[KNP+06]
Marta Kwiatkowska, Gethin Norman, David Parker, Oksana Tymchyshyn, John Heath and Eamonn Gaffney.
Simulation and Verification for Computational Modelling of Signalling Pathways.
In Proc. 2006 Winter Simulation Conference, pages 1666-1674.
December 2006.
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[Surveys techniques for the analysis of cell signalling pathways, including the simulation and model checking techniques in PRISM.]
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Abstract.
Modelling of the dynamics of biochemical reaction networks typically
proceeds by solving ordinary differential equations or stochastic
simulation via the Gillespie algorithm. More recently, computational
methods such as process algebra techniques have been successfully applied
to the analysis of signalling pathways. One advantage of these is that they
enable automatic verification of the models, via model checking, against
qualitative and quantitative temporal logic specifications, for example,
'what is the probability that the protein eventually degrades?'. Such
verification is exhaustive, that is, the analysis is carried out over all
paths, producing exact quantitative measures. In this paper, we give an overview of the
simulation, verification and differential equation approaches to modelling
biochemical reaction networks. We discuss the advantages and disadvantages
of the respective methods, using as an illustration a fragment of the FGF
signalling pathway.
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