AMICI is a software tool for efficient simulation and sensitivity of ODE models.
It provides forward, adjoint and steadystate sensitivity analysis with support
for models with parameter dependent events. To
Users can import models and problems specified using the
Systems Biology Markup Language, the BioNetGen Laguage, PySB or PETab.
Moreover, scalable gradient computation routines – facilitated by the
implemented sensitivity routines, are available from pyPESTO to provide
scalable gradient computation routines.
The software is written in python and c++ and also provides a MATLAB interface and a
Julia interface is currently under development. It is jointly developed with the Hasenauer Lab.
Development of AMICI is described in the following papers: