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.
- Automated generation of model specific native C code
- Modular structure for efficient compilation of systems with thousands of states and parameters
- First and second order forward sensitivity analysis
- Adjoint sensitivity analysis
- Steady state sensitivity analysis
- Time-to-event sensitivities
- Parameter dependent bolus injections
AMICI is a software package for MATLAB. It requires the Symbolic Math Toolbox and a correctly configured C Compiler.
Fabian Froehlich - email@example.com
Jan Hasenauer - firstname.lastname@example.org