Analysis of Signalling Pathways Using the PRISM Model Checker

Calder, M. , Vyshemirsky, V. , Gilbert, D. and Orton, R. (2005) Analysis of Signalling Pathways Using the PRISM Model Checker. In: Computational Methods in Systems Biology (CMSB'05), Edinburgh, United Kingdom, 03-05 Apr 2005, pp. 179-190.

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We describe a new modelling and analysis approach for signal transduction networks in the presence of incomplete data. We illustrate the approach with an example, the RKIP inhibited ERK pathway [1]. Our models are based on high level descriptions of continuous time Markov chains: reactions are modelled as synchronous processes and concentrations are modelled by discrete, abstract quantities. The main advantage of our approach is that using a (continuous time) stochastic logic and the PRISM model checker, we can perform quantitative analysis of queries such as if a concentration reaches a certain level, will it remain at that level thereafter? We also perform standard simulations and compare our results with a traditional ordinary differential equation model. An interesting result is that for the example pathway, only a small number of discrete data values is required to render the simulations practically indistinguishable.

Item Type:Conference Proceedings
Glasgow Author(s) Enlighten ID:Gilbert, Prof David and Calder, Professor Muffy and Vyshemirsky, Dr Vladislav and Orton, Dr Richard
Authors: Calder, M., Vyshemirsky, V., Gilbert, D., and Orton, R.
College/School:College of Medical Veterinary and Life Sciences > Institute of Infection Immunity and Inflammation
College of Science and Engineering > School of Computing Science
College of Science and Engineering > School of Mathematics and Statistics > Statistics
Publisher:University of Edinburgh

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