Hybrid Petri net based modeling for biological pathway simulation

Hiroshi Matsuno, Masao Nagasaki, Satoru Miyano

Research output: Contribution to journalArticlepeer-review

13 Citations (Scopus)


Hybrid Petri net (HPN) is an extension of the Petri net formalism, which enables us to handle continuous information in addition to discrete information. Firstly, this paper demonstrates how biological pathways can be modeled by the integration of discrete and continuous elements, with an example of the λ phage genetic switch system including induction and retroregulation mechanisms. Although HPN allows intuitive modeling of biological pathways, some fundamental biological processes such as complex formation cannot be represented with HPN. Thus, this paper next provides the formal definition of hybrid functional Petri net with extension (HFPNe), which has high potential for modeling various kinds of biological processes. Cell Illustrator is a software tool developed on the basis of the definition of HFPNe. Hypothesis creation by Cell Illustrator is demonstrated with the example of the cyanobacterial circadian gene clock system. Finally, our ongoing tasks, which include the development of a computational platform for systems biology, are presented.

Original languageEnglish
Pages (from-to)1099-1120
Number of pages22
JournalNatural Computing
Issue number3
Publication statusPublished - 2011 Sept


  • Cell Illustrator
  • Hybrid Petri net
  • Pathway simulation

ASJC Scopus subject areas

  • Computer Science Applications


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