[Bioperl-l] 1.0alpha2

[Jason Stajich]

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