title: Colored Petri net modeling and simulation of signal transduction pathways.
abstract: 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.
authors.affiliation: Metabolic and Biomolecular Engineering National Research Laboratory, Korea Advanced Institute of Science and Technology, 373-1 Guseong-dong, Yuseong-gu, Daejeon 305-701, Korea.
authors.forename: Dong-Yup
authors.initials: DY
authors.lastname: Lee
authors.forename: Ralf
authors.initials: R
authors.lastname: Zimmer
authors.forename: Sang Yup
authors.initials: SY
authors.lastname: Lee
authors.forename: Sunwon
authors.initials: S
authors.lastname: Park
mesh_terms: D000465:Algorithms; D000818:Animals; D003198:Computer Simulation; D004815:Epidermal Growth Factor / Q000378:metabolism*; D066246:ErbB Receptors / Q000378:metabolism*; D005786:Gene Expression Regulation / Q000502:physiology*; D006801:Humans; D008657:Metabolic Clearance Rate; D008954:Models, Biological; D009097:Multienzyme Complexes / Q000378:metabolism; D015398:Signal Transduction / Q000502:physiology*
chemical_list: D009097:Multienzyme Complexes; D004815:Epidermal Growth Factor; D066246:ErbB Receptors