Say what you will about Elsevier, they are certainly exploring ways to re-imagine the scientific article. In a comment on an earlier post Fabian Schreiber pointed out that Elsevier have released an app to display phylogenies in articles they publish. The app is based on jsPhyloSVGand is described here.
It is well known that phylogeny databases such as TreeBASE capture a small fraction of the published phylogenies. This raises the question of how to increase the number of trees that get archived.
For this weeks sessions of my phyloinformatics course I'm developing some phylogeny tools. The first is a simple AJAX-based BLAST tool.
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.
Matt Yoder (@mjyoder had a Twitter conversation yesterday about phylogeny viewers, prompted by my tweeting about my latest displacement activity, a 2D tree browser using the tiling approach made popular by Google Maps. As part of that conversation, Matt tweeted: Well, Matt's imagination has gone into overdrive, and he's blogged about his ideas. This issue deserves more exploration, but here are some quick thoughts.
My views on TreeBASE are pretty well known. Lately I've been thinking a lot about how to "fix" TreeBASE, or indeed, move beyond it. I've made a couple of baby steps in this direction. The first step is that I've created a group for TreeBASE papers on Mendeley.
Some serious displacement activity. I'm toying with adding phylogenies to iSpecies, probably sourced from the PhyLoTA browser. This raises the issue of how to display trees on a web page. PhyLoTA itself uses bitmap images, such as this one: but I'd like to avoid bitmaps. I toyed with using SVG, but that has it's own series of issues (it basically has to be served as a separate file). So, I've spent a couple of hours playing with the element.
Random half-formed idea time. Thinking about marking up an article (e.g., from PLoS) with a phylogeny (such as the image below, see doi:10.1371/journal.pone.0001109.g001), I keep hitting the fact that existing web-based tree viewers are, in general, crap. Given that a PLoS article is an XML document, it would be great if the tree diagram was itself XML, in particular SVG.
Stumbled across this cool visualisation project by Petra Isenberg at Calgary University. Collaborative tree comparison uses a tabletop system to enable two (or more) people to interact when comparing (in this case) phylogenies. I want one!
Over on the EOL blog is a summary of a meeting Visualizing the Evolutionary Tree of Life. This sounds like it was a fun meeting, but part of me is suffering from déjà vu. Our community has tossed this subject around for a while now.