{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,24]],"date-time":"2026-07-24T03:21:49Z","timestamp":1784863309050,"version":"3.55.0"},"reference-count":44,"publisher":"Oxford University Press (OUP)","issue":"24","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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.<\/jats:p>\n               <jats:p>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\u2013stochastic methods, and the importance of random number generator numerical resolution in stochastic simulation.<\/jats:p>\n               <jats:p>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 .<\/jats:p>\n               <jats:p>Contact: \u00a0mendes@vbi.vt.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl485","type":"journal-article","created":{"date-parts":[[2006,10,11]],"date-time":"2006-10-11T02:51:11Z","timestamp":1160535071000},"page":"3067-3074","source":"Crossref","is-referenced-by-count":2317,"title":["COPASI\u2014a COmplex PAthway SImulator"],"prefix":"10.1093","volume":"22","author":[{"given":"Stefan","family":"Hoops","sequence":"first","affiliation":[{"name":"Virginia Bioinformatics Institute, Virginia Tech 1 \u00a0 1 \u00a0 \u00a0 Washington St. 0477, Blacksburg, VA 24061, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sven","family":"Sahle","sequence":"additional","affiliation":[{"name":"Bioinformatics and Computational Biochemistry, EML Research 2 \u00a0 2 \u00a0 \u00a0 Schloss-Wolfsbrunnenweg 33, D-69118 Heidelberg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ralph","family":"Gauges","sequence":"additional","affiliation":[{"name":"Bioinformatics and Computational Biochemistry, EML Research 2 \u00a0 2 \u00a0 \u00a0 Schloss-Wolfsbrunnenweg 33, D-69118 Heidelberg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christine","family":"Lee","sequence":"additional","affiliation":[{"name":"Virginia Bioinformatics Institute, Virginia Tech 1 \u00a0 1 \u00a0 \u00a0 Washington St. 0477, Blacksburg, VA 24061, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J\u00fcrgen","family":"Pahle","sequence":"additional","affiliation":[{"name":"Bioinformatics and Computational Biochemistry, EML Research 2 \u00a0 2 \u00a0 \u00a0 Schloss-Wolfsbrunnenweg 33, D-69118 Heidelberg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natalia","family":"Simus","sequence":"additional","affiliation":[{"name":"Bioinformatics and Computational Biochemistry, EML Research 2 \u00a0 2 \u00a0 \u00a0 Schloss-Wolfsbrunnenweg 33, D-69118 Heidelberg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mudita","family":"Singhal","sequence":"additional","affiliation":[{"name":"Virginia Bioinformatics Institute, Virginia Tech 1 \u00a0 1 \u00a0 \u00a0 Washington St. 0477, Blacksburg, VA 24061, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liang","family":"Xu","sequence":"additional","affiliation":[{"name":"Virginia Bioinformatics Institute, Virginia Tech 1 \u00a0 1 \u00a0 \u00a0 Washington St. 0477, Blacksburg, VA 24061, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pedro","family":"Mendes","sequence":"additional","affiliation":[{"name":"Virginia Bioinformatics Institute, Virginia Tech 1 \u00a0 1 \u00a0 \u00a0 Washington St. 0477, Blacksburg, VA 24061, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ursula","family":"Kummer","sequence":"additional","affiliation":[{"name":"Bioinformatics and Computational Biochemistry, EML Research 2 \u00a0 2 \u00a0 \u00a0 Schloss-Wolfsbrunnenweg 33, D-69118 Heidelberg, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2006,10,10]]},"reference":[{"key":"2023012408502710600_b1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1051\/proc:2005001","article-title":"Adaptive simulation of hybrid stochastic and deterministic models for biochemical systems","volume":"14","author":"Alfonsi","year":"2005","journal-title":"ESAIM Proc."},{"key":"2023012408502710600_b2","doi-asserted-by":"crossref","DOI":"10.1137\/1.9780898719604","volume-title":"LAPACK Users' Guide","author":"Anderson","year":"1999"},{"key":"2023012408502710600_b3","doi-asserted-by":"crossref","first-page":"4059","DOI":"10.1063\/1.1778376","article-title":"Efficient formulation of the stochastic simulation algorithm for chemically reacting systems","volume":"121","author":"Cao","year":"2004","journal-title":"J. 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