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IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences 2006 E89-A(11):3166-3174; doi:10.1093/ietfec/e89-a.11.3166
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Copyright © 2006 The Institute of Electronics, Information and Communication Engineers

Special Section on Concurrent/Hybrid Systems: Theory and Applications -- Survey Paper

Petri Net Based Descriptions for Systematic Understanding of Biological Pathways

Hiroshi MATSUNO1, Chen LI1 and Satoru MIYANO2

1 The authors are with the Graduate School of Science and Engineering, Yamaguchi University, Yamaguchi-shi, 753-8512 Japan. E-mail: hmatsuno{at}yamaguchi-u.ac.jp, 2 The author is with Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639 Japan.

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.

Key Words: Petri net, systems biology, biological pathways, modeling, simulation

Manuscript received May 1, 2006. Final manuscript received July 7, 2006.


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