Gene Wiki Rainbow

Last summer I posted an image of the Gene Wiki hyperlink network, aptly titled "the gene wiki hairball".  The image was picked up by noted artist/scientist Martin Krzywinski and used as an example of why hairballs are a terrible visualization.  Perhaps out of guilt for making an example out of us and/or perhaps out of interest he has helped us improve our thinking about how to visualize networks substantially.  Here is a Circos view of the top 100 genes in the gene wiki, the editors that created the articles, and the diseases and compounds that the genes are linked to.  It will be presented as a guerilla poster[1] at ISMB this year so please stop by and have a closer look!

Aside from bringing an artistic aesthetic to scientific illustrations, one of Martin's main contributions (IHOP) is that he understands and uses space to convey meaning effectively.  In a hairball, the only consideration of space in the layout algorithm is to reveal as many nodes as possible.  In a Circos diagram, place can be attached to semantics.  This fundamental idea is used to an even greater extent in Martin's latest layout invention, Hive Plots.  Watch out for the Gene Wiki Hive Mind visualization - or better yet, write to us and help us build it!

[1] guer·ril·la post·er /gəˈrilə/ /ˈpōstər/

Noun: An uninvited poster displayed at a scientific conference.

TripleMap

I had fun playing with TripleMap today.  Its an RDF-backed Adobe Flash (Flex I assume) Web application for exploring graphical biomedical data.

Rapid conclusions

1. Its pretty - the visualization system worked well for my explorations
2. It has a few bugs (but it hasn't even reached a beta release yet so thats to be expected)
3. You are going to want to get more data into it as soon as you start using it.  While there is enough in there today to get you started, anyone familiar with bioinformatics will notice that a lot is still missing (but I know more is already on its way).
4. Its definitely something to keep an eye on as it develops.

Pretty Paper

Check out this visualization of the paper I'm working on at the moment. Very pretty, but I wish I could make the words link to something to make it more active and exploratory. Make your own at wordle.net. (Thanks to Egon for the tip).

seeing is believing

Wow, its been nearly a month since I wrote here.  I've been busy running in 5 directions at once - no surprise I haven't gotten anywhere lately.  But, just to get back in the habit, here is one of the tangential  things I've been thinking about when I should have been running in one direction as fast as I could.

Web3.0 needs a face.

Web2.0 has the profile page, the social network graph, and the tag cloud, what is the face of Web3.0?

The most popular and functional candidates thus far appear to be the products of the Simile group from MIT.  The main view I've seen appearing all over is the faceted browser (Longhorn, Exhibit) with fun enhancements like the Timeline component.  

These are great, but to me seem like fairly small steps from what we have already (at least from the user perspective, the code that runs them is pretty much magic).

Something new .

I wonder if something more along the lines of PhotoSynth will someday be making its way into our day to day desktop experience.  The thing that I see Photosynth doing, in a very intuitive way as it cheats by using reality, is to give huge collections of data such as that which can already be drawn from the giant global graph a nicely navigable, beautiful shape.  I wonder if there is some way to map large collections of other kinds of data such that the form underlying them is a) rendered in some beautiful way and b) rendered such that it actually contributes to the understanding and navigation of the collection.  [That will probably make more sense if you have seen this amazing demonstration of photosynth].  

the structure is the thing,

and it needs to be pretty!