As I am experimenting with the beaglebone, I came up with a solution to create applications in any language that will allow you to control the beaglebone. All I needed to do was to create a program that sends get requests to the beaglebone server and we get a response back. This allows the separation of the server and the control application. All you need during setup is the url where the server is running. As of right now I'm thinking about creating an application that controls certain defined pins on the beaglebone as an example application.