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

doi:10.1587/transfun.E93.A.2717

Special Section on Theory of Concurrent Systems and its Applications

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

Author information

Keywords: Petri net, signaling pathway, firing delay time, stochastic decision rule, conflict resolution

JOURNAL RESTRICTED ACCESS

2010 Volume E93.A Issue 12 Pages 2717-2729

DOI https://doi.org/10.1587/transfun.E93.A.2717

Details

Abstract

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.

Corresponding author

Register with J-STAGE for free!