I started this blog with the goal of documenting my own efforts to make a database of evolutionary trees, based on ideas sketched in hdl:10.1038/npre.2007.1028.1. I've felt that the major task is link phylogenies to other information, such as taxon names, specimens, localities, images, publications, etc. That is, to embed trees in a broader context.

The dissection of the colossal squid ( Mesonychoteuthis hamiltoni ) specimen from Antarctica has been getting a lot of coverage. Pangs of homesickness, especially seeing Steve O'Shea enthusing about the beast. Steve was a contemporary at Auckland Uni when I was a student.

Last month I was at the MBL in Woods Hole, taking part in the review of the Biodiversity Informatics Group. BIG is responsible for the EOL web site. I chair the Informatics Advisory Group, which provides advice to BIG, and it was our task to produce an evaluation of where things stood. I've written a post on the Encyclopaedia of Life blog about some of the big challenges facing EOL as it moves into its second year.

Bit of a rarity these days.

For some time now Google Code has been displaying the message: The web interface for wiki content is currently READ-ONLY for maintenance. You may still add comments, and members may add, edit, or delete wiki pages via svn. Learn more.

The manuscript for Briefings in Bioinformatics that I alluded to earlier has been accepted for publication. I've put a preprint up at Nature Preceding (hdl:10101/npre.2008.1760.1). The final version will appear in print later this year.

Greg Jordan and Bill Piel have released PhyloWidget, a Java applet for viewing phylogenetic trees. It's very slick, with some nice visual effects courtesy of Processing. PhyloWidget is open source, with code hosted by Google code. I'm a C++ luddite, so it took me a few moments to figure out how to build the applet, but it's simple enough, just typeant PhyloWidgetat the command prompt.

Vince Smith alerted me to "Systematics as Cyberscience", by Christine Hine, whose work I've mentioned earlier. Looks like an interesting read.

Google's Social Graph API was released earlier this year.The motivation:Apart from the obvious application to scientific databases (for example, utilising connections such as co-authorship), imagine the same idea applied to data.

Tom Pasley recently drew my attention to CrossRef's addition of a XML format parameter to their OpenURL resolver.