amici.petab.sbml_import
Functions
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Create AMICI model from PEtab problem |
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Log some model quantities |
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Turn a SBML species into parameters and replace species references inside the model instance. |
- amici.petab.sbml_import.import_model_sbml(sbml_model=None, condition_table=None, observable_table=None, measurement_table=None, petab_problem=None, model_name=None, model_output_dir=None, verbose=True, allow_reinit_fixpar_initcond=True, validate=True, non_estimated_parameters_as_constants=True, output_parameter_defaults=None, discard_sbml_annotations=False, **kwargs)[source]
Create AMICI model from PEtab problem
- Parameters:
sbml_model (
typing.Union[str,pathlib.Path,libsbml.Model]) – PEtab SBML model or SBML file name. Deprecated, passpetab_probleminstead.condition_table (
typing.Union[str,pathlib.Path,pandas.core.frame.DataFrame,None]) – PEtab condition table. If provided, parameters from there will be turned into AMICI constant parameters (i.e. parameters w.r.t. which no sensitivities will be computed). Deprecated, passpetab_probleminstead.observable_table (
typing.Union[str,pathlib.Path,pandas.core.frame.DataFrame,None]) – PEtab observable table. Deprecated, passpetab_probleminstead.measurement_table (
typing.Union[str,pathlib.Path,pandas.core.frame.DataFrame,None]) – PEtab measurement table. Deprecated, passpetab_probleminstead.petab_problem (
petab.problem.Problem) – PEtab problem.model_name (
typing.Optional[str]) – Name of the generated model. If model file name was provided, this defaults to the file name without extension, otherwise the SBML model ID will be used.model_output_dir (
typing.Union[str,pathlib.Path,None]) – Directory to write the model code to. Will be created if doesn’t exist. Defaults to current directory.verbose (
typing.Union[bool,int,None]) – Print/log extra information.allow_reinit_fixpar_initcond (
bool) – Seeamici.de_export.ODEExporter. Must be enabled if initial states are to be reset after preequilibration.validate (
bool) – Whether to validate the PEtab problemnon_estimated_parameters_as_constants – Whether parameters marked as non-estimated in PEtab should be considered constant in AMICI. Setting this to
Truewill reduce model size and simulation times. If sensitivities with respect to those parameters are required, this should be set toFalse.output_parameter_defaults (
typing.Optional[dict[str,float]]) – Optional default parameter values for output parameters introduced in the PEtab observables table, in particular for placeholder parameters. dictionary mapping parameter IDs to default values.discard_sbml_annotations (
bool) – Discard information contained in AMICI SBML annotations (debug).kwargs – Additional keyword arguments to be passed to
amici.sbml_import.SbmlImporter.sbml2amici().
- Return type:
- Returns:
The created
amici.sbml_import.SbmlImporterinstance.