[Bioperl-l] 1.0alpha2

[Jason Stajich]

On Tue, 5 Mar 2002, Brian Osborne wrote:

> Colleagues,
>
> There are 3 general approaches to flat-file indexing in Bioperl currently :
> the basic DB::Index* approach, the fully-featured but specialized DB::Fasta*
> approach, and the new OBDA approach.  Should the documentation steer users
> to OBDA and Flat*? Or shall "one hundred flowers bloom"?
>

OBDA will be the way to go if people want to access their indexes in
python,java, and c. I need to check with Lincoln to see what the future of
DB::Fasta is.  It has its own functionality that I'm not sure we support
anywhere else.  Once the OBDA flat indexes are testing a production
environment like the Sanger compute farm we'll probably really focus on
that. Albeit the original Index stuff will stick around for a while (at
least 2 or 3 releases).

So short answer is to steer people towards OBDA and we should have some
caveats about how this is a transition point in the toolkit.

> Also, Bio::Biblio seems destined to replace Bio::Annotation::Reference, yes?
> The increased detail in the objects and the ability to query bibliographic
> databases supports this notion. However, in the documentation for Seq
> objects we see that one can build an Annotation::Reference object and
> associate it with a Seq object with $seqobj->annotation($annrefobj). How
> will this work if one has a Bio::Biblio object in hand? Your thoughts?
>
Yes - but it won't happen for 1.0.  We definitely will be refactoring the
Annotation::Reference object to use Biblio objects - we should probably
try and at least get the inheritance scheme setup correctly now if not all
the functionality.  Ewan what was your thinking here on the timing here?

> I'm assuming, again, that the documentation should steer people away from
> Annotation::Reference. Yes?
>
Yeah - but that means we probably need to fix the sequence parsing code to
create proper Biblio objects.  I'll take a look.

> Brian O.
>
>
> ----- Original Message -----
> From: "Jason Stajich" <jason@cgt.mc.duke.edu>
> To: "Bioperl" <bioperl-l@bioperl.org>
> Sent: Sunday, March 03, 2002 9:25 PM
> Subject: [Bioperl-l] 1.0alpha2
>
>
> > I'm expecting to do a 1.0alpha2 release by the end of the week.  This will
> > include all the major changes that were rolled out during the hackathon
> > last week and the bug fixes and optimizations that were applied.
> >
> > A very brief summary of what will is new in 1.0alpha is below, we'll write
> > up a more detailed explaination and and vision of the projects that were
> > started at the hackathon in the coming week.
> >
> > The theme of the hackathon -- "Sequence Database Access"
> >
> > Changes to the corba server and client code were applied to
> > bring the code up to BSANE/BioCORBA 0.5 spec that is shared across
> > bioperl, biopython, and biojava.  These have been round-trip tested and
> > performance numbers have been analyzed.  A little more work to be done but
> > we'll have all that data in a nice little matrix for people to inspect.
> > Code is available in the CVS repositories bioperl-corba-server,
> > bioperl-corba-client.
> >
> > Bio Registry code was rolled out which is part of our whole Open
> > Bioinformatics Database Access (OBDA) spec.  This allows hooks to index
> > files, remote databases, corba servers, and sql dbs through biosql.  See
> > Bio::DB::Registry for implementation details.  Bio::DB::Failover allows
> > one to define failovers to cascade searching for a sequence by accession
> > or id.
> >
> > An in-memory and file-based cache of sequence objects has been written-
> > see Bio::DB::InMemory and Bio::DB::FileCache.
> >
> > BioSQL perl binding were rolled out in the bioperl-db CVS module.  Chris
> > Mungall and Ewan have been on point for this.
> >
> > Lincoln has committed his Bio::Graphics for rendering sequences using the
> > GD module.
> >
> > Martin Senger and Heikki have worked on Bibliographic modules - Heikki has
> > written the in-memory objects and Martin has written SOAP/XML -> bioperl
> > object parsers and attatched these to EBI Bibliopgrahic Query System (BQS)
> > (which returns medline soap/xml).  Bio::Biblio
> >
> > I've gotten a teeny bit of work done on the SearchIO to tune for more
> > format flexibilty.  Also written a Bio::SearchIO::Writer::HTMLResultWriter
> > which allows one to dump out any Bio::Search::Result::ResultI object as an
> > HTML report in the BLAST style.  Will try and add a couple more features
> > to this before 1.0.
> >
> > Michele Clamp wrote some modules in Bio::DB::Flat to handle the OBF new
> > flatfile indexing system which is cross platform and cross language
> > compatible.  Lincoln contributed a BDB implementation which after some
> > compatibility issues are ironed out should work from python and java
> > (unlike Bio::Index DB_File indexes).
> >
> > Perhaps other things I've skipped?
> >
> > I also updated the biodesign.pod so that it reflects the new bioperl
> > object design.  Those of you on the bioperl-guts list got a treat for
> > number of emails I'm sure.  *grin*
> >
> >
> >
> > -jason
> > --
> > Jason Stajich
> > Duke University
> > jason@cgt.mc.duke.edu
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> >
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
>

-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu