Description
CERENA is a 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. In addition, the Finite State Projection and Stochastic Simulation Algorithms implemented in CERENA can be used to provide microscopic descriptions of stochastic chemical kinetics.
By including such a unique variety of modeling approaches, CERENA enables comprehensive studies of reaction networks of realistic sizes. CERENA can be linked to optimization packages for parameter estimation. For that purpose, CERENA provides forward and adjoint sensitivity equations to facilitate efficient parameter estimation.