[Bioperl-l] 1.0alpha2

[Brian Osborne]

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"?

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?

I'm assuming, again, that the documentation should steer people away from
Annotation::Reference. Yes?

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
>