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http://bura.brunel.ac.uk/handle/2438/3784
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 ... |
Description: | http://dx.doi.org/10.1093/bib/bbn026 |
URI: | http://bura.brunel.ac.uk/handle/2438/3784 |
Appears in Collections: | Computer Science Dept of Computer Science Research Papers |
Files in This Item:
File | Description | Size | Format | |
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ode_tutorial[1].pdf | 531.45 kB | Adobe PDF | View/Open |
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