The light control is powered by Matlab. To be honest, this is one of the few time I have seen Matlab used in a project during my whole professional career. All code for Matlab is also on his site.
I have never found a definitive LED light cube design tutorial anywhere on the net. Schulze's page explains the concept in depth. Though, I still think the concept is not fully described as well as I would like. But if you build one from this project page, you will know.