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)