Why I want an iPad

OK, first of all, I want one, I want one real bad.

There's been a general sense of disappointment about the iPad, which I suspect is only natural given the enormous hype leading up to the announcement, as well as the fact that the applications shown were fairly conventional. Personally I don't think book reading is where the action is. For time-sensitive stuff like newspapers, and rich, complex documents such as scientific papers, sure, but physical books strike me as a piece of technology that we're not really going to improve on, rather like knives and forks.

But some grasp that this is magic. What I hope the iPad will do is finally move some visualisation tools into the main stream (as much as phylogenetics can be thought of as mainstream). The challenge of visualising large phylogenies has yielded some cool tools which, sadly, remained under-developed, such as TreeJuxtaposer, which seems clunky and counter-intuituve when using a mouse, but with a touch screen would just be awesome.



Tools such as Paloverde would also be more intuitive to use, as would the magnifier feature in Dendroscope. Imagine "pinch and zoom" in TreeJuxtaposer or Dendroscope, or for viewing large a sequence alignments.

Then there's the existing tabletop tools that I blogged about earlier:



And of course there's Perceptive Pixel's view of a taxonomic classification:



There would be some work involved porting these tools to the iPad (e.g., porting code from Java to Objective C in the case of TreeJuxtaposer and Dendroscope), but the person who does this is going to have an impact on this field comparable to Maddison brothers when they released MacClade in 1986.

Displaying taxonomic coverage using a treemap

A quick, and not altogether satisfactory hack, but I've added a simple interactive treemap to BioStor. It's essentially a remake of the Catalogue of Life treemap I created in 2008, but coloured by the number of references I've extracted from BHL. I wanted a quick way to visualise which groups were well represented (darker colours), and which weren't (lighter colours). For example, in the diagram below we can see that Annelida, Arthropoda, Chordata, Cnidaria, and Mollusca have most of the references.

The treemap at BioStor is interactive. You can click on a panel in the treemap to drill down. To go back up, click on the desired level in the tree displayed to the left of the treemap.

Why BHL needs automation and/or crowd sourcing

Jim Croft drew my attention to a cool crowd-sourcing project to convert scans of Australia's newspapers to text. The site has a nice chart showing the projects' coverage of the Australian newspapers, which motivated me to show something similar for BioStor. Each journal page now shows a chart of article coverage.

For example, the journal Breviora has most of its articles identified, mainly because the MCZ put a list of articles linked to BHL on their website. I harvested this to populate BioStor.

Other journals are looking a bit more sparse, such as the Bulletin of the British Museum (Natural History) (Entomology):

So, there's a lot to do, and a crying need for some combination of automation (whether driven by external metadata, which is my current approach, or trying to extract article information directly from the OCR text) and crowd sourcing if we're going to be able to make a significant dent in the task of finding articles in BHL.