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SUMMARY:Modelling and simulation of biological systems with COPASI - Prof.
  Pedro Mendes\, University of Manchester
DTSTART:20080625T130000Z
DTEND:20080625T140000Z
UID:TALK10654@talks.cam.ac.uk
CONTACT:Dr Fabien Petitcolas
DESCRIPTION:*Abstract*: With the increasing popularity of systems biology 
 it is becoming extremely important to support use of modelling and simulat
 ion by scientist who are not expert programmers. I will present COPASI\, w
 hich is a user-friendly and platform-independent software that provides po
 werful numerical methods for simulation and analysis of biochemical reacti
 on networks. COPASI allows a modeller to focus on the biological aspects o
 f a model rather than the mathematics\, yet it provides some of the most e
 fficient algorithms available.\n\nI will briefly present the basic feature
 s of this software\, which supports both deterministic simulations based o
 n ordinary differential equations (ODE)\, as well as stochastic simulation
 s using the Gillespie framework. This includes the unique capability to au
 tomatically convert an ODE-based model to its stochastic equivalent\, and 
 several other tools to facilitate complex simulations (parameter scans\, o
 ptimization and parameter estimation algorithms). Several analyses are als
 o available\, such as for stoichiometry\, sensitivity and stability. Altho
 ugh the most popular version of COPASI is based on a graphical user-interf
 ace\, it is also supplied in a command line version which allows for use o
 f COPASI as a simulation engine for other software. In this context I will
  describe our use of COPASI in two distributed computing environments: Con
 dor pools\, and web services.\n\n*Biography*: Pedro Mendes is Professor of
  Computational Systems Biology at The University of\nManchester and Associ
 ate Professor at the Virginia Bioinformatics Institute. He works in\nmodel
 ling and analysis of biological systems\, ranging from computer simulation
  of\nbiochemical systems to data management\, analysis\, and visualization
  of -omics data sets. Dr.\nMendes is a pioneer of Systems Biology: he is t
 he author of the widely used and popular\nbiochemical simulator Gepasi fir
 st created in 1989 (CABIOS 1993 9:563\; Trends Biochem.\nSci. 1997 22:361\
 ; Bioinformatics 1998 14:869)\, and co-leads the development of its\nsucce
 ssor COPASI (Bioinformatics 2006 22:3067)\, one of the most widely used so
 ftware\npackages for systems biology. He was a founder member of the SBML 
 community\n(Bioinformatics 2003 19:524) and is an author of the MIRIAM pro
 posal for model annotation\n(Nature Biotechnol. 2005 23:1509). He has been
  a member of the Scientific Board of several\nInternational Conferences on
  Systems Biology (starting with the first one in Tokyo in 2000).\nPedro Me
 ndes is a standing member of the US National Institutes of Health Study Se
 ction on\nModeling and Analysis of Biological Systems (MABS)\, and has ser
 ved as an ad hoc member\nin the National Institute of General Medical Scie
 nces Council. He has authored over 50\npublications\, of which 4 exceed 20
 0 citations and 2 have over 100 citations.
LOCATION:Microsoft Research Ltd\, 7 J J Thomson Avenue (Off Madingley Road
 )\, Cambridge
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