A lot of that stuff is incidental stuff; see .php, .html, .js, and so on. (Apparently there are some web-based tools that he mentions; not sure, though.) The bulk amounts to MATLAB plus Java libraries for remedying MATLAB's functionality gaps.
We used MATLAB. We organized the training data into a database (referred to as the "knowledge base") which was implemented in MYSQL with a web-based UI implemented in PHP. The various other scripts in shell and Perl were used to run the model on our Linux cluster.
I know exactly zilch about this field, so it very well could be something that mundane. However, for spreading calculations across a cluster of 128 computers, I sort of hope they're using something more specifically tailored for the task.
Keeping in mind that my knowledge is zilch, here are some exotic languages that appear to be designed for this sort of thing:
I went to a talk by Dr. Covert a few months ago and it was fascinating, all the moreso as a chalk-talk with an animation flip-book handout.
As an aside, since the topic of CS folks helping with biology research comes up often: apparently a Google engineer went on sabbatical to the Covert lab and helped re-architect and optimize the system to the point that it was feasible for this research. There are many other projects that would benefit from this type of expertise.
