Geography and genes: zoomable view of frog NCBI classification with linked map

More zoom viewer experiments (see previous post), this time with a linked map that updates as you browse the tree (SVG-capable browser required). As you browse the frog classification the map updates to show the location of georeferenced sequences in GenBank from the taxa in the part of the tree you are looking at. The map is limited to not more than 200 localities, and many frog sequences aren't georeferenced, but it's a fun way to combine classification and geography. You can try it at:

http://iphylo.org/~rpage/deeptree/7.html

or watch the video:

Zoomable tree with linked map from Roderic Page on Vimeo.

Zooming a large tree, now with thumbnails

Continuing experiments with a zoom viewer for large trees (see previous post), I've now made a demo where the labels are clickable. If the NCBI taxon has an equivalent page in Wikipedia the demo displays and link to that page (and, if present, a thumbnail image). Give it a try at

http://iphylo.org/~rpage/deeptree/3.html

or watch the short video clip below:

Zoomable viewer with Wikipedia thumbnails from Roderic Page on Vimeo.

Deep zooming a large 2D tree

Here's a quick demo of a 2D large tree viewer that I'm working on. The aim is to provide a simple way to view and navigate very large trees (such as the NCBI classification) in a web browser using just HTML and Javascript. At the moment this is simply a viewer, but the goal is to add the ability to show "tracks" like a genome browser. For example, you could imagine columns appearing to the right of the tree showing you whether there are phylogenies available for these taxa in TreeBASE, images from Wikipedia, sparklines for sequencing activity over time, etc. I'll blog some more on the implementation details when I get the chance, but it's pretty straightforward. Image tiles are generated from SVG images of tree using ImageMagick, labelling is applied on the fly using GIS-style queries to a MySQL database that holds the "world coordinates" of the nodes in the tree (see discussion of world coordinates on Google's Map API pages), and the zooming and tile fetching is based on Michal Migurski's Giant-Ass Image Viewer. Once I've tidied up a few things I'll put up a live demo so people can play with it.

Deep tree zooming from Roderic Page on Vimeo.