Controlling j5 assembly parameters
After starting a DeviceEditor session, you can set the j5 assembly parameters.

Demonstration video:

Here is a demonstration video that goes through this process (Control j5 assembly parameters.mov, right click this link to save the movie to disk for better viewing):


For more information on j5 assembly parameters, refer to the "j5 parameters file" page in the j5 user's manual.

Click the "j5" button at the top left of the DeviceEditor display. This will pop-up a new  "j5 Controls" dialog box. Within this dialog box, click on the "Run j5 on Server" tab. Within this tab, on the "j5 Parameters File" line, click on the "from parameters" link within the "Generate file from parameters" radio button label. This will pop-up a new  "j5 Parameters" dialog box, in which you can set many of the parameters that control how j5 designs DNA assemblies. To reset the parameters to their default values, click the "Return to Defaults" button. To reset the parameters to the values most recently used on the j5 server, click the "Return to Server Values" button. After you are satisfied with you changes, press the "OK" button, or press the "Cancel" button to reject your changes.

From here, you can either write the j5 parameters to disk, or you can progress to running j5 on the server from DeviceEditor directly, which will allow you to automatically generate a j5 assembly parameters file on-the-fly from the parameters you have just selected.