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 __________________________________________________ Do You Yahoo!? Everything you'll ever need on one web page from News and Sport to Email and Music Charts http://uk.my.yahoo.com _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
