I'm a big fan of the work Nature publishing group is doing in experimenting with new methods of publishing, such as their iOS apps (which inspired me to "clone" their iPhone app) and the Encode app with the concept of "threads". But there's an aspect of the iPad app that puzzles me: Nature's app doesn't know that a linked article elsewhere in Nature is also available using the app.

tl;dr Readmill might be a great platform for shared annotation and correction of Biodiversity Heritage Library content.Thinking about accessing the taxonomic literature I started revisiting previous ideas.

Prompted by a conversation with Vince Smith at the recent Online Taxonomy meeting at the Linnean Society in London I've been revisiting touch-based displays of large trees. There are a couple of really impressive examples of what can be done. Perceptive Pixel I've blogged about this before, but came across another video that better captures the excitement of touch-based navigation of a taxonomy.

The release of the ENCODE (ENCyclopedia Of DNA Element) project has generated much discussion (see Fighting about ENCODE and junk). Perhaps perversely, I'm more interested in the way Nature has packaged the information than the debate about how much of our DNA is "junk." Nature has a website (http://www.nature.com/encode/) that demonstrates the use of "threads" to navigate through a set of papers.

As part of a course on "phyloinformatics" that I'm about to teach I've been making some visualisations of classifications. Here's one I've put together using jQuery Mobile and the Encyclopedia of Life API. It's pretty limited, but is a simple way to explore EOL using three different classifications.

One of the things I keep revisiting is the way we display scientific articles. Apart from Nature's excellent iPhone and iPad apps, most efforts to re-imagine how we display articles are little more than glorified PDF viewers (e.g., the PLoS iPad app).Part of the challenge is that if we make the article more interactive we immediately confront the problem of how to link to other content.

Since I won't be able to be at the Biodiversity Heritage Library's Life and Literature meeting I thought I'd share some ideas for their Life and Literature Code Challenge. The deadline is pretty close (October 17) so having ideas now isn't terribly helpful I admit. That aside, here are some thoughts inspired by the challenge.

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Quick demo of the mockup I alluded to in the previous post. Here's a screen shot of the article "PhyloExplorer: a web server to validate, explore and query phylogenetic trees" (doi:10.1186/1471-2148-9-108) as displayed as a web-app on the iPad.

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