biosimulators_utils.model_lang.xpp package¶
Submodules¶
biosimulators_utils.model_lang.xpp.data_model module¶
Data model for XPP simulation methods
- Author
Jonathan Karr <karr@mssm.edu>
- Date
2021-08-08
- Copyright
2021, Center for Reproducible Biomedical Modeling
- License
MIT
biosimulators_utils.model_lang.xpp.utils module¶
Utilities for working with XPP models
- Author
Jonathan Karr <karr@mssm.edu>
- Date
2021-08-08
- Copyright
2021, Center for Reproducible Biomedical Modeling
- License
MIT
- biosimulators_utils.model_lang.xpp.utils.get_parameters_variables_outputs_for_simulation(model_filename, model_language, simulation_type, algorithm_kisao_id=None, set_filename=None, parameter_filename=None, initial_conditions_filename=None, native_ids=False, native_data_types=False, 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 or directory of XPP ODE, set, parameters, and initial conditions filesmodel_language (
str
) – model language (e.g.,urn:sedml:language:xpp
)simulation_type (
types.Type
) – subclass ofSimulation
algorithm_kisao_id (
str
, optional) – KiSAO id of the algorithm for simulating the model (e.g.,KISAO_0000019
for CVODE)set_filename (
str
, optional) – path to XPP set fileparameter_filename (
str
, optional) – path to XPP parameters fileinitial_conditions_filename (
str
, optional) – path to XPP initial conditions filenative_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 generatornative_data_types (
bool
, optional) – whether to return new_values in their native data typesinclude_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
ofSimulation
: simulations of the modellist
ofVariable
: possible observables for a simulation of the modellist
ofPlot
: possible plots of the results of a simulation of the model- Return type
list
ofModelAttributeChange
biosimulators_utils.model_lang.xpp.validation module¶
Methods for validating XPP files
- Author
Jonathan Karr <karr@mssm.edu>
- Date
2021-08-06
- Copyright
2021, Center for Reproducible Biomedical Modeling
- License
MIT
- biosimulators_utils.model_lang.xpp.validation.get_xpp_input_configuration_from_directory(dirname)[source]¶
Get input file configuration from a directory of files
*.ode
: Main model model*.set
: Set file*.par
: Parameters file*.ic
: Initial conditions file
- Parameters
dirname (
str
) – path to directory of XPP files- Returns
str
: path to main model filestr
: path to set filestr
: path to parameters filestr
: path to initial conditions filestr
: name of a set to usestr
: name of a set not to use
- Return type
tuple
- biosimulators_utils.model_lang.xpp.validation.validate_model(filename, set_filename=None, parameter_filename=None, initial_conditions_filename=None, name=None)[source]¶
Check that a model is valid
- Parameters
filename (
str
) – path to model file or directory with.ode
and possibly set (.set
), parameter (.par
), andd initial conditions (.ic
) filesset_filename (
str
, optional) – path to XPP set fileparameter_filename (
str
, optional) – path to XPP parameters fileinitial_conditions_filename (
str
, optional) – path to XPP initial conditions filename (
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)dict
: values of parameters of initial conditions of variables
- Return type
tuple