H1N1 Swine Flu TimeMap

Tweets from @ attilacsordas and @stew alerted me to the Google Map of the H1N1 Swine Flu outbreak by niman.

Ryan Schenk commented: "It'd be a million times more useful if that map was hooked into a timeline so you could see the spread.", which inspired me to knock together a timemap of swine flu. The timemap takes the RSS feed from niman's map and generates a timemap using Nick Rabinowitz's Timemap library.



Gotcha
Although in principle this should have been a trivial exercise (cutting and pasting into existing examples), it wasn't quite so straightforward. The Google Maps RSS feed is a GeoRSS feed, but initially I couldn't get Timemap to accept it. The contents of the <georss:point> tag in the Google Maps feed looks like this:

    <georss:point>
      33.041477 -116.894531
    </georss:point>

Turns out there's a minor bug in the file timemap.js, which I fixed by adding coords= TimeMap.trim(coords); before line 1369. The contents of the <georss:point> taginclude leading white space, and because timemap.js splits the latitude and longitude using whitespace, Google's feed breaks the code.

Postscript
Nick Rabinowitz has fixed this bug.

NCBI visualisations I - Genbank Timemap

Time for some fun. In between some tedious text mining I've been meaning to explore some visualisations of NCBI. Here's the first, inspired by Jörn Clausen's wonderful Live Earthquake Mashup (thanks to Donat Agosti for telling me about this). What I've done is take all the frog sequences in Genbank that are georeferenced, add the date those Genbank records were created, generate a KML file, and use Nick Rabinowitz's timemap to plot the KML. The result is here:



By dragging the time line you can see collections of sequences and where the frog samples came from. Clicking on a marker on the Google Map takes displays a link to the Genbank record. It's all pretty crude, but fun to play with. What I'm toying with is trying to do something like this for new taxa, i.e., a timemap showing where an when new species are described. Sort of a live biodiversity map like the earthquake mashup, albeit not quite so rapidly moving.