3.1.12. biosimulators_utils.sbml package

3.1.12.1. Submodules

3.1.12.2. biosimulators_utils.sbml.utils module

Utilities for working with SBML models

Author

Jonathan Karr <karr@mssm.edu>

Date

2021-04-05

Copyright

2021, Center for Reproducible Biomedical Modeling

License

MIT

biosimulators_utils.sbml.utils.get_parameters_variables_for_simulation(model_filename, model_language, simulation_type, algorithm, include_compartment_sizes_in_simulation_variables=False, include_model_parameters_in_simulation_variables=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:sbml)

  • simulation_type (types.Type) – subclass of Simulation

  • algorithm (str) – KiSAO id of the algorithm for simulating the model (e.g., KISAO_0000019 for CVODE)

  • include_compartment_sizes_in_simulation_variables (bool, optional) – whether to include the sizes of non-constant SBML compartments with assignment rules among the returned SED variables

  • include_model_parameters_in_simulation_variables (bool, optional) – whether to include the values of non-constant SBML parameters with assignment rules among the returned SED variables

Returns

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

Return type

list of ModelAttributeChange

3.1.12.3. biosimulators_utils.sbml.validation module

Utilities for validating SBML models

Author

Jonathan Karr <karr@mssm.edu>

Date

2021-04-13

Copyright

2021, Center for Reproducible Biomedical Modeling

License

MIT

biosimulators_utils.sbml.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)

Return type

tuple