David Parker
Reader, Computer Science, University of Birmingham
[KNP08a] Marta Kwiatkowska, Gethin Norman and David Parker. Using Probabilistic Model Checking in Systems Biology. ACM SIGMETRICS Performance Evaluation Review, 35(4), pages 14-21, Association for Computing Machinery. March 2008. [ps.gz] [pdf] [bib] [Illustrates the applicability of PRISM to systems biology, using a case study: the MAPK cascade.]
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Abstract. Probabilistic model checking is a formal verification framework for systems which exhibit stochastic behaviour. It has been successfully applied to a wide range of domains, including security and communication protocols, distributed algorithms and power management. In this paper we demonstrate its applicability to the analysis of biological pathways and show how it can yield a better understanding of the dynamics of these systems. Through a case study of the MAP (Mitogen-Activated Protein) Kinase cascade, we explain how biological pathways can be modelled in the probabilistic model checker PRISM and how this enables the analysis of a rich selection of quantitative properties.