I drew these Yeast protein interaction networks on a arc with the Javascript Protovis.js using the HTML5 canvas object as the pallet. Displayed are only a select number of edges though all the nodes of interest are listed. If you drill down on the baseline you can see the names of the ORFs. ORFs are clustered by gene, but otherwise there is little meaning in horizontal distance.

Ultimately, this should be an interactive tool for visual selection of biologically relevant interactions, resulting in tabular data retrieved from supporting databases.

(See also: protovis)

I watched, earlier this decade as Tamara Munzner’s H3Viewer came on the scene. Walrus is being developed by Young Hyun at CAIDA and builds on the idea. Although Walrus is based on research by Tamara Munzner, she is not connected with this effort in any way, nor does Walrus make use of any code from her H3Viewer.

The project appears to be dormant (since 2005) and claims it doesn’t run on modern Macintosh systems (no-longer the case). I’m looking for biological applications in non-directed graph visualization. Specifically, Yeast interaction networks.

(See also: walrus)

The Global edition of the New York Times has a nice tool on their site for tracking 2010 World Cup matches. Heat maps of field position, shot and possession timelines, updated every 15 seconds.

(See also: NYtimes: LIVE World Cup Match Tracker)

A tremendous image this morning. May your weather map appear less interesting.

(See also: www.wunderground.com)

Here is an early visualization I created of functional genomic interaction networks in yeast. I’m using Gephi 0.7 alpha3 to create the images and though this is a small subset of the greater hairball generated from 3531 nodes and 20,293 edges, it is perhaps the most beautiful.

Here is the same data rendered in Cytoscape v2.6.2, with labels turned on the nodes.

For my next trick, I will attempt to build a model of 4467 nodes and 8,394,136 edges. LGL appears to be built for large biological datasets like this.

(See also: DRYGIN: a database of quantitative genetic interactions of S. Cerevisiae)
(See also: gephi.org)
(See also: LGL is a compendium of applications for making the visualization of large networks and trees tractable.)
(See also: cytoscape.org)