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In Silico Biology 4, 0023 (2004); ©2004, Bioinformation Systems e.V.  



Constructing biological pathway models with hybrid functional Petri nets

Atsushi Doi1, Sachie Fujita1, Hiroshi Matsuno1*, Masao Nagasaki2 and Satoru Miyano2

1Faculty of Science, Yamaguchi University, Japan
  Email: matsuno@sci.yamaguchi-u.ac.jp
2Human Genome Center, Institute of Medical Science, University of Tokyo, Japan

*  corresponding author


Edited by E. Wingender; received January 16, 2004; revised and accepted March 12, 2004; published April 07, 2004


Abstract

In many research projects on modeling and analyzing biological pathways, the Petri net has been recognized as a promising method for representing biological pathways. From the pioneering works by Reddy et al. (Proc. Int. Conf. Intell. Syst. Mol. Biol. 1, 328336, 1993), and Hofestädt (SAMS 16, 113-122, 1994), that model metabolic pathways by traditional Petri net, several enhanced Petri nets such as colored Petri net, stochastic Petri net, and hybrid Petri net have been used for modeling biological phenomena. Recently, Matsuno et al. (In Silico Biol. 3, 0032, 2003), introduced the hybrid functional Petri net (HFPN) in order to give a more intuitive and natural modeling method for biological pathways than these existing Petri nets. Although the paper demonstrates the effectiveness of HFPN with two examples of gene regulation mechanism for circadian rhythms and apoptosis signaling pathway, there has been no detailed explanation about the method of HFPN construction for these examples. The purpose of this paper is to describe method to construct biological pathways with the HFPN step-by-step. The method is demonstrated by the well-known glycolytic pathway controlled by the lac operon gene regulatory mechanism.

Key words: hybrid functional Petri net, lac operon, biological pathway, simulation, Genomic Object Net