MOTIVATION: Simulation and modeling is becoming a standard approach to understand complex biochemical processes. Therefore, there is a big need for software tools that allow access to diverse simulation and modeling methods as well as support for the usage of these methods. RESULTS: Here, we present COPASI, a platform-independent and user-friendly biochemical simulator that offers several unique features. We discuss numerical issues with these features; in particular, the criteria to switch between stochastic and deterministic simulation methods, hybrid deterministic-stochastic methods, and the importance of random number generator numerical resolution in stochastic simulation. AVAILABILITY: The complete software is available in binary (executable) for MS Windows, OS X, Linux (Intel) and Sun Solaris (SPARC), as well as the full source code under an open source license from http://www.copasi.org.
MOTIVATION: Simulation and modeling is becoming a standard approach to understand complex biochemical processes. Therefore, there is a big need for software tools that allow access to diverse simulation and modeling methods as well as support for the usage of these methods. RESULTS: Here, we present COPASI, a platform-independent and user-friendly biochemical simulator that offers several unique features. We discuss numerical issues with these features; in particular, the criteria to switch between stochastic and deterministic simulation methods, hybrid deterministic-stochastic methods, and the importance of random number generator numerical resolution in stochastic simulation. AVAILABILITY: The complete software is available in binary (executable) for MS Windows, OS X, Linux (Intel) and Sun Solaris (SPARC), as well as the full source code under an open source license from http://www.copasi.org.
Authors: Maria Eugenia Monge; Thomas Rosenørn; Olivier Favez; Markus Müller; Gabriela Adler; Ali Abo Riziq; Yinon Rudich; Hartmut Herrmann; Christian George; Barbara D'Anna Journal: Proc Natl Acad Sci U S A Date: 2012-04-18 Impact factor: 11.205
Authors: Federico M Lauro; Matthew Z DeMaere; Sheree Yau; Mark V Brown; Charmaine Ng; David Wilkins; Mark J Raftery; John A E Gibson; Cynthia Andrews-Pfannkoch; Matthew Lewis; Jeffrey M Hoffman; Torsten Thomas; Ricardo Cavicchioli Journal: ISME J Date: 2010-12-02 Impact factor: 10.302