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COPASI -- a COmplex PAthway SImulator (2006)
| Venue: | BIOINFORMATICS |
| Citations: | 269 - 6 self |
BibTeX
@MISC{Hoops06copasi--,
author = {Stefan Hoops and Sven Sahle and Ralph Gauges and Christine Lee and Jürgen Pahle and Natalia Simus and Mudita Singhal and Liang Xu and Pedro Mendes and Ursula Kummer},
title = {COPASI -- a COmplex PAthway SImulator},
year = {2006}
}
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Abstract
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
Keyphrases
complex pathway simulator standard approach big need sun solaris full source code user-friendly biochemical simulator hybrid deterministic-stochastic method several unique feature deterministic simulation method complex biochemical process numerical issue complete software random number generator numerical resolution open source license m window stochastic simulation software tool
