[Bioperl-l] Bioperl 0.7 release.

[Ewan Birney]

On Mon, 5 Mar 2001, Chervitz, Steve wrote:

> 
> 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?
> 

I would have thought the "right" thing to do would be to provide a set of
add-ons/extensions to BPlite which made it more heavy - perhaps for
example making an in memory data structure first off.

If this was possible then I suspect that we can satisify both people who
ewant all the bells and whistles (like ->html_dump) with a lean-mean-core
of BLAST parsing.

Does this sync with you? would this be possible?



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