AMICI Python API

Modules

amici

AMICI

amici.amici

Core C++ bindings This module encompasses the complete public C++ API of AMICI, which was exposed via swig. All functions listed here are directly accessible in the main amici package, i.e., amici.amici.ExpData is available as amici.ExpData. Usage of functions and classes from the base amici package is generally recommended as they often include convenience wrappers that avoid common pitfalls when accessing C++ types from python and implement some nonstandard type conversions.

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.bngl_import

BNGL Import This module provides all necessary functionality to import a model specified in the BNGL 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.ode_model

Objects for AMICI's internal ODE model representation

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

amici.conserved_quantities_demartino

amici.conserved_quantities_rref

Find conserved quantities deterministically