Delay Time Determination for the Timed Petri Net Model of a Signaling Pathway Based on Its Structural Information

Yoshimasa MIWA  Yuki MURAKAMI  Qi-Wei GE  Chen LI  Hiroshi MATSUNO  Satoru MIYANO  

Publication
IEICE TRANSACTIONS on Fundamentals of Electronics, Communications and Computer Sciences   Vol.E93-A   No.12   pp.2717-2729
Publication Date: 2010/12/01
Online ISSN: 1745-1337
DOI: 10.1587/transfun.E93.A.2717
Print ISSN: 0916-8508
Type of Manuscript: Special Section PAPER (Special Section on Theory of Concurrent Systems and its Applications)
Category: 
Keyword: 
Petri net,  signaling pathway,  firing delay time,  stochastic decision rule,  conflict resolution,  

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Summary: 
This paper proposes a method to incorporate the concept of time for the inclusion of dynamics of signaling pathway in a Petri net model, i.e., to use timed Petri nets. Incorporation of delay times into a Petri net model makes it possible to conduct quantitative evaluation on a target signaling pathway. However, experimental data describing detailed reactions are not available in most cases. An algorithm given in this paper determines delay times of a timed Petri net only from the structural information of it. The suitability of this algorithm has been confirmed by the results of an application to the IL-1 signaling pathway.