biosimulators_utils.model_lang.sbml package#

Submodules#

biosimulators_utils.model_lang.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.model_lang.sbml.utils.get_package_namespace(package: str, namespaces: Dict[str | None, str]) → Tuple[str, str][source]#

Get the prefix and URI for the namespace of an SBML package

Parameters:

package (str) – SBML package id (e.g., fbc, qual)
namespaces (dict) – dictionary that maps namespace prefixes to URIs

Returns:

str: prefix
str: URI

Return type:

tuple

biosimulators_utils.model_lang.sbml.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, include_local_parameters_in_task_level_simulation_parameters=False, include_model_parameters_in_simulation_variables=False, include_compartment_sizes_in_simulation_variables=False, include_reaction_fluxes_in_kinetic_simulation_variables=False, validate=True, validate_consistency=True, config=None)[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_kisao_id (str, optional) – KiSAO id of the algorithm for simulating the model (e.g., KISAO_0000019 for CVODE)
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_value in their native data types
include_local_parameters_in_task_level_simulation_parameters (bool, optional) – whether to include the local parameters among the returned SED model changes for SED tasks
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
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_reaction_fluxes_in_kinetic_simulation_variables (bool, optional) – whether to include reaction fluxes among the returned SED variables for kinetic simulations
validate (str, optional) – whether to validate the model
validate_consistency (str, optional) – whether to check the consistency of the model
config (Config, optional) – whether to fail on missing includes

Returns:

possible attributes of a model that can be changed and their default values list of Simulation: simulation 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.sbml.validation module#

Utilities for validating SBML models

Author:: Jonathan Karr <karr@mssm.edu>
Date:: 2021-04-13
License:: MIT

biosimulators_utils.model_lang.sbml.validation.validate_model(filename, name=None, validate_consistency=True, config=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
validate_consistency (str, optional) – whether to check the consistency of the model
config (Config, optional) – whether to fail on missing includes

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)
libsbml.SBMLDocument: model

Return type:

tuple