Probabilistic model checking of complex biological pathways

Journal article

Probabilistic model checking is a formal verification technique that has been successfully applied to the analysis of systems from a broad range of domains, including security and communication protocols, distributed algorithms and power management. In this paper we illustrate its applicability to a complex biological system: the FGF (Fibroblast Growth Factor) signalling pathway. We give a detailed description of how this case study can be modelled in the probabilistic model checker PRISM, discussing some of the issues that arise in doing so, and show how we can thus examine a rich selection of quantitative properties of this model. We present experimental results for the case study under several different scenarios and provide a detailed analysis, illustrating how this approach can be used to yield a better understanding of the dynamics of the pathway. Finally, we outline a number of exact and approximate techniques to enable the verification of larger and more complex pathways and apply several of them to the FGF case study. © 2007 Elsevier Ltd. All rights reserved.

Authors: Heath, J; Kwiatkowska, M; Norman, G; Parker, D; Tymchyshyn, O

• Publication status: Published
• Peer review status: Peer reviewed
• Publisher: Elsevier
• Journal: THEORETICAL COMPUTER SCIENCE
• Volume: 391
• Issue: 3
• Pages: 239-257
• Publication date: 2008-02-14
• DOI: 10.1016/j.tcs.2007.11.013
• ISSN: 0304-3975
• Language: English
• Keywords: probabilistic verification; biological modelling; probabilistic model checking; biological pathways