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Home | Seminars and Symposia | Past seminars/symposia: Thursday, June 23, 2011

DTC Seminar Series

The Challenge of Discrete Event Simulation in Systems Biology

by

Gianfranco Balbo
University of Torino
Italy

Thursday, June 23, 2011
11:30 am

402 Walter Library

Balbo

The dynamics of Biological Systems seen at the level of molecular populations are characterized by random behaviors that are properly captured by modeling these phenomena with Stochastic Petri Nets (SPNs), and then translated into Continuous Time Markov Chains (CTMCs). The nice mathematical properties of SPNs and CTMCs are often difficult to exploit in Systems Biology, due to the size and the intricacy of these models, and Discrete Event Simulation frequently becomes the only analysis method that can be used in these cases. In principle, the simulation of CTMC is straightforward, but in practice it may turn out to be a real challenge when the model exhibits certain characteristics that are typical in Systems Biology. The talk will briefly introduce the SPN formalism together with some of their mathematical properties and then Gillespie's simulation algorithm together with many of its variations that contribute to make this approach the method of choice in this context. Subsequently the reasons that make classical Discrete Event Simulation methods questionable in these situations will be discussed with suggestions on research directions that could be pursued to overcome this difficulty, and to devise approximate simulation methods that could be more suitable for dealing with models characterized by huge state spaces and multi-scale transition speeds.

 

Gianfranco Balbo was born in Piossasco, Italy in 1946. He received his Doctor degree in Physics from the University of Torino, Italy, in 1970, and his M.S. and Ph.D. degrees in Computer Science from Purdue University, West Lafayette, Indiana, in 1975 and 1979, respectively, with a specialization in operating systems and evaluation methods for the study of their performance. Since 1978 he has been with the Computer Science Department of the University of Torino where he is now a Full Professor in charge of introductory courses on Computer Architecture, Operating System Theory, and Performance Evaluation of Computer Systems. Since 1984 he is a member of the board that manages the Ph.D. program organized by the Computer Science Department of the University of TorinoHe is active in the international scientific community as a member of the IFIP Working Group 7.3 "Computer System Modelling" and by participating in the Scientific Committees of several of the most important international conferences in Modelling and Performance Evaluation. From 1996 to 2002, he has been a member of the "Steering Committee" that coordinates the activities and the conferences in the fields of Petri net theory and applications. Since 2003 he is a member of the "Steering Committee" of "QEST: International Conference on the Quantitative Evaluation of Systems". He has been co-Chairman of the Scientific Committees of several international conferences. His current research interests are in the area of performance evaluation of computer systems, queueing network models, stochastic Petri net models, queueing theory, and in the application of stochastic analysis techniques in Systems Biology. He is co-author of more than 60 papers published in the proceedings of the most important international conferences of the field and on highly recognized scientific journals, and of the books "Computational Algorithms for Closed Queueing Networks", "Performance Models of Multiprocessor Systems", and "Modelling with Generalized Stochastic Petri Nets", published by Elsevier North Holland, MIT Press and Wiley, respectively. Most of his publications have been repeatedly cited at the international level and he is included in the list of the most cited researchers in Computer Science (http://hcr3.isiknowledge.com /formSearch.cgi). From 1989 to 1995 he has been Director of the Computer Science Department of the University of Torino. From October 1999 to December 2005 he has been President and Managing Director of the "Virtual Reality & Multi Media Park" which is a technology park that includes the promotion of advanced training and research in the audio-visual production field as one of its main objectives. Since November 2001, he is vice-rector of the University of Turin with the responsibility of the university information system. Since May 2003, he is a member of the Academy of Sciences of Torino. Since January 2011 he is president of the Scientific Committee of the Consortium for the Information System of the Piemonte Region (CSI Piemonte). Since January 2007 he is member of the Advisory Board of the Microsoft Research and the University of Trento Centre for Computational and Systems Biology. Dr. Balbo is a member of the Association for Computing Machinery.