Towards biopathway modeling and simulation

Hiroshi Matsuno, Sachie Fujita, Atsushi Doi, Masao Nagasaki, Satoru Miyano

Research output: Chapter in Book/Report/Conference proceedingChapter

36 Citations (Scopus)

Abstract

Petri net has been employed for modeling metabolic pathways as well as signal transduction pathways and gene regulatory networks. The purpose of this paper is to introduce an extension of Petri net called hybrid functional Petri net (HFPN) which allows us to model biopathways naturally and effectively. The method for creating biopathways with HFPN is demonstrated through a well-known biopathway example "lac operon gene regulatory mechanism and glycolytic pathway." In order to evaluate this biopathway model, simulations of five mutants of the lac operon are carried out by Genomic Object Net which is a biopathway simulator based on the HFPN architecture. The software Genomic Object Net and the HFPN files presented in this paper can be downloaded from http://www.GenomicObject.Net/.

Original languageEnglish
Title of host publicationLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
EditorsWil M.P. van der Aalst, Eike Best
PublisherSpringer Verlag
Pages3-22
Number of pages20
ISBN (Electronic)9783540403340
DOIs
Publication statusPublished - 2003

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume2679
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

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