ACADEMIA

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 at its Web site for non-commercial purposes. Pedro Mendes, Associate Professor at VBI, remarked: “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.” He added: “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. Dr. Ursula Kummer, Principal Investigator at EML Research, commented: “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.” She added: “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.”