CellDesigner Help

Connecting SBW 2.0 and CellDesigner 2.0
(Dec 31, 2004)

The SBW broker of SBW 2.0 has backward compatibility with SBW 1.0.5, but SBW 2.0 doesn't include some SBW-modules which are required to execute the simulation.
We're planning to release CellDesigner2.1, which will work with SBW 2.0, in Jan 2005.

In the meantime, if you want to connect CellDesigner2.0 with SBW 2.0, here is a workaround.

To install SBW 2.0 and CellDesigner 2.0:

  1. Install SBW 2.0. SBW 2.0 is available from http://sys-bio.org/.
  2. Install CellDesigner 2.0.
    * Please specify the path to SBWCore.jar as
    C:\Program Files\KGI\SBW\bin\SBWCore.jar

    or wherever you have installed SBW 2.0.
  3. Download SBW.zip from the following URL: http://systems-biology.org/~funa/SBW.zip
  4. Note: SBW.zip includes the SBW-modules which is mentioned
    above. These modules are from SBW 1.0.5 distribution. Without these
    modules, user can't execute the simulation.
  5. Unzip SBW.zip to C:\SBW.
  6. Launch SBW broker from
  7. [Start] -> [Systems Biology Workbench] -> [C++ Broker]
  8. Launch cmd.exe, and execute the following commands:
  9. cd C:\Program Files\CellDesigner2.0\jre\bin
    java -jar C:\SBW\modules\SimDriver.jar -sbwregister
    java -jar C:\SBW\modules\plot.jar -sbwregister
  10. Launch CellDesigner 2.0
  11. Open your SBML file, and select [Simulation Service] from [SBW] menu.

Please note that you have to launch the broker (C++ Broker) BEFORE you launch CellDesigner if you want to use SBW modules. This is caused by a problem of SBW 2.0. In SBW-1.0.5, the broker will be automatically kicked up by other SBW-powered application, so the user doesn't have to take care whether the broker is already running or not.

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