title: COPASI--a COmplex PAthway SImulator.
abstract: 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.
authors.affiliation: Virginia Bioinformatics Institute, Virginia Tech, Washington St. 0477, Blacksburg, VA 24061, USA.
authors.forename: Stefan
authors.initials: S
authors.lastname: Hoops
authors.forename: Sven
authors.initials: S
authors.lastname: Sahle
authors.forename: Ralph
authors.initials: R
authors.lastname: Gauges
authors.forename: Christine
authors.initials: C
authors.lastname: Lee
authors.forename: Jürgen
authors.initials: J
authors.lastname: Pahle
authors.forename: Natalia
authors.initials: N
authors.lastname: Simus
authors.forename: Mudita
authors.initials: M
authors.lastname: Singhal
authors.forename: Liang
authors.initials: L
authors.lastname: Xu
authors.forename: Pedro
authors.initials: P
authors.lastname: Mendes
authors.forename: Ursula
authors.initials: U
authors.lastname: Kummer
mesh_terms: 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
chemical_list: D020543:Proteome