Literature DB >> 15130807

Genomic Object Net: II. Modelling biopathways by hybrid functional Petri net with extension.

Atsushi Doi1, Masao Nagasaki, Sachie Fujita, Hiroshi Matsuno, Satoru Miyano.   

Abstract

This paper demonstrates how to create an HFPNe (hybrid functional Petri net with extension) model, using the lac operon gene regulatory mechanism and glycolytic pathway as an example. Using this example, readers can then model other biopathways of interest. Simulations of the HFPNe model were performed using the software package Genomic Object Net.

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Year:  2003        PMID: 15130807

Source DB:  PubMed          Journal:  Appl Bioinformatics        ISSN: 1175-5636


  5 in total

1.  An efficient biological pathway layout algorithm combining grid-layout and spring embedder for complicated cellular location information.

Authors:  Kaname Kojima; Masao Nagasaki; Satoru Miyano
Journal:  BMC Bioinformatics       Date:  2010-06-18       Impact factor: 3.169

2.  An efficient grid layout algorithm for biological networks utilizing various biological attributes.

Authors:  Kaname Kojima; Masao Nagasaki; Euna Jeong; Mitsuru Kato; Satoru Miyano
Journal:  BMC Bioinformatics       Date:  2007-03-06       Impact factor: 3.169

3.  Simulation-based model checking approach to cell fate specification during Caenorhabditis elegans vulval development by hybrid functional Petri net with extension.

Authors:  Chen Li; Masao Nagasaki; Kazuko Ueno; Satoru Miyano
Journal:  BMC Syst Biol       Date:  2009-04-27

4.  Application of approximate pattern matching in two dimensional spaces to grid layout for biochemical network maps.

Authors:  Kentaro Inoue; Shinichi Shimozono; Hideaki Yoshida; Hiroyuki Kurata
Journal:  PLoS One       Date:  2012-06-05       Impact factor: 3.240

5.  LucidDraw: efficiently visualizing complex biochemical networks within MATLAB.

Authors:  Sheng He; Juan Mei; Guiyang Shi; Zhengxiang Wang; Weijiang Li
Journal:  BMC Bioinformatics       Date:  2010-01-15       Impact factor: 3.169

  5 in total

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