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Provides a MATLAB interface for the SUNDIALS solvers CVODES and IDAS. 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 interface was designed to provide routines for efficient gradient computation in parameter estimation of biochemical reaction models but is also applicable to a wider range of differential equation constrained optimization problems.

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AMICI versioning

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AMICI classification

AMICI specifications

Software type:
Toolkit
Restrictions to use:
None
Programming languages:
C, C++, MATLAB
Computer skills:
Advanced
Interface:
Command line interface
Operating system:
Unix/Linux, Mac OS, Windows
License:
BSD 2-clause “Simplified” License
Stability:
Stable
Source code URL:
https://github.com/ICB-DCM/AMICI

Credits

Publications

  • (Fröhlich et al., 2016) Parameter estimation for dynamical systems with discrete events and logical operations. Bioinformatics.
    PMID: 28040696

Institution(s)

Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany; Center for Mathematics, Technische Universität München, Garching, Germany; Faculty of Physics, Ludwig-Maximilians Universität, München, Germany

Funding source(s)

This work was supported by the German Research Foundation (DFG) through the Graduate School of Quantitative Biosciences Munich (QBM), the German Federal Ministry of Education and Research (BMBF) within the SYS-Stomach project (Grant No. 01ZX1310B) and the Postdoctoral Fellowship Program of the Helmholtz Zentrum München.

Link to literature

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