Hi Andrew - it seems you and Sai's timezones are closer than mine !
thanks for your responses. These ideas are very cool.
In order for the DASTY server side DAS proxy system to be used by JalviewLite, does it necessarily mean that a proxy (the retrieval module) would need to be installed in people's own web server ?
It does, unless you provide a 'signed applet', and the user agrees to allow the applet free access to the internet. This page gives a good explanation of the different approaches :
If a JQuery/JalViewLite plugin is to be made successfully, does it mean that web developers can just give a bunch of (i.e.) uniprot ids as parameters to JalviewLite and JalviewLite would take care the rest of the communication and data retrieval steps with the DAS servers?
Not quite. As Andrew said, JalviewLite is really designed as a drop in visualization solution - and no DAS source browser or feature fetching code is currently included.
Will something like the following JS library for DAS be part of this proposed plugin?
Actually, yes. Jose Villavece's and Bernat Gel's code is quite new, and they will be talking about it at the next Das workshop (see http://www.ebi.ac.uk/training/onsite/DAS_070410.html ).
Currently, I've written some server-side codes on my server to retrieve uniprot sequences (based on selected uniprot ids) in a jsp file and then submit these sequences for alignment in JalviewLite by using this:
<param name="sequence1" value="yyyy TSPVV">
<param name="sequence2" value="zzzz TSPVV">
Just so I'm clear here, you also want to *align* the sequences retrieved from Uniprot ? JalviewLite only includes a pairwise alignment algorithm - so currently, you'd have to find some other way to align the retrieved sequences before sending them to the applet.
and as for getting sequence feature annotations, I'm writing server-side codes to retrieve gff file from uniprot (one by one for each sequences in the alignment)
and then I'd concatenate the contents from all of the gff files in order to make 1 single file to be applied into JalviewLite's alignment:
<param name="Features" value="file.gff">
(just a side question, can multiple Feature parameters be applied to sequence alignment in JalviewLite ? Haven't try this yet...)
Would this be a good project for "Google Summer of Code" Jim?
A great idea! Yes.
I'm interested to help to extend the DAS-connection of JalviewLite. But I am not sure if I'd qualify for doing this as a "Google Summer of Code" project.
I hope to take a closer look at jsDas during the developer meeting in the second week of April - I'll then let you know if there is something that can be done quickly, or whether it would need someone to spend several weeks on getting the applet to visualize DAS sequence and feature query results.
On 11/03/2010 02:47, Sai Tong wrote:
J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk
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