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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 type ant PhyloWidget at 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. Adding &format=xml to the OpenURL request retrieves bibliographic metadata in "unixref" format (for those who like this sort of thing, the XML schema is here). The biggest change is now the metadata lists more than one author for multi-author papers.
This will probably tempt fate, but I've an invited manuscript in review for Briefings in Bioinformatics on the topic of identifiers in biodiversity informatics. Readers of this blog will find much of it familiar (DOis, LSIDs, etc.). For fun I constructed a graph for three ant specimens of Probolomyrmex tani , and the images, DNA sequences, and publications that link to these specimens.
Stumbled across Project Xanadu, Ted Nelson's vision of the way the web should be (e.g., BACK TO THE FUTURE: Hypertext the Way It Used To Be). Nelson coined the term "transclusion", including one document in side another by reference.
Some thoughts on the first release of the Encyclopedia of Life. I am being deliberately critical. This is a high profile project with tens of millions of dollars in funding, lots of people involved, and is accompanied by some of the most overblown hype in organismal biology. In a sense I think EOL has set itself up by over promising and under delivering.
The first release of the Encyclopedia of Life is officially live today. I have promised to be very good...
My short note on the LSID Tester tool has been published in the Open Access journal Source Code for Biology and Medicine. The article has just come out so the DOI (doi:10.1186/1751-0473-3-2) isn't live yet, the direct link is http://www.scfbm.org/content/3/1/2/. Source code for the tester is available from Google Code.