Analysis of signalling pathways using the prism model checker

Muffy Calder, Vladislav Vyshemirsky, David Gilbert, Richard Orton

Research output: Contribution to conferencePaper

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.
Original languageEnglish
Number of pages12
Publication statusPublished - 2005
EventCMSB'2005 - Edinburgh, United Kingdom
Duration: 3 Apr 20055 Apr 2005

Conference

ConferenceCMSB'2005
CountryUnited Kingdom
CityEdinburgh
Period3/04/055/04/05

Keywords

  • analysis
  • signalling pathways
  • prism
  • model checker

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