amici.petab_import_pysb

PySB-PEtab Import

Import a model in the PySB-adapted petab (https://github.com/PEtab-dev/PEtab) format into AMICI.

Classes

PysbPetabProblem([pysb_model])

Representation of a PySB-model-based PEtab problem

Functions Summary

create_dummy_sbml(pysb_model[, observable_ids])	Create SBML dummy model for to use PySB models with PEtab.
import_model_pysb(petab_problem[, …])	Create AMICI model from PySB-PEtab problem

Functions

amici.petab_import_pysb.create_dummy_sbml(pysb_model, observable_ids=None)

Create SBML dummy model for to use PySB models with PEtab.

Model must at least contain PEtab problem parameter and noise parameters for observables.

Parameters

• pysb_model (pysb.core.Model) – PySB model

• observable_ids (typing.Optional[typing.Iterable[str]]) – Observable IDs

Return type

typing.Tuple[libsbml.Model, libsbml.SBMLDocument]

Returns

A dummy SBML model and document.

amici.petab_import_pysb.import_model_pysb(petab_problem, model_output_dir=None, verbose=True, **kwargs)

Create AMICI model from PySB-PEtab problem

Parameters

• petab_problem (amici.petab_import_pysb.PysbPetabProblem) – PySB PEtab problem

• model_output_dir (typing.Optional[str]) – 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.

• kwargs – Additional keyword arguments to be passed to amici.pysb_import.pysb2amici().

Return type

None