables_outputs_for_simulation(model_filename, model_language, simulation_type, algorithm_kisao_id=None, change_level=<class 'biosimulators_utils.sedml.data_model.SedDocument'>, native_ids=False, native_data_types=False)[source]

Get the possible observables for a simulation of a model

Parameters
  • model_filename (str) – path to model file

  • model_language (str) – model language (e.g., urn:sedml:language:rba)

  • simulation_type (types.Type) – subclass of Simulation

  • algorithm_kisao_id (str, optional) – KiSAO id of the algorithm for simulating the model (e.g., KISAO_0000669 for RBA)

  • change_level (types.Type, optional) – level at which model changes will be made (SedDocument or Task)

  • native_ids (bool, optional) – whether to return the raw id and name of each model component rather than the suggested name for the variable of an associated SED-ML data generator

  • native_data_types (bool, optional) – whether to return new_values in their native data types

Returns

possible attributes of a model that can be changed and their default values list of Simulation: simulations of the model list of Variable: possible observables for a simulation of the model list of Plot: possible plots of the results of a simulation of the model

Return type

list of ModelAttributeChange

biosimulators_utils.model_lang.rba.validation module

Methods for validating RBA files

Author

Jonathan Karr <karr@mssm.edu>

Date

2021-08-28

Copyright

2021, Center for Reproducible Biomedical Modeling

License

MIT

biosimulators_utils.model_lang.rba.validation.validate_model(filename, name=None)[source]

Check that a model is valid

Parameters
  • filename (str) – path to model

  • name (str, optional) – name of model for use in error messages

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)

  • rba.model.RbaModel: RBA model

Return type

tuple