AMICI provides a multi-language (Python, C++, Matlab) interface to the :term:`SUNDIALS` solvers :term:`CVODES` (for :term:`ODE`s) and :term:`IDAS` (for :term:`DAE`s). AMICI allows the user to read differential equation models specified as :term:`SBML` or :term:`PySB` and automatically compiles such models into Python modules, C++ libraries or .mex simulation files (Matlab).
In contrast to the (no longer maintained) sundialsTB Matlab interface, all necessary functions are transformed into native C++ code, which allows for a significantly faster simulation.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 it is also applicable to a wider range of differential equation constrained optimization problems.
- :term:`SBML` import
- :term:`PySB` import
- Generation of C++ code for model simulation and sensitivity computation
- Access to and high customizability of :term:`CVODES` and :term:`IDAS` solver
- Python, C++, Matlab interface
- Sensitivity analysis
- forward
- steady state
- adjoint
- first- and second-order (second-order Matlab-only)
- Pre-equilibration and pre-simulation conditions
- Support for discrete events and logical operations
The AMICI workflow starts with importing a model from either :term:`SBML` (Matlab, Python), :term:`PySB` (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 Matlab .mex file and is then used for model simulation.
The functionality of the Python, Matlab and C++ interfaces slightly differ, as shown in the following table:
| Feature \ Interface | Python | C++ | Matlab |
|---|---|---|---|
| :term:`SBML` import | yes (:ref:`details <amici_python_sbml_support>`) | no | yes (<=R2017b) |
| :term:`PySB` import | yes | no | no |
| :term:`DAE` import | no | no | yes |
| Forward sensitivities | yes | yes | yes |
| Adjoint sensitivities | yes | yes | yes |
| Steadystate sensitivities | yes | yes | yes |
| Second-order sensitivities | no | no | yes |
| Events | yes | yes | yes |
| :term:`preequilibration` | yes | yes | yes |
| :term:`presimulation` | yes | yes | no |