An Introduction to BioModel Engineering, Illustrated for Signal Transduction Pathways

Authors:
David Gilbert;Rainer Breitling;Monika Heiner;Robin Donaldson
Affiliations:
School of Information Science, Computing and Mathematics, Brunel University, UK;Groningen Bioinformatics Centre, University of Groningen, Haren, The Netherlands 9751 NN;Department of Computer Science, Brandenburg University of Technology, Cottbus, Germany;Bioinformatics Research Centre, University of Glasgow, Glasgow, UK G12 8QQ
Venue:
Membrane Computing
Year:
2009

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Abstract

BioModel Engineering is the science of designing, constructing and analyzing computational models of biological systems. It is inspired by concepts from software engineering and computing science. This paper illustrates a major theme in BioModel Engineering, namely that identifying a quantitative model of a dynamic system means building the structure, finding an initial state, and parameter fitting. In our approach, the structure is obtained by piecewise construction of models from modular parts, the initial state is obtained by analysis of the structure and parameter fitting comprises determining the rate parameters of the kinetic equations. We illustrate this with an example in the area of intracellular signalling pathways.