Yup, it's a bit of a hack right now b/c you need to merge several
branches and tools that are still in review, but it's not too bad.

You need to start from this branch:

https://github.com/ellisonbg/ipython/tree/jsonhandlers

and then grab this repo:

https://github.com/ipython/jsplugins

I would start by testing the d3graph plugin and verify that you can do
what I show here (watch ~ 40 seconds):

http://www.youtube.com/watch?v=F4rFuIb1Ie4&t=40m0s

That should give you the basics.  Then the webgl visualizer example is here:

https://github.com/RishiRamraj/seepymol
 
OK so I now have a very experimental proof of concept of how integrating Galry in the IPython notebook. There's a short demo here: http://www.youtube.com/watch?v=taN4TobRS-E

I'll put the code on github but there's of course much more to do.

I'll also work on a basic matplotlib-like high-level interface that will work in both standard python/ipython consoles, and in the IPython notebook.

Cheers,
Cyrille