For my thesis I had some similar ideas, but they were more abstract, sculpture-like. The user volume was a cylinder, with varying radii (mapped to activity) at different heights (time). The mappings you are talking about are very subjective, but it's good brainstorming. Refining and iterating over such ideas, brings innovation.
You are spot on that Github has very rich relationships of collaboration and sharing that are not all expressed by the data I chose. I wrote a longer post about my goals and motivation with Ekisto that addresses that concern:
http://processq.tumblr.com/post/69098066993/ekisto-design
I also write about future work which will improve the current version. I think some tagging functionality either precomputed or user-contributed will help a lot of newcomers understand the map better. Stackoverflow veterans immediately recognize the clusters and the avatars.
Yes, great feedback. StackOverflow does something similar, it displays a badge on mouse over a user link. Very helpful for seeing the top tags where the user posts.
There is a shortcut: Press Q + click. Pressing Q turns on query mode for one click. I only included it that in the mouseover tooltips, fearing abuse. The server seems to handle it well, so query away.
For Github you have to enter the username. For Stackoverflow you have to enter the numerical userid which can be found in the url of your profile page.
The Github API rate limiting made it impossible to keep up with the user/repository growth so I stopped in March 2012. Only users that were public at the date of the crawl, and are part of the largest connected component of the network will be shown.
I am the designer of Ekisto. Questions and feedback are welcome :)