[DAS] Re: DAS has been dastroyed?

[James Freeman]

Dear Dr. Lyttelton,

Everyone but me and thee is at the BOSC and ISMB:

http://bosc.open-bio.org/
http://www.ismb02.org/

I couldn't make it this year (wedding preparations), but registration is 
still open for the ISMB, you can bring up your points face to face 
there...

Regards,

Jim
--
James Freeman 
Bioinformatics Consultant at Biogen
Email: james_freeman@biogen.com
Voice: 617-914-5804
Mobile: 617-429-6352





"Oliver Lyttelton" <o_lyttelton@hotmail.com>
Sent by: owner-ensembl-dev@ebi.ac.uk
02-Aug-2002 06:07 AM

 
        To:     ensembl-dev@ebi.ac.uk
        cc: 
        Subject:        DAS has been dastroyed?


Sorry to see that the DAS mailing list appears to have been DNA'ed...

Has anyone got any info on what happened? On top of which I was hoping to 
hear some response on the following email I tried to post?


---------------------------------------------------------
Retrieving feature information


Dear Developers,
    Please consider this plea, it is heartfelt.

When I first heard about DAS, I was in a lecture at Imperial College on 
distributed Bioinformatics. The concept seemed perfect, the idea of 
allowing 
anyone with annotations to publish them in a standard format, which a 
single 
genome browser could interpret, creating a virtual free market on the 
internet, and thus improving the quality of annotation information for 
everyone.

Since I have been using the system, I have come across one massive problem 

with it, and that is the problem that there is no server-side conversion 
of 
coordinate systems during feature requests.

I understand the reason for wanting to store features at the lowest (and 
therefore most stable) level of granularity. However, I fail to see why 
this 
prevents real-time server-side conversion.

My basic premise is that a "dumb user" such as myself, ought to be able to 

query (programatically) a DAS annotation server in the coordinate system 
of 
their choice, and retrieve a list of all annotations stored on that 
server, 
in the same coordinate system. At the moment the amount of conversion 
required is prohibitive.

The task for the server is to translate the request location into 
chromosome 
coordinates, and then recurse down through the hierarchy picking up 
feature 
info at each level and translating it all into the client coordinate 
system. 
This strikes me as a server-side type job not client side, and if someone 
wrote the code once, it would save every client side program from having 
to 
do the same job.

To prevent queries returning too much info you could limit the number of 
features returned to a specific number...

Let me know what you think,

Best regards to everyone,

Oliver Lyttelton (MSc Project Imperial College)



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