Mauro Cavalcanti has released e-Species, "a taxonomically intelligent biodiversity search engine" written in Python that mimics much of the functionality of iSpecies. The project is open source, with a SourceForge page, although no files seem to be available yet. This is the second iSpecies clone I've seen, David Shorthouse having written a clone that uses only JSON.
Mauro Cavalcanti brought Chris Anderson's The End of Theory article in Wired to my attention, part of the July issue on "The End of Science". Of course, the end of science is hyperbole of the highest order (as, indeed, is the "end of theory"). It is also ironic that in the same issue Wired confess to having gotten 5 predictions of the death of something hopelessly wrong (including web browsers and online music swapping, no less). However, I
Hasan Jamil has released PhyQL, a visual system for querying phylogenetic information. To quote from the web site: There is also a YouTube screencast: I haven't had a chance to play with it yet. PhyQL was originally described by Jamil et al. "Querying phylogenies visually", BIBE 2001 (doi:10.1109/BIBE.2001.974405).
I've put the first version of "tvwidget" into Google Code. This is a HTML-only widget to display large evolutionary trees (you can see how my thoughts on how to do this unfolded by following my earlier posts starting with Visualising very big trees, Part V). tvwidget itself is a C++ program that takes a tree and generates the image tiles and Javascript for the viewer. It's poorly documented, I'll deal with tis once I get some time.
I've added a service to bioGUID that takes a PDF and attempts to extract latitude and longitude data from the PDF, returning those co-ordinates in either a Google Earth KML file, or in JSON format. This is one of a bunch of services that I'm adding to bioGUID to support some of the data mining that I'm doing.
Resurrecting iSpecies after moving it to a new folder{"=““} on one of my servers, and browsing popular searches, I keep coming across clearly erroneous distributions. FishBase seems a major culprit. For example, the common pandora Pagellus erythrinus is a marine fish, yet GBIF displays numerous occurrences in mainland Africa (dots with black centre on map below). What gives?
I have an "on again/off again" relationship with treemaps. Lately, I've been taking another look, partly inspired by Björn Engdahl's MSc thesis Ordered and Unordered Treemap Algorithms and Their Applications on Handheld Devices.
Something a little different, my dad's work features in the Winter 2008 issue of Art News New Zealand by Rob Garrett, who has a copy of the article on his web site. Dad designed eight stained glass windows for Westlake Boys High School in Auckland, New Zealand. Rob Garrett describes them thus: They are gorgeous to look at (the picture below shows them before they were mounted in the school hall).
As much as I like the idea of a globally unique, resolvable identifier, my recent experience with JSTOR is making me wonder. JSTOR has three identifiers for articles it archives, DOIs, SICIs, and stable URLs (the later being introduced with the new platform released April 4, 2008). Previously JSTOR would publish DOIs for many of its articles.
--Robert M. May, 1988, "How many species are there on Earth? doi:10.1126/science.241.4872.1441 Not much has changed in twenty years...
BioOne sucks. Really, really, sucks. I have lost count of the number of times they break DOIs. These are supposed to be the gold standard globally unique identifier, and BioOne continually buggers them. For example, take this URL: http://www.bioone.org/perlserv/?request=get-abstract&doi=10.1600/02-14.1. Note the doi=10.1600/02-14.1 bit at the end.