Talk @vizbi on phylogeny visualisation

The talks from the 2001 workshop on Visualizing Biological Data (VizBi 2011) are now available on Vimeo. There were some great talks at VizBi, especially the keynotes (the "featured videos" on the Vimeo page for VizBi).

My own (slightly breathless) talk was on phylogeny visualisation, which you can watch below.

Visualization of phylogenetics & phylogeography from Roderic Page on Vimeo.

In the talk I mention that the slides are also on SlideShare, and that is where you'll find URLs for the projects I mention. The URls aren't all that easy to get that way, so here they are:

• http://evolution.genetics.washington.edu/phylip/software.html#Plotting
• http://loco.biosci.arizona.edu/paloverde/paloverde.html
• http://www.wellcometreeoflife.org/
• http://dx.doi.org/10.1186/1471-2105-5-48
• http://dx.doi.org/10.1093/sysbio/46.3.523
• http://dx.doi.org/10.1186/1471-2105-8-213
• http://iphylo.blogspot.com/2007/06/earth-not-flat-official.html
• http://systbio.org/?q=node/184
• http://dx.doi.org/10.1080/10635150701266848
• http://www.ncbi.nlm.nih.gov/pubmed/17968069
• http://innovis.cpsc.ucalgary.ca/Research/CollaborativeTreeComparison
• http://www.perceptivepixel.com/
• http://iphylo.blogspot.com/2008/08/perceptive-pixel-taxonomy-demo.html
• http://www-ab.informatik.uni-tuebingen.de/software/dendroscope
• http://dx.doi.org/10.1126/science.300.5626.1692
• http://loco.biosci.arizona.edu/
• http://iphylo.blogspot.com/2007/08/visualising-very-big-trees-part-iv.html
• http://iphylo.blogspot.com/2011/02/live-demo-of-zooming-large-tree.html

Mendeley Hack4Knowledge: towards an "ego wall"

I'm taking a virtual part in Mendeley's Hack4Knowledge event. I'm using this a chance to explore some ideas about building novel interfaces to bibliographic data in Mendeley. One idea is to display a user's entire library in one screen. I think the user interfaces employed by most bibliographic software are too conservative and there some cool things that could be done. For example, see A fluid treemap interface for personal digital libraries (doi:10.1145/1065385.1065512, PDF available from CiteSeer).

One idea I'm playing with is to display all a Mendeley user's papers as a quantum treemap, with thumbnails of the papers and "badges" indicating, for example, how many readers each paper has. The idea is that at a glance you can see all your publications, and which ones are being read the most. You can think of it as an "ego wall" — a quick way to see what others think about your work. Below is part of my library. You can see the full treemap here as an SVG file. Imagine this as an iPad interface to a user's Mendeley library.



Eventually I'll make this live. I'm doing this yet as the script to create the visualisation is slow due to the multiple requests I need to make to get the necessary information. I have to get the list of a user's papers from Mendeley, then I call the API for each paper to get basic bibliographic details. I have to screen scrape the corresponding paper's web page to get the thumbnail and the paper's UUID, which I can then use to get the readership stats via Mendeley's API via yet another API call. Sigh.

Anyway, this is enough hacking for one day. Hope to spend some more time on this project tomorrow.

Adding Solr to BioStor: searching for real

Prompted by the appearance on the BHL blog of an article about BioStor I've thinking about how to improve what is basically a fairly clunky tool.

One major weakness is searching the collection of nearly 40,000 articles extracted from BHL. Note the word "extracted." BioStor isn't a tool like PubMed or Google Scholar where the goal is to find articles on a topic. Instead it addresses a more specific question, namely whether a given article is contained in an item scanned by BHL. Confusion about this was one reason publication of my paper on BioStor (doi:10.1186/1471-2105-12-187) took so long to pass through the review stage.

However, users (myself included) expect to be able to search for articles. So, it's time to explore ways to make it easier to find articles within the BioStor database. I've junked the previous pretty crappy code I wrote and have started to play with the Solr search engine. I'd experimented with Solr a while ago, but other stuff got in the way. Today I've managed to add it to BioStor and do a preliminary indexing of the articles in BioStor. So far I'm only indexing basic bibliographic metadata, and displaying the first 30 hits, but already it's making it much easier to find interesting stuff in BioStor.

Solr also supports faceted searching (i.e., clustering results by categories such as year, author, journal). I don't so much with this yet, but there's clearly a lot of scope. I could also add taxonomic names, and even the OCR text to Solr, greatly expanding the ability to find articles. But that's for the future. For now, here are some interesting searches:

• fig wasps
• lice
• Begonia
• frogs
• Madagascar