View source for COPASI

{{Short description|Mathematical biology software}}
{{Use dmy dates|date=April 2022}}
{{Infobox software
| name                   = COPASI
| logo                   = <!-- [[File: ]] -->
| screenshot             = <!-- [[File: ]] -->
| caption                =
| collapsible            =
| author                 =
| developer              =
| released               = {{Start date and age|2004|10|11}}
| latest release version = 4.40 (Build 278)
| latest release date    = {{Start date and age|2023|05|31}}
| programming language   = [[C++]]
| operating system       = [[Linux]], [[macOS]] and [[Microsoft Windows]]
| platform               = [[Qt (framework)|Qt]]
| size                   =
| language               =
| status                 =
| genre                  =
| license                = [[Artistic License]]
| website                = {{URL|http://www.copasi.org|copasi.org}}
}}
'''COPASI'''<ref>{{Cite journal | last1 = Hoops | first1 = S. | last2 = Sahle | first2 = S. | last3 = Gauges | first3 = R. | last4 = Lee | first4 = C. | last5 = Pahle | first5 = J. | last6 = Simus | first6 = N. | last7 = Singhal | first7 = M. | last8 = Xu | first8 = L. | last9 = Mendes | first9 = P. | doi = 10.1093/bioinformatics/btl485 | last10 = Kummer | first10 = U. | title = COPASI--a COmplex PAthway SImulator | journal = Bioinformatics | volume = 22 | issue = 24 | pages = 3067–3074 | year = 2006 | pmid =  17032683| doi-access = free }}</ref> (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.
== History ==
COPASI is based on the Gepasi<ref>{{Cite journal
| last1 = Mendes | first1 = P.
| author-link1 = Pedro Pedrosa Mendes
| title = GEPASI: A software package for modelling the dynamics, steady states and control of biochemical and other systems
| journal = Computer Applications in the Biosciences
| volume = 9
| issue = 5
| pages = 563–571
| year = 1993
| doi = 10.1093/bioinformatics/9.5.563
| pmid = 8293329
}}</ref> simulation software that was developed in the early 1990s by [[Pedro Pedrosa Mendes|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 Institutes 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 Pedrosa Mendes|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|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 (chemistry)|steady-state analysis]], [[Stochiometry|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)|C]] programming language, [[Berkeley Madonna]] files, and [http://www.math.pitt.edu/~bard/xpp/xpp.html XPPAUT] {{Webarchive|url=https://web.archive.org/web/20220418210023/http://www.math.pitt.edu/~bard/xpp/xpp.html |date=18 April 2022 }} files.
== See also ==
* [[List of systems biology modeling software]]
== References ==
<!--- See http://en.wikipedia.org/wiki/Wikipedia:Footnotes on how to create references using <ref></ref> tags which will then appear here automatically -->
{{Reflist}}
== External links ==
* [http://www.copasi.org COPASI home page]
* [http://www.comp-sys-bio.org Mendes group],
* [http://www.bioquant.uni-heidelberg.de/research/groups/modeling_of_biological_processes.html Department Modeling of Biological Processes], [[Heidelberg University]]
<!--- Categories --->
[[Category:Systems biology]]
[[Category:Ordinary differential equations]]
[[Category:Department of Computer Science, University of Manchester]]
[[Category:Software using the Artistic license]]