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Title: Analysis of signalling pathways using the prism model checker
Authors: Calder, M
Vyshemirsky, V
Gilbert, D
Orton, R
Issue Date: 2005
Publisher: University of Edinburgh
Citation: Proceedings of Third International CMSB 2005 (Computational Methods in Systems Biology), University of Edinburgh , 3-5 April 2005 , pp. 179-190
Abstract: 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.
Appears in Collections:Computer Science
Dept of Computer Science Research Papers

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