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Title: A structured approach for the engineering of biochemical network models, illustrated for signalling pathways
Authors: Breitling, R
Gilbert, D
Heiner, M
Orton, R
Issue Date: 2008
Publisher: Oxford University Press
Citation: Briefings in Bioinformatics, 9(5), 404-421.
Abstract: Quantitative models of biochemical networks (signal transduction cascades, metabolic pathways, gene regulatory circuits) are a central component of modern systems biology. Building and managing these complex models is a major challenge that can benefit from the application of formal methods adopted from theoretical computing science. Here we provide a general introduction to the field of formal modelling, which emphasizes the intuitive biochemical basis of the modelling process, but is also accessible for an audience with a background in computing science and/or model engineering. We show how signal transduction cascades can be modelled in a modular fashion, using both a qualitative approach { Qualitative Petri nets, and quantitative approaches { Continuous Petri Nets and Ordinary Differential Equations. We review the major elementary building blocks of a cellular signalling model, discuss which critical design decisions have to be made during model building, and present ...
Appears in Collections:Computer Science
Dept of Computer Science Research Papers

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