AMICI
Advanced Multilanguage Interface for CVODES and IDAS
About AMICI

AMICI provides a multilanguage (Python, C++, Matlab) interface for the SUNDIALS solvers CVODES (for ordinary differential equations) and IDAS (for algebraic differential equations). AMICI allows the user to read differential equation models specified as SBML and automatically compiles such models as .mex simulation files, C++ executables or python modules. In contrast to the SUNDIALSTB interface, all necessary functions are transformed into native C++ code, which allows for a significantly faster simulation. Beyond forward integration, the compiled simulation file also allows for forward sensitivity analysis, steady state sensitivity analysis and adjoint sensitivity analysis for likelihood based output functions.

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.

Online documentation is available as github-pages.

Publications

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Fröhlich, F., Kaltenbacher, B., Theis, F. J., & Hasenauer, J. (2017). Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks. Plos Computational Biology, 13(1), e1005331. doi: 10.1371/journal.pcbi.1005331

Fröhlich, F., Theis, F. J., Rädler, J. O., & Hasenauer, J. (2017). Parameter estimation for dynamical systems with discrete events and logical operations. Bioinformatics, 33(7), 1049-1056. doi: 10.1093/bioinformatics/btw764

Full list

Interfaces & workflow

The AMICI workflow starts with importing a model from either SBML (Matlab, Python) or a Matlab definition of the model (Matlab-only). From this input, all equations for model simulation are derived symbolically and C++ code is generated. This code is then compiled into a C++ library, a Python module, or a Matab mex file and is then used for model simulation.

AMICI workflow

Current build status

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