Calder, Muffy and Vyshemirsky, Vladislav and Gilbert, David and Orton, Richard (2006) Analysis of signalling pathways using continuous time Markov chains. Lecture Notes in Computer Science, 4220/2006. pp. 44-67. ISSN 0302-9743Full text not available in this repository. (Request a copy from the Strathclyde author)
We describe a quantitative modelling and analysis approach for signal transduction networks. We illustrate the approach with an example, the RKIP inhibited ERK pathway [CSK+03]. Our models are high level descriptions of continuous time Markov chains: proteins are modelled by synchronous processes and reactions by transitions. 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 such as what is the probability that if a concentration reaches a certain level, it will remain at that level thereafter? or how does varying a given reaction rate affect that probability? 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.
|Keywords:||systems biology, mathematical modelling, signalling pathways , Markov chain, Probabilities. Mathematical statistics, Theoretical Computer Science, Computer Science(all)|
|Subjects:||Science > Mathematics > Probabilities. Mathematical statistics|
|Department:||Faculty of Science > Mathematics and Statistics|
|Depositing user:||Pure Administrator|
|Date Deposited:||28 Nov 2011 09:42|
|Last modified:||04 May 2016 20:56|