3d International ICST Conference on Bio-Inspired Models of Network, Information, and Computing Systems

Research Article

An Algorithm to Estimate Delay Times in Petri Net Models of Signaling Pathways with Experimental Data

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  • @INPROCEEDINGS{10.4108/ICST.BIONETICS2008.4707,
        author={Kanji Hioka and Yoshimasa Miwa and Chen Li and Qi-Wei Ge and Hiroshi Matsuno and Satoru Miyano},
        title={An Algorithm to Estimate Delay Times in Petri Net Models of Signaling Pathways with Experimental Data},
        proceedings={3d International ICST Conference on Bio-Inspired Models of Network, Information, and Computing Systems},
        publisher={ICST},
        proceedings_a={BIONETICS},
        year={2010},
        month={5},
        keywords={Signaling pathway Petri nets Model decomosition Delay time estimation},
        doi={10.4108/ICST.BIONETICS2008.4707}
    }
    
  • Kanji Hioka
    Yoshimasa Miwa
    Chen Li
    Qi-Wei Ge
    Hiroshi Matsuno
    Satoru Miyano
    Year: 2010
    An Algorithm to Estimate Delay Times in Petri Net Models of Signaling Pathways with Experimental Data
    BIONETICS
    ICST
    DOI: 10.4108/ICST.BIONETICS2008.4707
Kanji Hioka1,*, Yoshimasa Miwa1,*, Chen Li2,*, Qi-Wei Ge3,*, Hiroshi Matsuno1,*, Satoru Miyano2,*
  • 1: Graduate School of Science and Engineering, Yamaguchi University 1677-1 Yoshida, Yamaguchi 753-8512, Japan
  • 2: Human Genome Center, University of Tokyo 4-6-1 Shirokanedai, Minatoku, Tokyo 108-8639, Japan
  • 3: Faculty of Education, Yamaguchi University 1677-1 Yoshida, Yamaguchi 753-8513, Japan
*Contact email: hioka@ib.sci.yamaguchi-u.ac.jp, miwa@ib.sci.yamaguchi-u.ac.jp, chenli@ims.u-tokyo.ac.jp, gqw@yamaguchi-u.ac.jp, matsuno@sci.yamaguchi-u.ac.jp, miyano@ims.u-tokyo.ac.jp

Abstract

In this paper, we propose an algorithm to estimate delay times in a Petri net model of signaling pathways based on biological experimental data. Firstly, we demonstrate a modeling method of signaling pathways with discrete Petri net using ErbB4 signaling pathway. Then, we propose a delay time estimation algorithm for Petri net models with experimental data. The estimated delay times are assigned to the transitions of the Petri net model of the ErbB4 signaling pathway that is simulated on Cell Illustrator 3.0. The simulation results are evaluated by comparing with the experimental data.