Download and Install CellDesigner


  CellDesigner 4.0.1 download from here in systems-biology.org.

CellDesigner4.0.1 is the bug fix version of CellDesigner 4.0.

Bug Fixes:

Known problems


System Requirements

The current version of CellDesigner requires Java2 Runtime Environment (JRE1.5.0 or later) on

*On WIndows "VISTA" and "7", the installer is for 32 bit version.
**On MacOSX 10.4 or later, Java 1.5.0_03 or later is required. On Mac OS X 10.3, Java 1.4.2_05 or later is required.
*** On Linux platform, due to the version of native libraries, Fedora Core 4 or later is recommended; some problems will arise if you use other than these.

The installer includes JRE (Java Runtime Environment 1.5.0_07-b03), so you do not have to install Java before your installation.

If SBW and its modules have already been installed, these modules are available. Especially time evolving simulation of editing models can be performed.


1. Install SBW and SBW modules

If you are interested in time evolving simulation and analysis on biochemical networks, we recommend you to install the Systems Biology Workbench (SBW) and SBW-powered software before you install CellDesigner (*).
Please check http://sys-bio.org/ and download the software from Software Downloads section.

To install SBW and SBW-powered software, follow their installation instructions.

If you would like to use CellDesigner alone right now, you can postpone this step until you need simulation and/or analysis.

(*) As of July, 2008, SBW 2.7.7 is available for Windows, 2.7.6 for MacOSX and Linux.
For details on SBW information: http://sys-bio.org/research/sbwIntro.htm

(**) Note: In case you have installed SBW 2.7.6 or later, and you encounter an error while installing CellDesigner, there might be a possibility that the C++ Broker is up which prevents CellDesigner to start. Please try to kill the broker using the Task Manager, or restart your system before you resume the

2. Install CellDesigner

Download the one for your operating system and follow instructions provided in 00READEME.txt or Startup Guide to install CellDesigner for each environment.

The current release is distributed in archived installer package for each operating system.

  • Windows: CellDesigner-401-windows-installer.exe
  • MacOSX: CellDesigner-4.0.1-osx-installer.zip
  • Linux:      CellDesigner-4.0.1-linux-installer.bin

* While J2RE is required for CellDesigner to run, the installers include it. Therefore, you do not need to download or install J2RE.

NOTICE: (2010/05/10) For Mac Snow Leopard (Mac OSX 10.6) Users
CellDesigner support 32 bit only. To run CellDesigner on Snow Leopard, you need to add -d32 option at Java VM startup.
from the command line from the CellDesigner directory:
"java -Djava.library.path=. -Xms32M -Xmx512M -d32 -cp $(ls exec/*.jar lib/*.jar | tr '\n' ':')

NOTICE: (2010/03/04) For 64bit Windows Users
CellDesigner support 32 bit only. Please install CellDesigner onto 32bit mode.

NOTICE: (2009/07/10) For Mac Leopard (10.5.7) 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 download the following zip file, and execute the fix patch according to the 00Readme.txt in the zip file.

>>> cd401-leopard_java-fix.zip

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

NOTICE: (2008/10/07) For Mac Leopard (10.5.5) Users
Due to the recent Mac update with the Java version update, CellDesigner 4.0.1 can no longer load correctly.
If you are familiar with command line interface (shell prompt), please execute the following 3 command lines which might 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

Note: Install Error

If you encounter the following error when you start CellDesigner on Windows platform
"Javaw.exe - entry point not found."
This error occurs when you have installed different libsbml on your Windows.
Both CellDesigner 4.0 uses libsbml-3. To solve this problem, there are 2 ways as follows:
  • 1. Uninstall libsbml
    This might work, but it may cause a problem if you have a software tool which requires that version of libsbml.
  • 2. Modify the registry on your Windows as follows:
    (Set the value of SafeDllSearchMode to 0)

If both of them didn't work for you, please also check whether you have xerces-c_2_7.dll under C:\Windows\systems32. If so, please remove the dll and restart CellDesigner.

3. Install Copasi

COPASI (http://www.copasi.org/)is a software application for simulation and analysis of biochemical networks. COPASI is free for Non-Commercial Use. If you want to use COPASI with CellDesigner, setup COPASI as follows:

  1. Visit the Copasi web site at http://www.copasi.org/.
  2. Download the Language Binding for Java (e.g. copasi-java-buildxx-win32.zip for Windows 32bit).
  3. Extract the downloaded file.
  4. In the extracted folder, find
    • CopasiJava.dll for Windows.
    • libCopasiJava.jnilib for MacOS X.
    • libCopasiJava.so for Linux.
  5. Copy the file into the CellDesigner’s root folder


File Compatibilities

When you read the files created by lower version of CellDesigner, CellDesigner 4.0 validates the file using libSBML consistency check utility.

  1. Open a file created by lower version of CellDesinger.
  2. Compartment's size attributes are automatically updated.
  3. File conversion needed dialog is open.
    "The file seems to be created by lower version of CellDesigner.
    Do you want to convert this model to work with the current version?"
  4. The file is converted and open with CellDesigner4.0.

Note: File compatibilities

Due to the CellDesigner 4.0 new notation scheme, the following components are no longer supported.
Please edit the original files and redraw them with 4.0 components.

  • Transcriptional activation -> catalysis shape
  • Transcriptional inhibition -> inhibition shape
  • Translational activation -> catalysis shape
  • Translational inhibition -> inhibition shape

  • Tag (4.0 beta files only) -> cannot open file.
    * delete it with 4.0beta and reopen it with CellDesigner4.0.

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