COPASI—a COmplex PAthway SImulator
Open accessAbstract
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 . Contact: mendes@vbi.vt.edu
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Model simulation time can be significantly reduced by using compiled simulation code.
“For the former, model simulation time is a primary concern which can be significantly reduced by using compiled simulation code [see COPASI (Hoops et al., 2006); ABC-SysBio (Liepe et al., 2010); Potters Wheel (Maiwald and Timmer, 2008); Sloppy Cell (Brown and Sethna, 2003)].”
From A bayesian approach to targeted experiment design (2012) · cites this paper as Hoops et al., 2006
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References 45 · Cited by 2,618
Research works printed but not linked: 1
- Pahle,J. (2002) Eine Hybridmethode zur Simulation biochemischer Prozesse (in German). Diploma thesis Universita¨t Karlsruhe (TH), Germany.
- Authors
- Hoops, S., Sahle, S., Gauges, R., Lee, C., Pahle, J., Simus, N., Singhal, M., Xu, L., Mendes, P., & Kummer, U.
- Affiliations
- Virginia Tech (US)
- European Media Laboratory (Germany) (DE)
- Corresponding author
- Mendes, Pedro
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2006-10-10
- Volume
- 22
- Issue
- 24
- Pages
- 3067-3074
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2102653059
- Cited by
- 2,618
- References
- 45
- Citations by year
- 2026: 87 · 2025: 150 · 2024: 147 · 2023: 130 · 2022: 150 · 2021: 157 · 2020: 145 · 2019: 148 · 2018: 163 · 2017: 140 · 2016: 153 · 2015: 148 · 2014: 135 · 2013: 164 · 2012: 131
- FWCI
- 30.76
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Bioinformatics (publishedVersion)
- PubMed (publishedVersion)
- Research Explorer (The University of Manchester) (publishedVersion)
- Funders
- Bundesministerium für Bildung und Forschung
- Klaus Tschira Stiftung
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Modeling and Simulation Systems
- Keywords
- COPASI, stochastic simulation, deterministic simulation, hybrid simulation
- MeSH terms
- Algorithms, Computer Graphics, Computer Simulation, Models, Biological, Programming Languages, Software, User-Computer Interface, Signal Transduction, Proteome, Protein Interaction Mapping
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