Computational methodologies for modelling, analysis and simulation of signalling networks

Gilbert, D., Fuss, H., Gu, X., Orton, R. , Robinson, S., Vyshemirsky, V., Kurth, M.J., Downes, C.S. and Dubitzky, W. (2006) Computational methodologies for modelling, analysis and simulation of signalling networks. Briefings in Bioinformatics, 7(4), pp. 339-353. (doi:10.1093/bib/bbl043)

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Abstract

This article is a critical review of computational techniques used to model, analyse and simulate signalling networks. We propose a conceptual framework, and discuss the role of signalling networks in three major areas: signal transduction, cellular rhythms and cell-to-cell communication. In order to avoid an overly abstract and general discussion, we focus on three case studies in the areas of receptor signalling and kinase cascades, cell-cycle regulation and wound healing. We report on a variety of modelling techniques and associated tools, in addition to the traditional approach based on ordinary differential equations (ODEs), which provide a range of descriptive and analytical powers. As the field matures, we expect a wider uptake of these alternative approaches for several reasons, including the need to take into account low protein copy numbers and noise and the great complexity of cellular organisation. An advantage offered by many of these alternative techniques, which have their origins in computing science, is the ability to perform sophisticated model analysis which can better relate predicted behaviour and observations.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Gilbert, Prof David and Vyshemirsky, Dr Vladislav and Orton, Dr Richard
Authors: Gilbert, D., Fuss, H., Gu, X., Orton, R., Robinson, S., Vyshemirsky, V., Kurth, M.J., Downes, C.S., and Dubitzky, W.
Subjects:Q Science > QA Mathematics > QA75 Electronic computers. Computer science
College/School:College of Science and Engineering > School of Computing Science
Journal Name:Briefings in Bioinformatics
Publisher:Oxford University Press
ISSN:1467-5463
ISSN (Online):1477-4054
Published Online:01 January 2006

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