I've refined my first efforts to now highlight where you are in the tree. The trees on display here now show the new look.Basically I've abandoned image maps as they don't allow me to highlight the part of the tree being selected. After some fussing I switched to using HTML DIVs, which sit on top of the image. This took a little while to get working, CSS and DIV placement drives me nuts.
OK, time to put my money where my mouth is. Here's a first stab at displaying big trees in a browser. Not terribly sophisticated, but reasonably fast. Take a look at Big Trees. Approach Given a tree I simply draw it in a predetermined area (in these examples 400 x 600 pixels). If there are more leaves than can be drawn without overlapping I simply cull the leaf labels.
One of the striking pictures in Tamara Munzner et al.'s paper "TreeJuxtaposer: Scalable Tree Comparison using Focus+Context with Guaranteed Visibility" (doi:10.1145/882262.882291, also available here) is that of a biologist struggling to visualise a large phylogeny.
The PC hosting linnaeus.zoology.gla.ac.uk and darwin.zoology.gla.ac.uk has died, and this spells the end of my interest in (a) using generic PC hardware and (b) running Linux. The former keeps breaking down, the later is just harder than it needs to be (much as I like the idea). From now on, it's Macs only. No more geeky knapsacks for me.Because of this crash a lot of my experimental web sites are offline.
This October 22-24 there is a phyloinformatics workshop at the e-Science Institute in Edinburgh, Scotland, hosted in conjunction with the Isaac Newton Institute for Mathematical Sciences's Phylogenetics Programme. The invited speakers are:Prof.
Based on my recent experience developing an OpenURL service (described here, here, and here), linking this to a reference parser and AJAX tool (see David Shorthouse's description of how he did this), and thoughts on XMP, maybe it's time to try and articulate how this could be put together to make taxonomic literature more accessible.Details below, but basically I think we could make major progress by:Creating an OpenURL service that knows about
The TDWG-GUID mailing list for this month has a discussion of whether TDWG should commit to LSIDs as the GUID of choice.
Oops. One big problem with drawing trees in Google Earth is that the Earth, sadly, is not flat. This means that widely distributed clades cause problems if I draw straight lines between nodes in the tree. For geographically limited clades (such as the Hawaiian kaytidids shown earlier) this is not really a problem.
Now, for something completely different. I've been playing with Google Earth as a phylogeny viewer, inspired by Bill Piel's efforts, the cool avian flu visualisation Janies et al. published in Systematic Biology (doi:10.1080/10635150701266848), and David Kidd's work.As an example, I've taken a phylogeny for Banza katydids from Shapiro et al. (doi:10.1016/j.ympev.2006.04.006), and created a KML file.