COPASI--a COmplex PAthway SImulator.
BACKGROUND
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.


BACKGROUND
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.
Hoops
Stefan
S
Virginia Bioinformatics Institute, Virginia Tech, Washington St. 0477, Blacksburg, VA 24061, USA.
Sahle
Sven
S
Gauges
Ralph
R
Lee
Christine
C
Pahle
Jürgen
J
Simus
Natalia
N
Singhal
Mudita
M
Xu
Liang
L
Mendes
Pedro
P
Kummer
Ursula
U
D000465:Algorithms; D003196:Computer Graphics; D003198:Computer Simulation; D008954:Models, Biological; D011381:Programming Languages; D025941:Protein Interaction Mapping / Q000379:methods*; D020543:Proteome / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*; D012984:Software; D014584:User-Computer Interface
D020543:Proteome