Virginia Bioinformatics Institute launches new simulation software
June 16, 2006
EML Research and the Virginia Bioinformatics Institute (VBI) at Virginia Tech today announced the launch of the COPASI simulation software. COPASI (Complex Pathway Simulator) is a major software package that allows users to model, simulate and analyze biochemical and systems biology networks.
COPASI, which supports the Systems Biology Markup Language (SBML) standard for systems biology software, enables researchers to investigate how a system is working by allowing them to construct biochemical models, reproduce experimental results and justify the validity of the chosen model. The software may be freely downloaded on the COPASI website for non-commercial purposes.
“The first official release of COPASI represents a key milestone in delivering a fully comprehensive software solution for modeling and simulation to the life science community,” Remarked Pedro Mendes, associate professor at Virginia Bioinformatics Institute. “We have been working closely with Ursula Kummer’s group at EML Research to deliver an open-source software package that aids in the understanding of cellular and molecular behavior and which facilitates the quantitative interpretation of modern experiments. COPASI is the culmination of six years of intense development work to deliver a package that meets the real needs of life scientists. The future development of COPASI will continue to strive towards providing a powerful package that every biologist can use, not just experts in systems biology.”
COPASI simplifies the task of model building by assisting the user in translating the language of chemistry (reactions) to mathematics (matrices and differential equations). The user-friendly interface is combined with a set of sophisticated numerical algorithms that assure the results are obtained quickly and accurately. COPASI simulates the kinetics of systems of biochemical reactions and provides a number of tools to fit models to data, optimize any function of the model, perform metabolic control analysis and linear stability analysis.
“Simulation and modeling are becoming increasingly important tools in systems biology research and can be used to test the physical and chemical limitations as well as feasibility of a wide range of biochemical reactions. We anticipate that COPASI will prove invaluable to researchers not only in simulating increasingly complex networks but also in helping to understand how external factors, for example drugs, impact metabolic systems,” commented Dr. Ursula Kummer, principal investigator at EML Research. “We have already seen many applications from our existing user community and expect many more due to COPASI’s inherent flexibility for top-down and bottom-up modeling.”
COPASI (Complex Pathway Simulator) is a software package that allows the simulation and detailed analysis of biochemical networks. The package, which is available for use on Windows, Macintosh, Linux and Solaris operating systems, is based on original software developed by Pedro Mendes (Gepasi) and on the STODE software developed at EML Research. The main authors of COPASI are Drs. Stefan Hoops, Sven Sahle, and Ralph Gauges. COPASI incorporates a model editor, different simulation techniques (e.g. deterministic and stochastic), optimization routines, sensitivity analysis and user-friendly visualization techniques. Some of the current features include: stochastic and deterministic time course simulation; steady state analysis (including stability); metabolic control analysis/sensitivity analysis; elementary mode analysis; mass conservation analysis; parameter scans; optimization of arbitrary objective functions; parameter estimation using data from time course and/or steady state experiments; sliders for interactive parameter changes; global parameters to change multiple kinetic rates at once; import and export of SBML; fully compatible with Gepasi files; command line version for batch processing.
About the Virginia Bioinformatics Institute
The Virginia Bioinformatics Institute (VBI) at Virginia Tech has a research platform centered on understanding the “disease triangle” of host–pathogen–environment interactions in plants, humans and other animals. By successfully channeling innovation into transdisciplinary approaches that combine information technology and biology, researchers at VBI are addressing some of today’s key challenges in the biomedical, environmental and plant sciences.
About the EML Research gGmbH
The EML Research gGmbH is a non-profit institute conducting research in Information Technology and its applications. A strong focus is set on bioinformatics. Research is carried out in close collaboration with universities and other research institutes. EML Research projects are supported by the Klaus Tschira Foundation(KTS), as well as by the European Union, the German Ministry of Research and Education (BMBF) and by the German Research Foundation (DFG). EML Research is a partner in the first German Center for Modeling and Simulation in the Biosciences (BIOMS). KTS and EML Research are housed in the Villa Bosch in Heidelberg, the former residence of Nobel Prize laureate Carl Bosch (1874 – 1940).