[Bioperl-announce-l] Bioperl 1.0.2 Released

Jason Stajich jason@cgt.mc.duke.edu
Mon, 15 Jul 2002 19:59:01 -0400 (EDT)

I am pleased to announce the release of Bioperl 1.0.2 a bug fix release
which corrects several issues in the previous release.  This release is
API compliant with the 1.0 branch so all scripts which have been written
for modules in the 1.0 or 1.0.1 releases should also work with this

As per usual you can obtain the release from the usual channels, primarily
our server at
    or FTP

Additionally Windows ActiveState Perl users can use the PPM utillity
   PPM> set repository Bioperl http://bioperl.org/DIST/
   PPM> search bioperl             (this will show you what are the available
                                    bioperl versions)
   PPM> install bioperl            (will install the default version

The package will be released onto CPAN and will be available from your
local CPAN mirror in the next few days depending on the synchronization

This release contains 413 modules and over 169k lines of code and
represents the work of dozens of developers.

Some notable problems with IRIX and Makefiles have been reported for this
release series because of the number of modules in our distribution.
Please see the PLATFORMS file for information on workarounds.

I would also like to encourage any user, will little or lots of experience
with the toolkit to help us gauge the project's use throughout industry
and academia by participating in the user survey [Yes you Bioperl
developers too - there's a Question just for you!].  This is available at
http://bioperl.org/survey.html or from the toolbar at the lefthand side of
the project website http://bioperl.org.

This release represents the last release on the 1.0 series.  The
developers have begun work 1.1 developer/preview releases which will lead
to the next stable Bioperl release 1.2 which we expect to release in the
late Fall of 2002.  Expect the first 1.1 release by the beginning of

Please note that because of the expected changeover for NCBI Entrez URLs
at the end of 2002, some modules (Bio::DB::GenBank, Bio::DB::GenPept) will
not work after 2002.  The necessary fixes have already been applied and
tested on the 1.1 branch and will be available in the 1.2 release.

We expect a number of major components to be added to the toolkit in the
coming months and encourage any user interested in specific functionality
being added to the toolkit to join the mailing list discussion.

The Changes for 1.0.2 are appended below.

Jason Stajich on behalf of the Bioperl developers.  Please see the
AUTHORS file in the distribution for a complete list of individuals who
made this release possible.


1.0.2 Bug fix release

    o Note: The modules Bio::DB::GenBank and Bio::DB::GenPept provided
      in this release will not work after December 2002 when NCBI
      shuts off the old Entrez cgi scripts.  We have already fixed
      on our main development branch and the functionality will be
      available in the next stable bioperl release (1.2) slated for
      Fall 2002.

    o Numerous parsing bugs in Bio::SearchIO::fasta found through
      testset by Robin Emig.  These were fixed as was the get_aln
      method in Bio::Search::HSP::GenericHSP to handle the extra
      context sequence that is provided with a FastA alignment.

    o Migrating differences between Bio::Search::XX::BlastXX to
      Bio::Search::XX::GenericXX objects.  This included mechanism
      to retrieve whole list of HSPs from Hits and whole list of Hits from
      Results in addition to the current next_XX iterator methods that
      are available.  Added seq_inds() method to GenericHSP which identifies
      indexes in the query or hit sequences where conserved,identical,gaps,
      or mismatch residues are located (adapted from Steve Chervitz's
      implementation in BlastHSP).

    o Bio::DB::GFF bugs fixed and are necessary for latest GBrowse release.
      Bio::DB::GFF::RelSegment is now Bio::SeqI compliant.

    o Bio::Graphics glyph set improved and extended for GBrowse release

    o Bio::Tree::Tree get_nodes implementation improvement thanks
      to Howard Ross notice performance problem when writing out
      unbalanced trees.

    o Bio::Location::Fuzzy::new named parameter -loc_type became
      -location_type, Bio::Location::Simple::new named parameter
      -seqid becamse -seq_id.

    o Fixed major Bio::AlignIO::emboss parsing bug on needle output,
      was mis-detecting that gaps should be placed at the beginning of
      the alignment when the best alignment starts internally in the

Jason Stajich
Duke University
jason at cgt.mc.duke.edu