CellDesigner Help

Simulation by SBW

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

If SBW has been installed on your machine, you can work directly from CellDesigner with other SBW compliant applications. SBW menu of CellDesigner is enabled when SBW is available.

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 CellDesigner installation.

To install SBW and SBW-powered software

  1. Go to http://sys-bio.org/.
  2. Downloal applications and follow their installation instructions.

To confirm the installation of SBW

  1. To check if the SBW is properly installed, start CellDesigner and open a file.
  2. The SBW menu in the Menu should be activated if your setup has correctly been done.
  3. Check if there are any simulators listed in the SBW menu.
  4. If you have installed the simulators of your choice correctly, they are listed under SBW menu.

To register with SBW

  1. Open a file.
  2. In the Menu, select SBW, then Register with SBW.

To call an SBW module

  1. Open a file.
  2. In the Menu, select SBW.
  3. See that the menu items offered by the SBW are listed.
  4. Select an appropriate menu item from the list.
  5. Jarnac Simulation Service appears if Jarnac has been installed. The others are default-installed.

To simulate a model using SBW

  1. Open the sample file MAPK.xml in "samples" directory.
  2. In the Menu, select SBWJarnac Simulation Service. This launches Jarnac Simulator.
  3. Change TimeEnd value to "1000".
  4. Change Number of Points value to "100".
  5. Click Simulate
    Jarnac Simulator
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