Celldesigner: A modeling tool for biochemical networks

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

Research output: Chapter in Book/Report/Conference proceedingConference contribution

18 Citations (Scopus)

Abstract

Understanding of 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 SBML compliant, and is SBW-enabled software so that it can import/export SBML described documents and can integrate with other SBW-enabled simulation/analysis software packages. CellDesigner also supports simulation and parameter search, which is supported by integration with SBML ODE Solver, enabling us to simulate through our sophisticated graphical user interface. We could 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 via the Web.

Original languageEnglish
Title of host publicationProceedings of the 2006 Winter Simulation Conference, WSC
Pages1707-1712
Number of pages6
DOIs
Publication statusPublished - 2006 Dec 1
Event2006 Winter Simulation Conference, WSC - Monterey, CA, United States
Duration: 2006 Dec 32006 Dec 6

Publication series

NameProceedings - Winter Simulation Conference
ISSN (Print)0891-7736

Other

Other2006 Winter Simulation Conference, WSC
CountryUnited States
CityMonterey, CA
Period06/12/306/12/6

    Fingerprint

ASJC Scopus subject areas

  • Software
  • Modelling and Simulation
  • Computer Science Applications

Cite this

Funahashi, A., Matsuoka, Y., Jouraku, A., Kitano, H., & Kikuchi, N. (2006). Celldesigner: A modeling tool for biochemical networks. In Proceedings of the 2006 Winter Simulation Conference, WSC (pp. 1707-1712). [4117804] (Proceedings - Winter Simulation Conference). https://doi.org/10.1109/WSC.2006.322946