[Bioperl-l] slippy map for genomic features.

Mitch Skinner mitch_skinner at berkeley.edu
Thu Jul 5 17:22:38 EDT 2007


Hi,

FWIW, we've been working on something similar:
http://genome.biowiki.org/dmel/static/browser/prototype_gbrowse.html
based on GBrowse/Bio::Graphics and javascript that Andrew wrote from 
scratch (with the prototype library).  When our project was starting up 
(fall 05) Andrew looked but didn't find openlayers; I'm not sure if it 
was public back then but their current svn only goes back to 2006.

I think that things like layout (bumping) ought to be done in advance on 
a chromosome-wide basis; otherwise it's difficult to keep features from 
ending up at different heights on neighboring tiles.  And it would be 
difficult for the server to know what was being clicked on.  So we've 
been doing some up-front work to either do layout or to just render all 
the tiles in advance:
http://gmod.cvs.sourceforge.net/gmod/Generic-Genome-Browser/ajax/server/TileGenerator.pm?revision=1.1&view=markup
which is driven by this script:
http://gmod.cvs.sourceforge.net/gmod/Generic-Genome-Browser/ajax/server/generate-tiles.pl?revision=1.14&view=markup

Or you could just not bump at all, I guess.  I think of that as 
important functionality but I'd be interested in hearing about use cases 
where it's not necessary.  It's not just bumping, though; things like 
text labels also make it difficult to predict exactly what pixels a 
feature will span if you only have its genomic coordinates.

To make features clickable we've been using imagemaps; it simplifies the 
server code but it bogs down the client quite a bit.

I'd certainly be interested in seeing if there are ways we could work 
together; if you're at Berkeley maybe we could meet.

Regards,
Mitch

Brent Pedersen wrote:
> 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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