Affiliations: Faculty of Science, Yamaguchi University, Japan.
E-mail: [email protected] | Human Genome Center, Institute of Medical Science,
University of Tokyo, Japan
Note:  Corresponding author
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., 1993, and Hofestädt, 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., 2003b, 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.
Keywords: Hybrid functional Petri net, lac operon, biological pathway, simulation, Genomic Object Net