From time to time, it might be useful to view the Java standard out text console. The BioCoRE Control Panel can send debugging information there as can other Web Start programs that you might want to run. In its default configuration, you won't ever see the Java console. To enable it, you need to go into the Java Web Start application manager (On Windows you probably have an application called 'Java Web Start' in your Start menu, and on unix it is probably an application called 'javaws' that might or might not be in your path). On Mac OS X, the console is automatically enabled, and console messages can be found in ~/Library/Logs/Java Console.log, and can be viewed using the Console application in Applications/Utilities.

In the application manager, you can go to File | Preferences and navigate to the Advanced tab where you can enable the Java console. You have the option of having it pop open every time you that you run an application (Show Java Console), or you can have it automatically log the output to a file (Log Output). Personally, I would recommend just having it log the output to a file. That way you don't have an extra window everytime you run an application, but you can still look at the output if you wish to do so. Just choose a log file name that is somewhere that you can remember it. The BioCoRE Control Panel shouldn't ever put too much text there, but some programs can, so you might want to check the size of the log file on occasion.