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Exactness and Approximation of the Stochastic Simulation Algorithm

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Abstract: In 1976, a paper by Daniel T. Gillespie proposed a novel computational approach to effectively analyze the time behavior of chemical/biochemical systems through an easy-to-implement simulation algorithm. The success of Gillespie’s method for the study of biochemical systems dynamics is well demonstrated by the plethora of studies, papers and computational tools based on it that have appeared since the original publication. This talk intends to clarify the applicability of the Stochastic Simulation Algorithm proposed by Gillespie. The derivation of Gillespie’s results is revisited to pinpoint those steps at which, depending on the validity of the assumptions adopted about the system to be studied, approximations may be introduced. We discuss and present some examples about the ways the inaccuracies entailed by the approximations may propagate and affect simulation results.

Biography: Dr. Ivan Mura got his M.S. degree in Computer Science, summa cum laude, from the University of Pisa in 1994, and a PhD in Computer Science Engineering from the University of Pisa in 1999. He worked for the Italian National Research Council as a junior researcher until September 1999, when he joined the Motorola Research and Development Centre in Turin, Italy. He first held a Project Lead and later a Project Manager position at Motorola, managing several research projects dealing with performance and availability modeling of telecommunications systems as well as the involvement of the company in various research and development projects funded by the European Commission in the V Framework Research Programme. Dr. Ivan Mura joined the CoSBi Centre in January 2007.

This talk is part of the CoSBi Computational and Systems Biology Series series.

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