amici 0.6a3

Advanced multi-language Interface to CVODES and IDAS

About AMICI

AMICI provides a multilanguage 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 fiels, c++ executables and 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.

Current build status

Linux/Mac: Coverage:

FAQ

Q: My model fails to build.

A: Remove the corresponding model directory located in AMICI/models/yourmodelname and compile again.

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Q: It still does not compile.

A: Make an issue and we will have a look.

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Q: I get an out of memory error while compiling my model on a Windows machine.

A: This may be due to an old compiler version. See issue #161 for instructions on how to install a new compiler.

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Q: The simulation/sensitivities I get are incorrect.

A: There are some known issues, especially with adjoint sensitivities, events and DAEs. If your particular problem is not featured in the issues list, please add it!