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AMICI

Advanced Matlab Interface to CVODES and IDAS

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AMICI (Advanced MATLAB Interface for CVODES and IDAS) is a MATLAB interface for the SUNDIALS solvers CVODES (for ordinary differential equations) and IDAS (for algebraic differential equations). AMICI allows the user to specify differential equation models in terms of symbolic variables in MATLAB and automatically compiles such models as .mex simulation files. In contrast to the SUNDIALSTB interface, all necessary functions are transformed into native C code, which allows for a significantly faster compilation.

The compiled .mex simulation files support various sensitivity methods thereby provides routines for efficient gradient computation taylored for parameter estimation of biochemical reaction models. Yet, AMICI is also applicable to a wider range of differential equation constrained optimization problems.

Features

Requirements

AMICI is a software package for MATLAB. It requires the Symbolic Math Toolbox and a correctly configured C Compiler.

Documentation

The documentation of AMICI is available as PDF or as HTML The documentation includes an Installation Guide, a Model Specification Guide, several Examples and a detailed Code Overview.

Support

Fabian Froehlich - fabian.froehlich@helmholtz-muenchen.de

Jan Hasenauer - jan.hasenauer@helmholtz-muenchen.de