Genomic Object Net: I. A platform for modelling and simulating biopathways.

Masao Nagasaki, Atsushi Doi, Hiroshi Matsuno, Satoru Miyano

Research output: Contribution to journalArticle

85 Citations (Scopus)

Abstract

Genomic Object Net (GON) 1.0 is a software package for creating models and simulations of biopathways. Its core architecture employs the notion of a hybrid functional Petri net with extension (HFPNe). HFPNe can seamlessly handle discrete and continuous objects and events while keeping the model components themselves simple. With the feature and graphical model editor, biopathways can be modelled intuitively and simulated on GON. The subsequent output of the simulation results can be evaluated in customised views on GON Visualizer by writing an XML file. Additionally, GON provides a tool to transform biopathway models in KEGG and BioCyc to the GON XML files for modelling and simulation. The tool avoids a lot of tedious work by users, enabling them to focus on the biological model.

Original languageEnglish
Pages (from-to)181-184
Number of pages4
JournalApplied bioinformatics
Volume2
Issue number3
Publication statusPublished - 2003

ASJC Scopus subject areas

  • Information Systems
  • Agricultural and Biological Sciences(all)
  • Computer Science Applications

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    Nagasaki, M., Doi, A., Matsuno, H., & Miyano, S. (2003). Genomic Object Net: I. A platform for modelling and simulating biopathways. Applied bioinformatics, 2(3), 181-184.