CERENA (ChEmical REaction Network Analyzer) is a MATLAB-based toolbox for the simulation and analysis of chemical reaction networks using approximations of the Chemical Master Equation solution statistics.
CERENA includes a variety of methods for the analysis of stochastic biochemical reaction networks, focusing on mesoscopic and macroscopic descriptions, namely Reaction Rate Equation (RRE), Method of Moments (MM), and System Size Expansion (SSE).
Also, CERENA provides the first implementation of the Method of Conditional Moments (MCM), and offers a wide range of options, amongst others variable truncation orders and different closure schemes.
- Automatic import from Systems Biology Markup Language (SBML)
- Export to Data2Dynamics software for parameter estimation
- Derivation and solution of 1st and 2nd-order forward sensitivity equations for all ODE-based and DAE-based models
- Derivation and solution of adjoint sensitivity equations for all ODE-based models
- Various moment closure schemes, and variable truncation order, for MM and MCM
- Broad applicability by allowing for multiple compartments, non- mass action kinetics, and time-dependent propensities
The CERENA toolbox Wiki provides a short summary of the toolbox's Features as well as an in-depth Description of the whole project.
Additionally, there is an Installation guide and an Usage helper with Examples.
For common questions see FAQ.
Hasenauer, J., Wolf, V., Kazeroonian, A., and Theis, F. J. (2014). Method of conditional moments (MCM) for the chemical master equation. Journal of Mathematical Biology, 69(3), 687–735.
Citation link: http://link.springer.com/article/10.1007%2Fs00285-013-0711-5