You may run jAmaSeis without a GUI in headless mode. To run a Java program in headless mode you need to add "-Djava.awt.headless=true" to the command line arguments such as: java -Djava.awt.headless=true -Xmx1024m -jar jAmaseis.jar To edit the configuration you normally need to run with a GUI in order to modify the Java preferences. On Ubuntu Linux (should be the same for others as well) the configuration is normally found under the "~/.java/.userPrefs/edu/iris/epo/jamaseis/options" directory. The settings are in "prefs.xml" in the top directory and the sources are in "prefs.ml" under a source directory e.g., source0. For Windows and Mac you can also have Java use the Linux file preferences instead of the registry or plist file by starting jAmaSeis with the following command: java -Djava.util.prefs.PreferencesFactory=java.util.prefs.FileSystemPreferencesFactory -Xmx1024m -jar jAmaseis.jar For the Linux file preferences the directory may be specified by setting the java.util.prefs.userRoot property: mkdir /Users/kevin/jamaseis/userPrefs java -Djava.util.prefs.PreferencesFactory=java.util.prefs.FileSystemPreferencesFactory -Djava.util.prefs.userRoot=/Users/kevin/jamaseis/userPrefs -Xmx1024m -jar jAmaseis.jar Example preferences files: prefs.xml source0//prefs.xml: