[Bioperl-l] Bioperl Release 1.4

[Hilmar Lapp]

Congratulations Heikki, you got this out the door ready for being 
wrapped and put under the tree :) Great work. -hilmar

On Tuesday, December 23, 2003, at 01:11  AM, Heikki Lehvaslaiho wrote:

>
>    Bioperl Release  1.4
>    --------------------
>
> The stable Bioperl release 1.4 is available for immediate use at:
>
>     http://bioperl.org/DIST
>
> We are releasing simultaneously three modules:
>
> bioperl-core - core bioperl modules
>              http://bioperl.org/DIST/current_core_stable.tar.gz
>              http://bioperl.org/DIST/current_core_stable.tar.bz2
> bioperl-ext  - C compiled extensions
>              http://bioperl.org/DIST/current_ext_stable.tar.gz
>              http://bioperl.org/DIST/current_ext_stable.tar.bz2
> bioperl-run  - wrappers for external programs
>              http://bioperl.org/DIST/current_run_stable.tar.gz
>              http://bioperl.org/DIST/current_run_stable.tar.bz2
>
>
> They will also appear shortly at IUBIO mirror
> <http://iubio.bio.indiana.edu/soft/molbio/perl/bioperl/> (later today)
> and in CPAN <http://search.cpan.org/dist/bioperl/>.
>
> Remember, all the external modules needed by bioperl-core can be
> installed from CPAN under name Bundle-BioPerl
> <http://search.cpan.org/dist/Bundle-BioPerl/>.
>
>
> Changes
> -------
>
> Over 3000 file changes have gone into this release since the 1.2
> development tree was branched off from the main. These are the
> main feature enhancements:
>
>    o installable scripts
>    o global module version from Bio::Root:Version
>    o Bio::Graphics - major improvements; added SVG support
>    o Bio::Popgen - population genetics
>    o Bio::Restriction - new restrion analysis modulues
>    o Bio::Tools::Analysis - web based DNA and Protein analysis
>      framework and several implementaions
>    o Bio::Seq::Meta - per residue annotable sequences
>    o Bio::Matrix
>    o Bio::Matrix::PSM - Position Scoring Matrix
>    o Bio::Ontology - major contributions
>    o Bio:Tree
>    o Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA - small inhibitory RNA
>    o Bio::SeqFeature::Tools - seqFeature mapping tools,
>      e.g. Bio::SeqFeature::Tools::Unflattener.pm
>    o Bio::Tools::dpAlign - pure perl dynamic programming sequence 
> alignment
>      (needs Bioperl-ext)
>    o new Bio::SearchIO formats
>    o new Bio::SeqIO formats: tab, kegg, tigr, game; important fixes for
>      old modulues
>    o Bio::AlignIO: maf
>    o improved Bio::Tools::Genewise
>    o Bio::SeqIO now can recognize sequence formats automatically from 
> stream
>    o new parsers in Bio::Tools:
>       Blat,  Geneid, Lagan, Mdust, Promoterwise, PrositeScan,
>    o several new HOWTOs: SimpleWebAnalysis, Trees, Feature Annotation,
>      OBDA Access, Flat Databases
>    o hundreds of new and improved files
>
> For detailed documentation, see individual module documentation in the
> distribution or in http://doc.bioperl.org/. The tutorials are
> available at http://bioperl.org/HOWTOs/.
>
>
> This release is a result of hard work by the bioperl core team, nearly
> hundred developers and countless suggestions and bug reports at the
> bioperl mailing list (bioperl-l at bioperl.org) or the the bioperl bug
> tracking system (http://bugzilla.bioperl.org/).
>
>
> Wishing you all Peaceful Christmas,
>
>         -Heikki and all the bioperl developers
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
>
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------