COPASI (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 simulation software that was developed in the early 1990s by

Pedro Mendes Pedro is a masculine given name. Pedro is the Spanish, Portuguese, and Galician name for ''Peter''. Its French equivalent is Pierre while its English and Germanic form is Peter. The counterpart patronymic surname of the name Pedro, meaning ...

. The initial development of COPASI was funded by the

Virginia Bioinformatics Institute The Biocomplexity Institute of Virginia Tech (formerly the Virginia Bioinformatics Institute) is a research organization specializing in bioinformatics, computational biology, and systems biology. The institute has more than 250 personnel, inclu ...

, and the

Klaus Tschira Foundation The Klaus Tschira Stiftung (KTS) is a German foundation established by the physicist Klaus Tschira in 1995 as a non-profit organization. Its primary objective is to support projects in the natural and computer sciences as well as mathematics. The ...

. Current development efforts are supported by grants from the

National Institutes of Health The National Institutes of Health, commonly referred to as NIH (with each letter pronounced individually), is the primary agency of the United States government responsible for biomedical and public health research. It was founded in the late ...

, the

BBSRC Biotechnology and Biological Sciences Research Council (BBSRC), part of UK Research and Innovation, is a non-departmental public body (NDPB), and is the largest UK public funder of non-medical bioscience. It predominantly funds scientific rese ...

, and the German Ministry of Education.

Development team

COPASI is the result of an international collaboration between the

University of Manchester , mottoeng = Knowledge, Wisdom, Humanity , established = 2004 – University of Manchester Predecessor institutions: 1956 – UMIST (as university college; university 1994) 1904 – Victoria University of Manchester 1880 – Victoria Univer ...

(UK), the

University of Heidelberg } Heidelberg University, officially the Ruprecht Karl University of Heidelberg, (german: Ruprecht-Karls-Universität Heidelberg; la, Universitas Ruperto Carola Heidelbergensis) is a public research university in Heidelberg, Baden-Württemberg, ...

(Germany), and the

(USA). The project principal investigators are

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 A chemical reaction is a process that leads to the chemical transformation of one set of chemical substances to another. Classically, chemical reactions encompass changes that only involve the positions of electrons in the forming and breaking ...

between molecular species. The dynamics of the model is determined by

Rate law In chemistry, the rate law or rate equation for a reaction is an equation that links the initial or forward reaction rate with the concentrations or pressures of the reactants and constant parameters (normally rate coefficients and partial reactio ...

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 Metabolic control analysis (MCA) is a mathematical framework for describing metabolic, signaling, and genetic pathways. MCA quantifies how variables,elastsuch as fluxes and species concentrations, depend on network parameters. In particular, it is a ...

, computation of

Lyapunov exponent In mathematics, the Lyapunov exponent or Lyapunov characteristic exponent of a dynamical system is a quantity that characterizes the rate of separation of infinitesimally close trajectories. Quantitatively, two trajectories in phase space with ini ...

, time scale separation, parameter scans, optimization, and parameter estimation. * Importing and Exporting: COPASI can read models in

SBML The Systems Biology Markup Language (SBML) is a representation format, based on XML, for communicating and storing computational models of biological processes. It is a free and open standard with widespread software support and a community of use ...

format as well as in Gepasi format. COPASI can write models in several different formats including the

, source code in the C programming language,

Berkeley Madonna Berkeley Madonna is a mathematical modelling software package, developed at the University of California at Berkeley by Robert Macey and George Oster. It numerically solves ordinary differential equations and difference equations, originally deve ...

files, an
XPPAUT
files.

References

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External links

COPASI home page

Mendes group

Heidelberg University } Heidelberg University, officially the Ruprecht Karl University of Heidelberg, (german: Ruprecht-Karls-Universität Heidelberg; la, Universitas Ruperto Carola Heidelbergensis) is a public research university in Heidelberg, Baden-Württemberg, ...

Systems biology Ordinary differential equations Department of Computer Science, University of Manchester Software using the Artistic license

History

Development team

Features

See also

References

External links