CellDesigner

CellDesigner^TM: A modeling tool of biochemical networks

Current Release Version: CellDesigner 4.0.1
CD 4.0 implemented most of Systems Biology Graphical Notation (SBGN) Process Diagram level 1 draft proposal. find out more...

NOTICE: (2008/10/07) For Mac Leopard (10.5.5) Users
Due to the recent Mac Java update, there is a problem of CellDesigner launch. We will release the fixed version shortly. In the meantime, please execute the following 3 command lines from command line interface (shell prompt), which would fix the problem.

cd /Applications/CellDesigner4.0.1/CellDesigner4.0.1.app/Contents/MacOS
mv JavaApplicationStub JavaApplicationStub.bak
cp /System/Library/Frameworks/JavaVM.framework/Versions/A/Resources/MacOS/JavaApplicationStub ./
NOTICE: (2009/01/26) For Ubuntu Linux Users
If compiz is enabled, it might cause the GUI problem. Please try the following commands to run CellDesigner.:
$ export AWT_TOOLKIT="MToolkit"
$ ~/runCellDesigner4.0.1

Check also:

Plugins / Utilities

BioModels.net models simulation results with CellDesigner 4

What is CellDesigner^TM

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.