AMICI Python API

Modules

amici	Top-level module.
amici.importers.sbml	SBML Import This module provides all necessary functionality to import a model specified in the Systems Biology Markup Language (SBML).
amici.importers.sbml.splines	Splines This module provides helper functions for reading/writing splines with AMICI annotations from/to SBML files and for adding such splines to the AMICI C++ code.
amici.importers.pysb	PySB Import This module provides all necessary functionality to import a model specified in the pysb.core.Model format.
amici.importers.bngl	BNGL Import This module provides all necessary functionality to import a model specified in the BNGL format.
amici.importers.antimony	Import of Antimony models into AMICI.
amici.importers.petab	PEtab import related code.
amici.importers.petab.v1	PEtab v1 import related code.
amici.importers.utils	Miscellaneous functions related to model import, independent of any specific model format
amici.sim.jax	Functionality for simulating JAX-based AMICI models.
amici.sim.sundials	Functionality for simulating AMICI models using SUNDIALS solvers.
amici.sim.sundials.plotting	Plotting Plotting related functions
amici.sim.sundials.gradient_check	Finite Difference Check This module provides functions to automatically check correctness of amici computed sensitivities using finite difference approximations
amici.sim.sundials.petab	Functionality for simulating PEtab problems.
amici.sim.sundials.petab.v1
amici.adapters.fiddy	Adapters for using AMICI with the fiddy package for finite difference checks.