Transcription Factor Regulatory Networks pp 121-145

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

Modeling and Simulation Using CellDesigner

  • Yukiko Matsuoka
  • Akira Funahashi
  • Samik Ghosh
  • Hiroaki Kitano
Protocol

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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Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • Yukiko Matsuoka
    • 1
    • 2
  • Akira Funahashi
    • 3
  • Samik Ghosh
    • 1
  • Hiroaki Kitano
    • 1
    • 2
    • 4
    • 5
  1. 1.The Systems Biology InstituteMinato-kuJapan
  2. 2.JST ERATO Kawaoka Infection Induced Host Response ProjectMinato-kuJapan
  3. 3.Department of Biosciences and InformaticsKeio UniversityYokohama, 223-8522Japan
  4. 4.Open Biology UnitOkinawa Institute of Science and TechnologyKunigamiJapan
  5. 5.Laboratory for Disease Systems ModelingRIKEN Center for Integrative Medical SciencesTsurumi-ku, YokohamaJapan

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