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Transcription Factor Regulatory Networks

Volume 1164 of the series Methods in Molecular Biology pp 121-145

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Modeling and Simulation Using CellDesigner

  • Yukiko MatsuokaAffiliated withThe Systems Biology InstituteJST ERATO Kawaoka Infection Induced Host Response Project
  • , Akira FunahashiAffiliated withDepartment of Biosciences and Informatics, Keio University
  • , Samik GhoshAffiliated withThe Systems Biology Institute
  • , Hiroaki KitanoAffiliated withThe Systems Biology InstituteJST ERATO Kawaoka Infection Induced Host Response ProjectOpen Biology Unit, Okinawa Institute of Science and TechnologyLaboratory for Disease Systems Modeling, RIKEN Center for Integrative Medical Sciences Email author 

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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