Petri Net Based Descriptions for Systematic Understanding of Biological Pathways

Hiroshi MATSUNO  Chen LI  Satoru MIYANO  

IEICE TRANSACTIONS on Fundamentals of Electronics, Communications and Computer Sciences   Vol.E89-A   No.11   pp.3166-3174
Publication Date: 2006/11/01
Online ISSN: 1745-1337
DOI: 10.1093/ietfec/e89-a.11.3166
Print ISSN: 0916-8508
Type of Manuscript: INVITED SURVEY PAPER
Petri net,  systems biology,  biological pathways,  modeling,  simulation,  

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Petri nets have recently become widely accepted as a description method for biological pathways by researchers in computer science as well as those in biology. This paper gives an overview of Petri net formalisms to describe biological pathways and discusses their use in modelings and simulations for the systematic understandings of biological pathways. After reviewing the use of various types of Petri nets for the biological pathway modelings, we showed the examples that analyze fundamental properties of biological pathways using T-invariant, P-invariant, siphon, and trap. Applications of hybrid Petri nets for producing new biological hypotheses through simulations are also illustrated.