[Biojava-dev] Biojava Interface to BLAST web/remote services

[Scooter Willis]

Looks like the rolled their own URL interface and did not do a WSDL. Not a big deal but does appear they have some sort of submit get a "ticket" and then check back with the "ticket" identifier for the results. The BioJava API would hide the transport layer so you could use a custom URL approach or web services. 
 
Not sure how the other WSDL interfaces handle long running tasks but I assume the Web Services can handle a call that takes say 5 minutes to respond without timing out. Some process would need to distinguish between a long running server task and a server that is no longer responding.
 
Scooter

________________________________

From: biojava-dev-bounces at lists.open-bio.org on behalf of Andreas Prlic
Sent: Thu 6/4/2009 5:12 AM
To: Sylvain Foisy
Cc: biojava-dev at lists.open-bio.org
Subject: Re: [Biojava-dev] Biojava Interface to BLAST web/remote services



Hi Sylvain,

Do you mean the URL api for the NCBI Blast searches? Could not find a
link for a WSDL...
http://www.ncbi.nlm.nih.gov/BLAST/developer.shtml

Andreas


On Tue, Jun 2, 2009 at 6:26 PM, Sylvain Foisy
<sylvain.foisy at diploide.net> wrote:
> Hi,
>
> In response to Scooter and from using some of these BLAST implementations in
> the past, I would suggest that we use the QBlast service from NCI first for
> a number of reasons:
>
> - It has been in operation for a long time and its usage is well documented;
>
> - Because of this, there is few chances that it will change;
>
> - Coming from NCBI, it will probably be there for some time to come ;-)
>
> Our friends at BioPerl have been using this technique for a long time now
> with the BioPerl Module:Bio::Tools::Run::RemoteBlast module. We might try to
> emulate at first and of course, do better :-)
>
> Any inputs?
>
> Best regards
>
> Sylvain
>
> ===================================================================
>
>  Sylvain Foisy, Ph. D.
>  Consultant Bio-informatique / Bioinformatics
>  Diploide.net - TI pour la vie / IT for Life
>
>  Courriel: sylvain.foisy at diploide.net
>  Web: http://www.diploide.net <http://www.diploide.net/> 
>
> ===================================================================
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