CellDesigner: A graphical biological network editor and workbench interfacing simulator

Akira Funahashi, Mineo Morohashi, Yukiko Matsuoka, Akiya Jouraku, Hiroaki Kitano

研究成果: Chapter

2 被引用数 (Scopus)

抄録

Understanding the logic and dynamics of gene-regulatory and biochemical networks is a major challenge of systems biology. To facilitate this research topic, we have developed CellDesigner, a modeling tool of gene-regulatory and biochemical networks. CellDesigner supports users to easily create such networks, using solidly defined and comprehensive graphical representation (SBGN, systems biology graphical notation). CellDesigner is systems biology markup language (SBML) compliant, and has Systems Biology Workbench(SBW)-enabled software so that it can import/export SBML-described documents and integrate with other SBW-enabled simulation/analysis software packages. CellDesigner also supports simulation and parameter search, which is supported by integration with SBML ordinary differential equation (ODE) Solver, enabling us to simulate through our sophisticated graphical user interface. We can also browse and modify existing SBML models with references to existing databases. CellDesigner is implemented in Java; thus, it runs on various platforms such as Windows, Linux, and MacOS X. CellDesigner is freely available from our Web site at http://celldesigner.org/.

本文言語English
ホスト出版物のタイトルIntroduction to Systems Biology
出版社Humana Press
ページ422-434
ページ数13
ISBN(印刷版)9781588297068
DOI
出版ステータスPublished - 2007 12 1
外部発表はい

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)

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