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

Kanji Hioka; Yoshimasa Miwa; Chen Li; Qi-Wei Ge; Hiroshi Matsuno; Satoru Miyano

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.

Keywords: Signaling pathway Petri nets Model decomosition Delay time estimation

Published: 2010-05-16
Publisher: ICST
Modified: 2010-05-16

: http://dx.doi.org/10.4108/ICST.BIONETICS2008.4707