[Biojava-l] biojava BLAST parser proposal

[Matthew Pocock]

Simon,

Thank you very much for taking this on. It sounds like you have a pretty
good idea what you would like to do. The time-line sounds great.

What package were you going to put this stuff under? I came up with
org.biojava.bio.program.blast (leaves room to add other program.* packages)
but maybe somebody has a better idea. It would be cool if you could add a
bioperl-live/demos/blast directory with some simple demo programs & blast
reports. I should move the corba demos into a corba directory...

I look forward to reading the docs & running some demo apps.

All the best,
Matthew

Simon Brocklehurst wrote:

> Dear All,
>
> Just to keep everyone up to date with where we are on this.  I have now
> reviewed existing publically available Java frameworks for parsing
> BLAST, and believe that what we will be proposing for biojava represents
> one of the more elegant solutions that I've seen (although beauty is
> obviously in the eye of the beholder!).
>
> We're on track to have a fully working system and extensive
> documentation available to everyone next week.  I think we're
> incorporating just about everything that people said they wanted.
>
> Potential users can expect to find:
>
> o A facade layer that provides *really easy to use* classes for:
>      o grabbing predefined BLAST-related biojava value objects
>      o HTML-based visualization of BLAST results that allows extensive
> configuration of:
>                 o look and feel
>                 o marked up links to other information sources
>
> o A SAX layer that allows people to trivially:
>       o Populate their own object models for BLAST output. For example,
> grab only particular pieces of information from a large BLAST output.
>       o Access the system in a language- and platform-neutral entry via
> XSLT transforms if they are starting with existing XMLised BLAST output.
>
> o A low-level parsing layer to allow for us to deal with the differences
> between different versions of BLAST
>
> o An even more low level code re-use layer will make it easier for
> people to parse BLAST-like output from other programs e.g. HMMER
>
> Further comments and ideas are still welcome. Whether there is now time
> to incorporate much else before an initial release, I'm not sure (it's
> gonna be a busy weekend's coding as it is!).
>
> Simon
> --
> Simon M. Brocklehurst, Ph.D.
> Head of Bioinformatics
> Cambridge Antibody Technology
> The Science Park, Melbourn, Cambridgeshire, UK
> http://www.CambridgeAntibody.com/
> mailto:simon.brocklehurst@CambridgeAntibody.com
>
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