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Biomodel engineering – from structure to behavior. (English) Zbl 1275.92022

Priami, Corrado (ed.) et al., Transactions on Computational Systems Biology XII. Special issue on modeling methodologies. Berlin: Springer (ISBN 978-3-642-11711-4/pbk). Lecture Notes in Computer Science 5945. Lecture Notes in Bioinformatics. Journal Subline, 1-12 (2010).
Summary: Biomodel engineering is the science of designing, constructing and analyzing computational models of biological systems. It forms a systematic and powerful extension of earlier mathematical modeling approaches and has recently gained popularity in systems biology and synthetic biology. In this brief review for systems biologists and computational modelers, we introduce some of the basic concepts of successful biomodel engineering, illustrating them with examples from a variety of application domains, ranging from metabolic networks to cellular signaling cascades. We also present a more detailed outline of one of the major techniques of biomodel engineering – Petri net models – which provides a flexible and powerful tool for building, validating and exploring computational descriptions of biological systems.
For the entire collection see [Zbl 1204.92037].

MSC:

92C42 Systems biology, networks
68Q85 Models and methods for concurrent and distributed computing (process algebras, bisimulation, transition nets, etc.)
92-08 Computational methods for problems pertaining to biology

Software:

COBRA Toolbox
PDFBibTeX XMLCite
Full Text: DOI

References:

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