title: Constructing biological pathway models with hybrid functional Petri nets.
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.
authors.affiliation: Faculty of Science, Yamaguchi University, Japan.
authors.forename: Atsushi
authors.initials: A
authors.lastname: Doi
authors.forename: Sachie
authors.initials: S
authors.lastname: Fujita
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Matsuno
authors.forename: Masao
authors.initials: M
authors.lastname: Nagasaki
authors.forename: Satoru
authors.initials: S
authors.lastname: Miyano
mesh_terms: D000244:Adenosine Diphosphate / Q000378:metabolism; D000255:Adenosine Triphosphate / Q000378:metabolism; D005690:Galactose / Q000378:metabolism; D005947:Glucose / Q000378:metabolism; D006019:Glycolysis; D006868:Hydrolysis; D007763:Lac Operon; D007785:Lactose / Q000378:metabolism; D008954:Models, Biological; D009243:NAD / Q000378:metabolism; D019289:Pyruvic Acid / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D009243:NAD; D000244:Adenosine Diphosphate; D019289:Pyruvic Acid; D000255:Adenosine Triphosphate; D005947:Glucose; D007785:Lactose; D005690:Galactose