CellDesigner 3.5: A versatile modeling tool for biochemical networks

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

Research output: Contribution to journalArticle

285 Citations (Scopus)

Abstract

Understanding of the logic and dynamics of generegulatory and biochemical networks is a major challenge of systems biology. To facilitate this research topic, we have developed a modeling/simulating tool called CellDesigner. CellDesigner primarily has capabilities to visualize, model, and simulate gene-regulatory and biochemical networks. Two major characteristics embedded in CellDesigner boost its usability to create/import/export models: 1) solidly defined and comprehensive graphical representation (systems biology graphical notation) of network models and 2) systems biology markup language (SBML) as a model-describing basis, which function as intertool media to import/export SBML-based models. In addition, since its initial release in 2004, we have extended various capabilities of CellDesigner. For example, we integrated other Systems Biology Workbench enabled simulation/analysis software packages. CellDesigner also supports simulation and parameter search, supported by integration with SBML ODE Solver, enabling users to simulate through our sophisticated graphical user interface. Users can also browse and modify existing models by referring to existing databases directly through CellDesigner. Those extended functions empower CellDesigner as not only a modeling/ simulating tool but also an integrated analysis suite. Cell-Designer is implemented in Java and thus supports various platforms (i.e., Windows, Linux, and MacOS X). CellDesigner is freely available via our Web site.

Original languageEnglish
Article number4567412
Pages (from-to)1254-1265
Number of pages12
JournalProceedings of the IEEE
Volume96
Issue number8
DOIs
Publication statusPublished - 2008 Aug

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Markup languages
Graphical user interfaces
Software packages
Systems Biology
Websites
Genes

Keywords

  • Biochemical simulation
  • Kinetic modeling
  • SBGN
  • SBML
  • Systems biology

ASJC Scopus subject areas

  • Electrical and Electronic Engineering

Cite this

Funahashi, A., Matsuoka, Y., Jouraku, A., Morohashi, M., Kikuchi, N., & Kitano, H. (2008). CellDesigner 3.5: A versatile modeling tool for biochemical networks. Proceedings of the IEEE, 96(8), 1254-1265. [4567412]. https://doi.org/10.1109/JPROC.2008.925458

CellDesigner 3.5 : A versatile modeling tool for biochemical networks. / Funahashi, Akira; Matsuoka, Yukiko; Jouraku, Akiya; Morohashi, Mineo; Kikuchi, Norihiro; Kitano, Hiroaki.

In: Proceedings of the IEEE, Vol. 96, No. 8, 4567412, 08.2008, p. 1254-1265.

Research output: Contribution to journalArticle

Funahashi, A, Matsuoka, Y, Jouraku, A, Morohashi, M, Kikuchi, N & Kitano, H 2008, 'CellDesigner 3.5: A versatile modeling tool for biochemical networks', Proceedings of the IEEE, vol. 96, no. 8, 4567412, pp. 1254-1265. https://doi.org/10.1109/JPROC.2008.925458
Funahashi A, Matsuoka Y, Jouraku A, Morohashi M, Kikuchi N, Kitano H. CellDesigner 3.5: A versatile modeling tool for biochemical networks. Proceedings of the IEEE. 2008 Aug;96(8):1254-1265. 4567412. https://doi.org/10.1109/JPROC.2008.925458
Funahashi, Akira ; Matsuoka, Yukiko ; Jouraku, Akiya ; Morohashi, Mineo ; Kikuchi, Norihiro ; Kitano, Hiroaki. / CellDesigner 3.5 : A versatile modeling tool for biochemical networks. In: Proceedings of the IEEE. 2008 ; Vol. 96, No. 8. pp. 1254-1265.
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