AMICI: high-performance sensitivity analysis for large ordinary differential equation models

Fröhlich F, Weindl D, Schälte Y, Pathirana D, Paszkowski Ł, Lines GT, Stapor P, Hasenauer J, Bioinformatics 37 (20) :3676-3677 (2021).
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# Abstract

Ordinary differential equation models facilitate the understanding of cellular signal transduction and other biological processes. However, for large and comprehensive models, the computational cost of simulating or calibrating can be limiting. AMICI is a modular toolbox implemented in C++/Python/MATLAB that provides efficient simulation and sensitivity analysis routines tailored for scalable, gradient-based parameter estimation and uncertainty quantification.