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Probabilistic Model Checking of Complex Biological ... - PRISM

Probabilistic Model Checking of Complex Biological ... - PRISM

Probabilistic Model Checking of Complex Biological ... -

Probabilistic Model Checking of Complex Biological Pathways John Heath a , Marta Kwiatkowska b,⋆ , Gethin Norman b , David Parker b , Oksana Tymchyshyn c a School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom b Oxford University Computing Laboratory, Wolfson Building, Parks Road, Oxford OX1 3QD, United Kingdom c School of Computer Science, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom Abstract Probabilistic model checking is a formal verification technique that has been successfully applied to the analysis of systems from a broad range of domains, including security and communication protocols, distributed algorithms and power management. In this paper we illustrate its applicability to a complex biological system: the FGF (Fibroblast Growth Factor) signalling pathway. We give a detailed description of how this case study can be modelled in the probabilistic model checker PRISM, discussing some of the issues that arise in doing so, and show how we can thus examine a rich selection of quantitative properties of this model. We present experimental results for the case study under several different scenarios and provide a detailed analysis, illustrating how this approach can be used to yield a better understanding of the dynamics of the pathway. Finally, we outline a number of exact and approximate techniques to enable the verification of larger and more complex pathways and apply several of them to the FGF case study. Key words: Probabilistic model checking, probabilistic verification, biological pathways, biological modelling ⋆ Corresponding author. Email: marta.kwiatkowska@comlab.ox.ac.uk Tel: +44- 1865-283509; Fax: +44-1865-273839 Preprint submitted to Elsevier Science 29 August 2007

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