Modeling and simulation using cellDesigner

Yukiko Matsuoka, Akira Funahashi, Samik Ghosh, Hiroaki Kitano

Research output: Contribution to journalArticlepeer-review

59 Citations (Scopus)


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 Cell Designer, adopting the standards such as SBML and SBGN.

Original languageEnglish
Pages (from-to)121-145
Number of pages25
JournalMethods in Molecular Biology
Publication statusPublished - 2014 Jan 1
Externally publishedYes


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

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics


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