[Bioperl-l] Bioperl 0.7 release.

[Chervitz, Steve]

Ewan, Chris, Hilmar, and Jason,

Kudos on getting the 0.7 release off. It looks like another quantum jump in
functionality and quality. And congrats on the twins, Hilmar. I know what
and drain and joy just one new baby can be, having recently becoming a
father myself (http://home.pacbell.net/chervitz/baby). (I can't image what
it would be like having two new ones AND putting a Bioperl release together!
I have these visions of laptops wearing diapers and babies draped in code
printouts...)

Regarding the Blast modules, I'm glad to see Ian's code make it into the
release, since the maintenance of my modules has been lagging. I have been
working on revamping them for improved maintainability, but progress  has
slowed lately (new baby, new company, etc.). Is there still an interest to
have a heavyweight Blast parser such as Bio::Tools::Blast, or  will BPLite
suffice for all Blast parsing/running needs?

Cheers,
Steve Chervitz


-----Original Message-----
From: Ewan Birney [mailto:birney@ebi.ac.uk]
Sent: Monday, March 05, 2001 10:57 AM
To: bioperl-announce@bioperl.org; bioperl-l@bioperl.org
Subject: [Bioperl-l] Bioperl 0.7 release.




We are very pleased to announce the Bioperl 0.7 release. This release
represents a very significant improvement to the previous 0.6 series
and brings a number of important new features to bioperl. The ChangeLog
is at the end of this message.


The release is available at

   ftp://bio.perl.org/pub/DIST/bioperl-0.7.0.tar.gz

and has also been uploaded to CPAN. The release will shortly be available
through our web site at 

   http://bio.perl.org/


Alongside the release a number of satellite packages are also being
released being:

   bioperl-gui - classes for building Perl::Tk visualisation on top of
                 bioperl

   bioperl-ext - C extensions for alignments to bioperl

   bioperl-corba-client - CORBA wrappings of the biocorba 0.2 standard for
                          bioperl

   bioperl-corba-server - Wrappings of Bioperl objects compliant to the
                          biocorba 0.2 standard

Bioperl-gui has already been released on the ftp site and CPAN site. The
other packages will make their way over this week.



Bioperl 0.7 is predominantly the effort of Jason Staijch and Hilmar Lapp
who worked to build on top of the Bioperl 0.6 effort. Lorenz Pollack and
Peter Schattner also provided significant pieces of code. The effort was
supported by general bioperl developers, in particular Ewan Birney and
Chris Dadigidan. Many thanks also goes to our Mac (Todd Richmond) and NT
(Shelly Mistry) testers.



We'd also collectively like to congratulate Hilmar for the additions to
his family recently (twins I believe!). I hope Hilmar can take it easy for
the next couple of weeks.




The Bioperl Core Group, who coordinate Bioperl, is:

Ewan Birney, Chris Dadigidan, Hilmar Lapp and Jason Staijch. 


ChangeLog:



0.7  Large number of changes, including refactoring of the
     Object system, new parsers, new functionality and
     all round better system. Highlights are:


     o Refactored root of inheritance: moved to a lightweight
Bio::Root::RootI;
       Bio::Root::IO for I/O and file/handle capabilities.

     o Imported BPlite modules from Ian Korf for BLAST
       parsing. This is considered the supported BLAST parser;
       Bio::Tools::Blast.pm will eventually phase out due to lack of
       support.

     o Improved Sequence Feature model. Added complete location
       modelling (with fuzzy and compound locations).  See
       Bio::LocationI and the modules under Bio/Location.  Added
       support in Genbank/EMBL format parsing to completely parse
       feature tables for complex locations.

     o Moved special support for databanks etc to specialized modules under
       Bio/Seq/. One of these supports very large sequences through 
       a temporary file as a backend.

     o Explicit Gene, Transcript and Exon SeqFeature objects, supporting
       CDS retrieval and exon shuffling.

     o More parsers: Sim4, Genscan, MZEF, ESTScan, BPbl2seq, GFF

     o Refactored Bio/DB/GenBank+GenPept. There is now also DB/SwissProt and
       DB/GDB (the latter has platform-specific limitations).

     o New analysis parser framework for HT sequence annotation (see
       Bio::SeqAnalysisParserI and Bio::Factory::SeqAnalysisParserFactory)

     o New Alignment IO framework

     o New Index modules (Swissprot)

     o New modules for running Blast within perl
       (Bio::Tools::Run::StandAloneBlast). Added modules for running
       Multiple Sequence Alignment tools ClustalW and TCoffee
       (Bio::Tools::Run::Alignment).

     o New Cookbook-style tutorial (see bptutorial.pl). Improved
       documentation across the package.

     o Much improved cross platform support. Many known incompatibilities
       have been fixed; however, NT and Mac do not work across the entire
       setup (see PLATFORMS).

     o Many bug fixes, code restructuring, etc. Overall stability and
       maintainability benefit a lot.

     o A total of 957 automatic tests


Enjoy!    

-----------------------------------------------------------------
Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney@ebi.ac.uk>. 
-----------------------------------------------------------------


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