What's new in CellDesigner 4.0
CD 4.0 implemented most of Systems Biology Graphical Notation (SBGN) level 1 proposal.
CellDesignerTM: A modeling tool of biochemical networks
Current Release Version: 
CellDesigner 4.0.1:
NOTICE: (2008/08/12) We have found serious bugs in CellDesigner4.0.
Ver.4.0.1 fixes the following bugs.
- Notes data may be lost when saving the file.
- SBW connection: CellDesigner annotation data is not passed to SBW modules.
- Database link to Genome Network Platform is not working
- Incorrect error messages for simulation.
- Cannot set stoichiometry value other than 1
What is CellDesignerTM
CellDesigner is a structured diagram editor for drawing gene-regulatory and biochemical networks. Networks are drawn based on the process diagram, with graphical notation system proposed by Kitano, and are stored using the Systems Biology Markup Language (SBML), a standard for representing models of biochemical and gene-regulatory networks. Networks are able to link with simulation and other analysis packages through Systems Biology Workbench (SBW).
CellDesigner supports simulation and parameter scan by an integration with SBML ODE Solver.and Copasi.
By using CellDesigner, you can browse and modify existing SBML models with references to existing databases, simulate and view the dynamics through an intuitive graphical interface. 
How to Cite CellDesigner
- Funahashi, A., Tanimura, N., Morohashi, M., and Kitano, H., CellDesigner: a process diagram editor for gene-regulatory and biochemical networks, BIOSILICO, 1:159-162, 2003
[doi:10.1016/S1478-5382(03)02370-9] - 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 Volume 96, Issue 8, Aug. 2008 Page(s):1254 - 1265
[doi 10.1109/JPROC.2008.925458] Abstract | Full Text: PDF (1379 KB)
- Kitano, H.et al. "Using process diagram for the graphical representation of biological networks", Nature Biotechnology 23(8), 961-966 (2005)
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