I just wanted to use the end of the year as a chance to reflect on what we’ve accomplished in 2004 and think about what 2005 holds for Bioperl. List Message What happened in 2004? First of all, this year has been really has been productive at a level perhaps only appreciated by the folks who read the bioperl-guts-l list which lists the CVS commits.

Bioperl developers are preparing a 1.5 release, you can grab the pre-release for testing at http://bioperl.org/DIST. We would greatly appreciate you downloading and testing this code before it is released by running ‘make test’. See Aaron’s post announcing the RC1 candidate.

I’m happy to announce a new release of Biopython 1.30, available today from http://biopython.org. This release contains a number of new modules and substantial changes to older modules. As a result of the changes, we’ve bumped up to a brand new major number.

The Mailing list post Continuing on the BioJava Bootcamp of 2003, The Quebec Bioinformatics Network (BioneQ) is organizing its first BioPerl Bootcamp, to be held at the Universite de Montreal from June 21-25 2004.

Bioperl version 1.4 for Windows is available. Thanks once again to Nigam Shah for creating and testing the PPM and PPD files.

BioKnoppix is a new live CD linux, based on KNOPPIX, with EMBOSS 2.8.0, jemboss, artemis, clustalx, Cn3D, ImageJ, BioPython, Rasmol, Bioperl, Bioconductor. It being made available by The University of Puerto Rico High Performance Computing facility (HPCf) and the Puerto Rico Biomedical Research Infrastructure Network (BRIN-PR). Great stuff!

I’m happy to announce the 1.24 release of Biopython. As normal Biopython is available from http://biopython.org.

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 ( gz b2z) bioperl-ext - C compiled extensions ( gz b2z) bioperl-run - wrappers for external programs ( gz b2z) They will also appear shortly at the IUBIO mirror (later today) and in CPAN.

Todd Harris has released GD::SVG in CPAN. This module implements support for most features of GD that are used by Bio::Graphics (together with the SVG module). Try out the publication publication quality graphics directly from CVS and help to squash the last bugs before stable bioperl release. See all_glyphs.pl and dynamic_glyphs.pl in examples/biographics directory.

Need to write a wrapper around sequence analysis service in a web form? Richard Adams has written a HOWTO document about his Bio::Tools::Analysis modules. Available in CVS or in the latest developer release. See into BIOPERL/doc/howto/{sgml|html|pdf|txt} for the SimpleWebAnalysis document in your favourite format.

Jeff announces a new release of Biopython: Biopython 1.23 is now available from the website at: http://www.biopython.org/ This is mostly a maintenance release, which fixes some problems in the installation. You do not need to update from 1.22 unless you are using the Bio.Cluster, Bio.KDTree, or Bio.PDB.mmCIF packages.