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http://bura.brunel.ac.uk/handle/2438/3026
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. |
URI: | http://bura.brunel.ac.uk/handle/2438/3026 |
Appears in Collections: | Computer Science Dept of Computer Science Research Papers |
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