We've been building http://www.github.com/graphistry/pygraphistry to enable doing this from most browsers and notebooks. The idea is to use WebGL to render the big graphs (pan/zoom/etc.), and offload most of the real-time compute (layout, filter, etc.) to a GPU cloud. It's similar to Gephi and Cytoscape, but with more of a focus on scaling to big graphs and streamlining data analysis, and integrating into web apps and notebook environments.
