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Transcription Factor Regulatory Networks pp 121–145Cite as

Modeling and Simulation Using CellDesigner

Part of the Methods in Molecular Biology book series (MIMB,volume 1164)

Abstract

In silico modeling and simulation are effective means to understand how the regulatory systems function in life. In this chapter, we explain how to build a model and run the simulation using CellDesigner, adopting the standards such as SBML and SBGN.

Key words

  • CellDesigner
  • Transcription regulatory network
  • SBML (systems biology markup language)
  • SBGN (systems biology graphical notation)
  • Garuda platform

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Acknowledgements

This work is, in part, supported by funding from the Genome Network Project of the Ministry of Education, Culture, Sports, Science, and Technology (MEXT), New Energy and Industrial Technology Development Organization (NEDO), International Strategic Collaborative Research Program (BBSRC-JST) of the Japan Science and Technology Agency (JST), the Exploratory Research for Advanced Technology (ERATO) program of JST to the Systems Biology Institute (SBI) and from a strategic cooperation partnership between the Luxembourg Centre for Systems Biomedicine and SBI.

Author information

Authors and Affiliations

  1. The Systems Biology Institute, 5-6-9 Shirokanedai, Minato-ku, Tokyo, 108-0071, Japan

    Yukiko Matsuoka, Samik Ghosh & Hiroaki Kitano

  2. JST ERATO Kawaoka Infection Induced Host Response Project, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan

    Yukiko Matsuoka & Hiroaki Kitano

  3. Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kouhoku-ku, Yokohama, 223-8522, Japan

    Akira Funahashi

  4. Open Biology Unit, Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna-son, Kunigami, Okinawa, 904-0495, Japan

    Hiroaki Kitano

  5. Laboratory for Disease Systems Modeling, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan

    Hiroaki Kitano

Authors
  1. Yukiko Matsuoka
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  2. Akira Funahashi
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  3. Samik Ghosh
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  4. Hiroaki Kitano
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Corresponding author

Correspondence to Hiroaki Kitano .

Editor information

Editors and Affiliations

  1. Division of Interactome Medical Science, The University of Tokyo, The Institute of Medical Science, Minato-ku, Tokyo, Japan

    Etsuko Miyamoto-Sato

  2. Division of Interactome Medical Science, The University of Tokyo, The Institute of Medical Science, Minato-ku, Tokyo, Japan

    Hiroyuki Ohashi

  3. Division of Interactome Medical Science, The University of Tokyo, The Institute of Medical Science, Minato-ku, Tokyo, Japan

    Hirotaka Sasaki

  4. Division of Interactome Medical Science, The University of Tokyo, The Institute of Medical Science, Minato-ku, Tokyo, Japan

    Jun-ichi Nishikawa

  5. Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, Kohoku-ku, Yokohama, Japan

    Hiroshi Yanagawa

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Matsuoka, Y., Funahashi, A., Ghosh, S., Kitano, H. (2014). Modeling and Simulation Using CellDesigner. In: Miyamoto-Sato, E., Ohashi, H., Sasaki, H., Nishikawa, Ji., Yanagawa, H. (eds) Transcription Factor Regulatory Networks. Methods in Molecular Biology, vol 1164. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-0805-9_11

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  • DOI: https://doi.org/10.1007/978-1-4939-0805-9_11

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-0804-2

  • Online ISBN: 978-1-4939-0805-9

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