CellDesigner 3.5: A versatile modeling tool for biochemical networks

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

研究成果: Article

295 引用 (Scopus)

抜粋

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.

元の言語English
記事番号4567412
ページ(範囲)1254-1265
ページ数12
ジャーナルProceedings of the IEEE
96
発行部数8
DOI
出版物ステータスPublished - 2008 8

ASJC Scopus subject areas

  • Electrical and Electronic Engineering

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  • これを引用

    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