[Biojava-l] BLAST/Java interface

[Matthew Pocock]

Schreiber, Mark wrote:
> I think that a web service of BLAST or a binary installation are
> preferable to submitting BLAST to NCBI for anything over 30 or so
> sequences. You can quite quickly find your domain blocked from NCBI's
> web servers if you send large numbers of messages to NCBI. (Speaking
> from personal experience).
> 
> The question really is can this sort of service be bundled with BioJava
> or does it contain so many dependencies that each install would have to
> be a custom job? Seems to be getting into the realms of Enterprise
> BioJava (don't laugh Brian!)
> 
> - Mark

Enterprise BioJava? EBJ? Now, there's an idea. Lims, web service 
wrappers for apps, servlet wrapper for sequence gui package, jsp stubs 
for database access. Hmm.

One option to the more immediate problem of locating and running the 
blast executable is to glue in all the dependancies via jndi - I'd like 
to be able to resolve urn:biojava.org:executable/blastn to an object 
that can be used to run blast. For different installs, this could 
resolve to a local blast binary, a blast farm or some blast web service. 
It boils down to just how much is per-site customization and how much 
can be pre-canned.

We were thinking that the prefix for our names should be 
urn:biojava.org, and that from then on each element (seperated by /) 
would be id:version where version is optional. e.g.

* urn:biojava.org:executable/blastn
* urn:biojava.org:alphabet/DNA/tokenization:iupac/a
* urn:biojava.org:alphabet/protein
* urn:biojava.org:seqdb/embl:35/A12345

I'm fairly sure we can convince JNDI to use its federation support to 
mary this scheim to LSIDs as necisary. I've updated the BioJava V2 
wishlist to include this, but we could add this sort of stuff to the 
current BioJava without too much hardship. Now, time to go through the 
jndi tutorial again...

Matthew

-- 
BioJava Consulting LTD - Support and training for BioJava
http://www.biojava.co.uk

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