CellDesigner: A graphical biological network editor and workbench interfacing simulator

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

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Citation (Scopus)

Abstract

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/.

Original languageEnglish
Title of host publicationIntroduction to Systems Biology
PublisherHumana Press
Pages422-434
Number of pages13
ISBN (Print)9781588297068
DOIs
Publication statusPublished - 2007
Externally publishedYes

Fingerprint

Systems Biology
Simulators
Markup languages
Language
Gene Regulatory Networks
Software
Genes
Graphical user interfaces
Ordinary differential equations
Software packages
Websites
Databases
Research

Keywords

  • biochemical simulation
  • Pathway editor
  • SBGN
  • SBML
  • SBW
  • systems biology
  • XML

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Funahashi, A., Morohashi, M., Matsuoka, Y., Jouraku, A., & Kitano, H. (2007). CellDesigner: A graphical biological network editor and workbench interfacing simulator. In Introduction to Systems Biology (pp. 422-434). Humana Press. https://doi.org/10.1007/978-1-59745-531-2_21

CellDesigner : A graphical biological network editor and workbench interfacing simulator. / Funahashi, Akira; Morohashi, Mineo; Matsuoka, Yukiko; Jouraku, Akiya; Kitano, Hiroaki.

Introduction to Systems Biology. Humana Press, 2007. p. 422-434.

Research output: Chapter in Book/Report/Conference proceedingChapter

Funahashi, A, Morohashi, M, Matsuoka, Y, Jouraku, A & Kitano, H 2007, CellDesigner: A graphical biological network editor and workbench interfacing simulator. in Introduction to Systems Biology. Humana Press, pp. 422-434. https://doi.org/10.1007/978-1-59745-531-2_21
Funahashi A, Morohashi M, Matsuoka Y, Jouraku A, Kitano H. CellDesigner: A graphical biological network editor and workbench interfacing simulator. In Introduction to Systems Biology. Humana Press. 2007. p. 422-434 https://doi.org/10.1007/978-1-59745-531-2_21
Funahashi, Akira ; Morohashi, Mineo ; Matsuoka, Yukiko ; Jouraku, Akiya ; Kitano, Hiroaki. / CellDesigner : A graphical biological network editor and workbench interfacing simulator. Introduction to Systems Biology. Humana Press, 2007. pp. 422-434
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