Colored Petri net modeling and simulation of signal transduction pathways

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Presented herein is a methodology for quantitatively analyzing the complex signaling network by resorting to colored Petri nets (CPN). The mathematical as well as Petri net models for two basic reaction types were established, followed by the extension to a large signal transduction system stimulated by epidermal growth factor (EGF) in an application study. The CPN models based on the Petri net representation and the conservation and kinetic equations were used to examine the dynamic behavior of the EGF signaling pathway. The usefulness of Petri nets is demonstrated for the quantitative analysis of the signal transduction pathway. Moreover, the trade-offs between modeling capability and simulation efficiency of this pathway are explored, suggesting that the Petri net model can be invaluable in the initial stage of building a dynamic model. (c) 2005 Elsevier Inc. All rights reserved.
Publisher
ACADEMIC PRESS INC ELSEVIER SCIENCE
Issue Date
2006-03
Language
English
Article Type
Article
Keywords

GROWTH-FACTOR RECEPTOR; PROTEIN-KINASE; FEEDBACK-REGULATION; DRUG DISCOVERY; MAPK PATHWAY; CASCADE; SYSTEMS; ACTIVATION; DYNAMICS; BIOLOGY

Citation

METABOLIC ENGINEERING, v.8, pp.112 - 122

ISSN
1096-7176
DOI
10.1016/j.ymben.2005.10.001
URI
http://hdl.handle.net/10203/19836
Appears in Collection
CBE-Journal Papers(저널논문)
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