COPASI

COPASI[1] (COmplex PAthway SImulator) is an open-source software application for creating and solving mathematical models of biological processes such as metabolic networks, cell-signaling pathways, regulatory networks, infectious diseases, and many others.

COPASI
Initial releaseOctober 11, 2004 (2004-10-11)
Stable release
4.25 (Build 207) / March 15, 2019 (2019-03-15)
Repository
Written inC++
Operating systemLinux, macOS and Microsoft Windows
PlatformQt
LicenseArtistic License
Websitecopasi.org

History

COPASI is based on the Gepasi[2] simulation software that was developed in the early 1990s by Pedro Mendes. The initial development of COPASI was funded by the Virginia Bioinformatics Institute, and the Klaus Tschira Foundation. Current development efforts are supported by grants from the National Institute of Health, the BBSRC, and the German Ministry of Education.

Development team

COPASI is the result of an international collaboration between the University of Manchester (UK), the University of Heidelberg (Germany), and the Virginia Bioinformatics Institute (USA). The project principal investigators are Pedro Mendes and Ursula Kummer. The chief software architects are Stefan Hoops and Sven Sahle.

Features

COPASI includes features to define models of biological processes, simulate and analyze these models, generate analysis reports, and import/export models in SBML format.

  • Model definition: Models are defined as chemical reactions between molecular species. The dynamics of the model is determined by Rate law associated with individual reactions. Models can also include compartments, events, and other global variables that can help specify the dynamics of the system.
  • Tasks: Tasks are different types of analysis that can be performed on a model. They include steady-state analysis, stoichiometric analysis, time course simulation using deterministic and stochastic simulation algorithms, metabolic control analysis, computation of Lyapunov exponent, time scale separation, parameter scans, optimization, and parameter estimation.
  • Importing and Exporting: COPASI can read models in SBML format as well as in Gepasi format. COPASI can write models in several different formats including the SBML, source code in the C programming language, Berkeley Madonna files, and XPPAUT files.
gollark: It is hard to know in advance whether you'll be interested in stuff which needs that several years later.
gollark: Yeees? I mean, I don't know how hard first aid is, but mortgages are trivial.
gollark: Anyway, maths is useful basically anywhere you'll need to analyze stuff quantitatively. Science, programming, engineering, finance, data science. School maths probably less so.
gollark: Your solution to a bad system is to make it involved in *more* important roles?
gollark: People should probably be expected to learn some things independently at some point.

References
  1. Hoops, S.; Sahle, S.; Gauges, R.; Lee, C.; Pahle, J.; Simus, N.; Singhal, M.; Xu, L.; Mendes, P.; Kummer, U. (2006). "COPASI--a COmplex PAthway SImulator". Bioinformatics. 22 (24): 3067–3074. doi:10.1093/bioinformatics/btl485. PMID 17032683.
  2. Mendes, P. (1993). "GEPASI: A software package for modelling the dynamics, steady states and control of biochemical and other systems". Computer Applications in the Biosciences (CABIOS). 9 (5): 563–571. doi:10.1093/bioinformatics/9.5.563. PMID 8293329.
This article is issued from Wikipedia. The text is licensed under Creative Commons - Attribution - Sharealike. Additional terms may apply for the media files.