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Modelling and simulation of biological systems with COPASI

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Abstract: With the increasing popularity of systems biology it is becoming extremely important to support use of modelling and simulation by scientist who are not expert programmers. I will present COPASI , which is a user-friendly and platform-independent software that provides powerful numerical methods for simulation and analysis of biochemical reaction networks. COPASI allows a modeller to focus on the biological aspects of a model rather than the mathematics, yet it provides some of the most efficient algorithms available.

I will briefly present the basic features of this software, which supports both deterministic simulations based on ordinary differential equations (ODE), as well as stochastic simulations using the Gillespie framework. This includes the unique capability to automatically convert an ODE -based model to its stochastic equivalent, and several other tools to facilitate complex simulations (parameter scans, optimization and parameter estimation algorithms). Several analyses are also available, such as for stoichiometry, sensitivity and stability. Although the most popular version of COPASI is based on a graphical user-interface, it is also supplied in a command line version which allows for use of COPASI as a simulation engine for other software. In this context I will describe our use of COPASI in two distributed computing environments: Condor pools, and web services.

Biography: Pedro Mendes is Professor of Computational Systems Biology at The University of Manchester and Associate Professor at the Virginia Bioinformatics Institute. He works in modelling and analysis of biological systems, ranging from computer simulation of biochemical systems to data management, analysis, and visualization of -omics data sets. Dr. Mendes is a pioneer of Systems Biology: he is the author of the widely used and popular biochemical simulator Gepasi first created in 1989 (CABIOS 1993 9:563; Trends Biochem. Sci. 1997 22:361; Bioinformatics 1998 14:869), and co-leads the development of its successor COPASI (Bioinformatics 2006 22:3067), one of the most widely used software packages for systems biology. He was a founder member of the SBML community (Bioinformatics 2003 19:524) and is an author of the MIRIAM proposal for model annotation (Nature Biotechnol. 2005 23:1509). He has been a member of the Scientific Board of several International Conferences on Systems Biology (starting with the first one in Tokyo in 2000). Pedro Mendes is a standing member of the US National Institutes of Health Study Section on Modeling and Analysis of Biological Systems (MABS), and has served as an ad hoc member in the National Institute of General Medical Sciences Council. He has authored over 50 publications, of which 4 exceed 200 citations and 2 have over 100 citations.

This talk is part of the Microsoft Research Computational Science Seminars series.

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