[Bioperl-l] slippy map for genomic features.

Brent Pedersen bpederse at gmail.com
Thu Jul 5 13:58:24 EDT 2007


hi,
here's a side project i've been tinkering on in googlecode svn that
may be useful to some.
http://code.google.com/p/genome-browser/
it's a simple hack on top of OpenLayers (openlayers.org) to provide a
javascript slippy map interface and API to view and browse genomic
features. It can be used with any image generation program that can
accept &xmin= and &xmax= parameters through the url. -- though i
havent had it working it bioperl as bioperl generates images of
different height depending on the number of tracks.

there's a live example of the code in SVN here:
http://toxic.berkeley.edu/bpederse/genome-browser/
with images generated by a colleague's modules on first request. those
images are then cached by a simple perl script included in the SVN
repo. all subsequent requests are returned from the cache.
an image request (automatically generated by the javascript) looks like:
http://toxic.berkeley.edu/bpederse/genome-browser/tiler.pl?chr=1&version=6&layers=mRNA&organism=arabidopsis&xmin=491520&xmax=499712&width=512
but any implementation need only implement xmin and xmax. all other
parameters will be used for caching but are not required.

if anyone is interested in getting this going with bioperl image
generation--or improving the project in any way, let me know and i'll
add you as a committer and provide any javascript support that i can.

-brent

tar ball download:
http://genome-browser.googlecode.com/files/genome-browser-0.02.tar


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