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 filemodel_language (
str
) – model language (e.g.,urn:sedml:language:sbml
)simulation_type (
types.Type
) – subclass ofSimulation
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 variablesinclude_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
ofVariable
: possible observables for a simulation of the model- Return type
list
ofModelAttributeChange
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 modelname (
str
, optional) – name of model for use in error messages
- Returns
nested
list
ofstr
: nested list of errors (e.g., required ids missing or ids not unique)nested
list
ofstr
: nested list of errors (e.g., required ids missing or ids not unique)
- Return type
tuple