[BiO BB] Bioperl 0.7 release.
Gary Van Domselaar
gvd at penguin.pharmacy.ualberta.ca
Mon Mar 5 17:16:14 EST 2001
This message from Ewan Birney has been forwarded from the Bioperl mailing
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
and has also been uploaded to CPAN. The release will shortly be available
through our web site at
Alongside the release a number of satellite packages are also being
bioperl-gui - classes for building Perl::Tk visualisation on top of
bioperl-ext - C extensions for alignments to bioperl
bioperl-corba-client - CORBA wrappings of the biocorba 0.2 standard for
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.
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
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
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
Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney at ebi.ac.uk>.
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