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Bioinformatics Advance Access published online on October 10, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl485
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received June 29, 2006
Revised August 29, 2006
Accepted September 14, 2006

Article

COPASI - a COmplex PAthway SImulator

Stefan Hoops 1 *, Sven Sahle 2 *, Ralph Gauges 2, Christine Lee 1, Jürgen Pahle 2, Natalia Simus 2, Mudita Singhal 1, Liang Xu 1, Pedro Mendes 1 *, and Ursula Kummer 2

1 Virginia Bioinformatics Institute, Virginia Tech, Washington St. 0477, Blacksburg, VA 24061, USA
2 Bioinformatics and Computational Biochemistry, EML Research, Schloss-Wolfsbrunnenweg 33, D-69118 Heidelberg, Germany

* To whom correspondence should be addressed.
Pedro Mendes, E-mail: mendes{at}vbi.vt.edu


  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 http://www.copasi.org.

Associate Editor: Jonathan Wren

*these authors contributed equally


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