There is a C++/Cuda library with a python frontend that I am starting to play with that is from one of the guys who works with Hinton. It is written by Alex Krizhevsky and has lots of tools for training feed forward networks with lots of different connection topologies and neuron types. If I am not mistaken this was the library that was used in the recent Kaggle drug competition that is referenced in the article. There is some good starting point documentation here as well to look into, as long as you know enough about the mechanics of Artificial Neural Networks it has some really interesting stuff in there.

Here is the link: http://code.google.com/p/cuda-convnet/