AMICI Python API

Modules

amici	AMICI
amici.amici
amici.sbml_import	SBML Import This module provides all necessary functionality to import a model specified in the Systems Biology Markup Language (SBML).
amici.pysb_import	PySB Import This module provides all necessary functionality to import a model specified in the pysb.core.Model format.
amici.petab_import	PEtab Import Import a model in the petab (https://github.com/PEtab-dev/PEtab) format into AMICI.
amici.petab_import_pysb	PySB-PEtab Import Import a model in the PySB-adapted petab (https://github.com/PEtab-dev/PEtab) format into AMICI.
amici.petab_objective	PEtab Objective Functionality related to running simulations or evaluating the objective function as defined by a PEtab problem
amici.petab_simulate	PEtab Simulate Functionality related to the use of AMICI for simulation with PEtab's Simulator class.
amici.import_utils	Miscellaneous functions related to model import, independent of any specific model format
amici.ode_export	C++ Export This module provides all necessary functionality specify an ODE model and generate executable C++ simulation code. The user generally won't have to directly call any function from this module as this will be done by amici.pysb_import.pysb2amici(), amici.sbml_import.SbmlImporter.sbml2amici() and amici.petab_import.import_model()
amici.plotting	Plotting Plotting related functions
amici.pandas	Pandas Wrappers This module contains convenience wrappers that allow for easy interconversion between C++ objects from amici.amici and pandas DataFrames
amici.logging	Logging This module provides custom logging functionality for other amici modules
amici.gradient_check	Finite Difference Check This module provides functions to automatically check correctness of amici computed sensitivities using finite difference approximations
amici.parameter_mapping	Parameter mapping