One of the things that keeps bothering me is the lack of compelling ways to visualise information in phylogenetic databases. Trees themselves are, I feel, pretty awful objects to work with. They are large, and displaying them takes up a lot of screen real estate. Yet, in many ways, the more one sees of the tree the less one gains from the experience.

Not a huge fan of IE, but this post on David Patten's blog nicely illustrates the ease of use of A9's OpenSearch with IE 7. I'd previously played with OpenSearch as a quick way to integrate biodiversity sources, and put together a couple that have been registered with A9 (search for "taxonomy" and you'll find them). It's essentially adding a few tags to RSS or Atom feeds, coupled with a simple way to describe the search engine.

A quick Google found this Firefox extension for turning built-in SVG on and off, posted on or maybe something uplifting. Really useful little extension, because Firefox SVG support is actually pretty awful very good. (Just discovered that FireFox couldn't handle my original SVG, but if I put in the namespaces as attributes of the svg tag, everything worked fine.

Well, that was fun. I've just installed AT&T's WebDot, a Tcl CGI program for generating images of graphs on the fly using Graphviz. Although there are RPMs for Fedora Core 4 available from AT&T's site, they didn't work. Here's what I did to get this working: Installed Graphviz from the RPM. Installed WebDot from the source tarball, not the RPM.

The Human-Computer Interaction Lab at the University of Maryland has produced numerous nice visualisation tools, and has a page devoted to biodiversity visualisation.

My suspicion is that most queries biologists would make concerning trees are fundamentally LCA queries (as opposed to pattern matching, for example). For instance, "find me trees where group x is monophyletic" is a LCA query.

All My Eye is a new blog by staff at Ingenta involved in RDF and related projects. Worth keeping an eye on, especially as the Ingenta fields are metadata rich, and have been used by uBio's RSS project.

Continuing the theme of visualising phylogenies, one thing which strikes me is the parallel between genome browsers that display annotation "tracks" (such as the UCSC Genome Browser) and illustrations of "chronograms" with geological periods and accompanying data, such as sea levels, isotope levels, etc. In my haste I couldn't find an example with a sea-level track, but I know they exist. The chronogram at right comes from Steppan et al.

VLDB2005 has some interesting papers. One which caught my eye is Efficiently Processing Queries on Interval-and-Value Tuples in Relational Databases [PDF] by Enderle et al. Why?

Amber Frid-Jimenez: has a really nice page showing document icons that reflect the words contained in the document. Neat idea, and has a lot of potential. One obvious extension to phylogenetics would be to represent the taxonomic coverage in a similar style, so people could very quickly find studies on related sets of organisms simply by browsing.

I've updated my extension to resolve LSIDs in Firefox so that it works with version 1.5.0.1 (the most recent version of Firefox). The extension is available from Mozdev. It may take a little while for the mirrors to update with the new version, so if you get a "404" when trying to download, you may need to come back later. IBM's LSID project have their own Firefox extension LSID Launchpad for Firefox, which is a lot slicker than mine.