AMICI
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.
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.
Papers
AMICI: high-performance sensitivity analysis for large ordinary differential equation models
Optimization and profile calculation of ODE models using second order adjoint sensitivity analysis
Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks
Parameter estimation for dynamical systems with discrete events and logical operations