[Jalview-discuss] question about using DAS service and JalviewLite

[Jim Procter]

Hi Andrew - it seems you and Sai's timezones are closer than mine !

On 11/03/2010 02:47, Sai Tong wrote:
> 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 :
http://www.raditha.com/java/sandbox/



> 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?
> http://code.google.com/p/jsdas/
>
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)
>
> http://www.uniprot.org/uniprot/Q65GN7.gff
>
> 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...)
Nope - but you can add more features using the loadAnnotation javascript 
function - so if you wrote some client side javascript to retrieve 
features with jsLib, then you could parse them into gff and add them to 
the current Jalview view directly.

>> 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.
:) that's understandable - taking 3 months out of your research to do 
java/javascript software development is not everyone's cup of tea. 
Having said that - if you have any friends or colleagues who do have the 
time, then it might be worth suggesting it to them.

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.

Cheers,
Jim.

-- 
-------------------------------------------------------------------
J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.