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dc.contributor.authorBreitling, R-
dc.contributor.authorGilbert, D-
dc.contributor.authorHeiner, M-
dc.contributor.authorOrton, R-
dc.identifier.citationBriefings in Bioinformatics, 9(5), 404-421.en
dc.description.abstractQuantitative 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 ...en
dc.publisherOxford University Pressen
dc.titleA structured approach for the engineering of biochemical network models, illustrated for signalling pathwaysen
Appears in Collections:Computer Science
Dept of Computer Science Research Papers

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