[Bioperl-announce-l] Bioperl 1.2 Released

Ewan Birney birney@ebi.ac.uk
Tue, 31 Dec 2002 14:22:02 +0000 (GMT)

I am pleased to announce the release of the Bioperl 1.2 package, which
is a stable release of Bioperl. Our recommendation is to upgrade from the
1.0 series to the 1.2 series (for production environments, we would of
course advise side by side testing first off, and cannot take
responsibilty for whether 1.2 is a drop in replacement for 1.0. Please
do your own testing).

The release can be retrieved from http: via


(use wget or curl from the command line)

[FTP access is currently not very good due to some firewall issues.

The release has also been uploaded to CPAN and will be propagating around
CPAN mirrors now.

Bioperl 1.2 has a number of features and improvements, listed below. In

   o The Bio::Perl module, which flattens the learning curve for newcomers
has been extended and improved

   o Documentation resources have been updated and there is more of focus
on making sure the documentation is consistent across the package

   o Access to the Entrez system at NCBI over http: now uses the EUtils
system and is more robust

   o The SearchIO system for parsing search results (BLAST, HMMER and the
like) has had many minor fixes, meaning that it is more useful in
production environments

   o The Bio::Graphics system has had a number of small improvements,
including alignment viewing

   o There is documentation on Windows installation

I'd like to thank the large number of developers who helped in this
release, in particular the ever present Jason Staijch, Peter Schattner,
Lincoln Stein and Hilmar Lapp, along with Paul Boutros for his windows
work. Bioperl is an open, collaborative project and we welcome
improvements and contributions.

Ewan Birney, on behalf of the Bioperl developers.

Changes file:

1.2  Stable major release

    o More functionality added to Bio::Perl, the newbie module

    o Bug fixes in Bio::TreeIO::newick fixes bug introduced in 1.0.2
      Support for New Hampshire Extended (NHX) format parsing.

    o Bio::Tools added support for parsing Genomewise, Pseudowise, Est2Genome,
      Tmhmm, SignalP, Seg, RepeatMasker, FootPrinter, and a lightweight
      Hmmpfam parser.

    o New ontology parsing Bio::Ontology

    o Bug fixes in Bio::SearchIO for HMMer parsing, support for
      multi-report (mlib) fasta reports, support for waba and exonerate.

    o Bio::ClusterIO for parsing Unigene clusters

    o Bio::Assembly added for representing phrap and ace assembly clusters.

    o Rudimentary support for writing Chado XML (see
      GMOD project: www.gmod.org for more information)

    o Bio::Coordinate for mapping between different coordinate systems such
      as protein -> cDNA -> Exon -> DNA and back.  Useful for mapping
      features into different coordinate systems.

    o Bio::DB::GenBank/Bio::DB::GenPept now support Entrez queries
      with the get_Stream_by_query method and supports the latest
      NCBI eutils interface.

    o Bugs fixed in Bio::SeqFeature::Collection an in-memory fast
      object for extracting subsets of features : currently only
      supports extraction by location.