AMICI Python API

Modules

`amici`	AMICI
`amici.amici`	Core C++ bindings
`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`	PEtab import related code.
`amici.petab.conditions`	PEtab conditions to AMICI ExpDatas.
`amici.petab.import_helpers`	General helper functions for PEtab import.
`amici.petab.parameter_mapping`
`amici.petab.petab_import`	PEtab Import Import a model in the petab (https://github.com/PEtab-dev/PEtab) format into AMICI.
`amici.petab.pysb_import`	PySB-PEtab Import Import a model in the PySB-adapted petab (https://github.com/PEtab-dev/PEtab) format into AMICI.
`amici.petab.sbml_import`
`amici.petab.simulations`	Functionality related to simulation of PEtab problems.
`amici.petab.simulator`	PEtab Simulator Functionality related to the use of AMICI for simulation with petab.Simulator.
`amici.petab_import`	PEtab Import Import a model in the petab (https://github.com/PEtab-dev/PEtab) format into AMICI.
`amici.petab_import_pysb`	PEtab import for PySB models
`amici.petab_objective`	Evaluate a PEtab objective function.
`amici.petab_simulate`	Simulate a PEtab problem
`amici.import_utils`	Miscellaneous functions related to model import, independent of any specific model format
`amici.jax`	JAX
`amici.de_export`	C++ Export This module provides all necessary functionality to specify a differential equation 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.de_model`	Symbolic differential equation model.
`amici.de_model_components`	Objects for AMICI's internal differential equation 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 between AMICI and PEtab.
`amici.conserved_quantities_demartino`
`amici.conserved_quantities_rref`	Find conserved quantities deterministically
`amici.numpy`	C++ object views This module provides views on C++ objects for efficient access.
`amici.sbml_utils`	SBML Utilities This module provides helper functions for working with SBML.
`amici.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.