COPASI
Encyclopedia
COPASI 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. The name COPASI stands for COmplex PAthway SImulator.
, the Klaus Tschira Foundation
, the Biotechnology and Biological Sciences Research Council
, and the Engineering and Physical Sciences Research Council
. Current development efforts are supported by a grant from the National Institute of Health and the German Ministry of Education.
(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.
.
History
COPASI is based on the GEPASI simulation software that was developed in the early 1990's by Pedro Mendes. The initial development of COPASI was funded by the Virginia Bioinformatics InstituteVirginia Bioinformatics Institute
The Virginia Bioinformatics Institute at Virginia Tech is a bioinformatics, computational biology, and systems biology research facility that uses transdisciplinary approaches combining information technology, biology and medicine to interpret and apply vast amounts of biological data generated...
, the Klaus Tschira Foundation
Klaus Tschira Foundation
The Klaus Tschira Foundation was established by the physicist Klaus Tschira in 1995 as a non-profit organization. Its primary objective is to support projects in natural and computer sciences as well as mathematics. The KTF places strong emphasis on the public understanding in these fields...
, the Biotechnology and Biological Sciences Research Council
Biotechnology and Biological Sciences Research Council
Biotechnology and Biological Sciences Research Council is a UK Research Council and NDPB and is the largest UK public funder of non-medical bioscience...
, and the Engineering and Physical Sciences Research Council
Engineering and Physical Sciences Research Council
The Engineering and Physical Sciences Research Council is a British Research Council that provides government funding for grants to undertake research and postgraduate degrees in engineering and the physical sciences , mainly to universities in the United Kingdom...
. Current development efforts are supported by a grant from the National Institute of Health and the German Ministry of Education.
Development Team
COPASI is the result of an international collaboration between the University of ManchesterUniversity of Manchester
The University of Manchester is a public research university located in Manchester, United Kingdom. It is a "red brick" university and a member of the Russell Group of research-intensive British universities and the N8 Group...
(UK), the University of Heidelberg (Germany), and the Virginia Bioinformatics Institute
Virginia Bioinformatics Institute
The Virginia Bioinformatics Institute at Virginia Tech is a bioinformatics, computational biology, and systems biology research facility that uses transdisciplinary approaches combining information technology, biology and medicine to interpret and apply vast amounts of biological data generated...
(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 formatSBML
The Systems Biology Markup Language 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 users and developers...
.
- 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 analysisSteady state (chemistry)In chemistry, a steady state is a situation in which all state variables are constant in spite of ongoing processes that strive to change them. For an entire system to be at steady state, i.e. for all state variables of a system to be constant, there must be a flow through the system...
, stoichiometric analysis, time course simulation using deterministic and stochastic simulation algorithms, metabolic control analysisMetabolic control analysisMetabolic control analysis is a mathematical framework for describingmetabolic, signaling and genetic pathways. MCA quantifies how variables,such as fluxes and species concentrations, depend on network parameters....
, computation of Lyapunov exponentLyapunov exponentIn 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...
, time scale separation, parameter scans, optimization, and parameter estimation. - Importing and Exporting: COPASI can read models in SBMLSBMLThe Systems Biology Markup Language 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 users and developers...
format as well as in Gepasi format. COPASI can write models in several different formats including the SBMLSBMLThe Systems Biology Markup Language 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 users and developers...
, source code in the CC (programming language)C is a general-purpose computer programming language developed between 1969 and 1973 by Dennis Ritchie at the Bell Telephone Laboratories for use with the Unix operating system....
programming language, Berkeley Madonna files, and XPPAUT files.
External links
- COPASI home page
- Mendes group, University of ManchesterUniversity of ManchesterThe University of Manchester is a public research university located in Manchester, United Kingdom. It is a "red brick" university and a member of the Russell Group of research-intensive British universities and the N8 Group...
- Department Modeling of Biological Processes, University of Heidelberg