AJAXification of genome browsers
Euan Adie
Saturday, 24 February 2007 19:51 UTC
Does anybody who’s more in the loop know if the big genome browsers (Ensembl, UCSC) are doing anything about AJAXifying their interfaces?
Mainly this’d be cool so that you don’t have to reload huge pages of features every time you want to shift the viewport a little bit to the left. That definitely puts people off.
There was a bit of interest in this a while back on the blogs (Pierre whipped something up, I think?), GBrowse got started in the Holmes lab and somebody said that Ensembl were looking into something similar.
What’s the latest? Any other ideas about how the browsers could be made easier to use by judicial application of web 2.0 technologies?
-
Replies
Jump to resultsResults
-
Um, judicious use, not judicial. Sorry. :)
-
I’d be very curious too. ENSEMBL for one still looks very old school, although given the facelift that the EBI search engine got, I wouldn’t be surprised if ENSEMBL got an upgrade as well.
-
Do they have enough of an API that someone could build an interface externally?
-
Yeah, Ensembl does, anyway – all the data is open so you could just download the MySQL dumps and work from those.
You could use the (nice but fairly crappily documented if you’re looking to do something quickly) API, too, but that’d be sloooow.
-
An undergraduate that worked with me to develop some code to do simple visualization and downstream refactoring of virus genomes a while back that was inspired by google maps. Didn’t get that far, but one could always take a look at the code. His thesis can be found here
Also, in the course of his work, he came across GBrowse, which is the only other AJAX browser he could find and was meant for larger scale genomes.
-
Ian Holmes’ lab is working AJAX-ification of Gbrowse.
The Blog entry about Google Summer of Code entry has more details as well.
-
I do not think of any lab doing it. However, here is a “ajaxified” (I don’t think there is a word like this.. :-) )web site for table of contents of many scientific journals and science jobs.
www.sciencetodayonline.com
Sreenu
-
>> Yeah, Ensembl does, anyway – all the data is open so you could just download the MySQL dumps and work from those.
This is exactly what we did for the X:Map Genome browser
We were interested in the new Affymetrix Exon arrays, so we developed a browser to show us where the probes were hitting the genome and it all grew from there.. 10.27 million tiled images later, and we had a google maps based view of the human, mouse and rat genomes..
-
I agree, an AJAX/interactive genome browser would be cool. But does it really put people off having to load views page-by-page?
We use GBrowse and have never had a single complaint.
I think — at least with the genomes we are presenting — people look at single snapshots corresponding to something like the span of a gene. We typically pad links into the browser so people get enough up and downstream view to be meaningful.
Personally, I’d rather see the interactivity for zooming in and out (ie into the sequence) than for panning.
-
i’ve recently converted openlayers to draw our bioinformatics stuff.
a demo is here
and the source is herei’d love to have users/contributors to the project.
Results
-
