Flipboard and BHL

Flipboard is a new application for the iPad that is pitching itself as a personalised social magazine. It's launch created a lot of buzz, so much so that many users were unable to add their Facebook and Twitter accounts to it, much to their chagrin. I was one of these annoyed users, but now that I've been able to login I've been having a play and it's a lot of fun.

Nice typography and a clever layout is part of the attraction, and there has been some discussion about whether the Biodiversity Heritage Library (BHL) could be integrated.

@chrisfreeland @rdmpage #bhlib integration on @flipboard? The fb interface is very polished, familiar and comfortableless than a minute ago via Twitter for iPhoneJim Croft
Jim_Croft

Personally I'm sceptical. For me the key to Flipboard is not so much the nice interface, but the fact that the content is timely and relevant: timely because it's taken from live streams, and relevant because it comes from sources you select, including those form your social network. BHL doesn't have any of these characteristics. It's a huge digital archive with very little structure, and what structure it does have is largely bibliographic. For this content to work in a Flipboard-like environment I think BHL would need to develop "streams" based on, say taxa, geography, or readership, and these would have to be personalised. In a sense, Flipboard is displaying streams of content assembled by a combination of editors and your social network, and BHL has neither.

Wikipedia paper out

My short note on "Wikipedia as an Encyclopaedia of Life" has appeared in Organisms Diversity & Evolution (doi:10.1007/s13127-010-0028-9) (yes, I do occasionally write papers). A preprint of this paper is available on Nature Precedings (hdl: 10101/npre.2010.4242.1).

My presentation at iEvoBio covers much the same ground, and is included below, although the paper was written before I made the mapping from NCBI taxa to Wikipedia pages.

Phyloinformatics in the age of Wikipedia (warning, do not view if easily offended)

View more presentations from Roderic Page.

Show me the trees! Playing with the TreeBASE API

Being in an unusually constructive mood, I've spent the last couple of days playing with the TreeBASE II API, in an effort to find out how hard it would be to replace TreeBASE's frankly ghastly interface.

After some hair pulling and bad language I've got something to work. It's very crude, but gives a glimpse at what can be done. If you visit http://iphylo.org/~rpage/mytreebase/ and enter a taxon name, my code paddles off and queries TreeBASE to see if it has any phylogenies for that taxon. Gears grind, RSS feeds are crunched, a triple store is populated, NEXUS files are grabbed and Newick trees extracted, small creatures are needlessly harmed, and at last some phylogeny thumbnails are rendered in SVG (based on code I mentioned earlier), grouped by study. Functionality is limited (you can't click on the trees to make them bigger, for example), and the bibliographic information TreeBASE stores for studies is a bit ropey, but you get the idea.



What I'm looking for at this stage is a very simple interface that answers the question "show me the trees", which I think is the most basic question you can ask of TreeBASE (and one its own web interface makes unnecessarily hard). I've also gained some inspiration from the BioText search engine.

If you want to give it a try, here are some examples. These examples should be fairly responsive as the data is cached, but if you try searching for other taxa you may have a bit of a wait while my code talks to TreeBASE.

• Engystomops (Túngara Frog)
• Apteryx (kiwi)
• Coursetia
• Viburnum
• Physeter (sperm whale)