Bioperl 1.2.3 On behalf of the Bioperl developers, we are pleased to announce the release of Bioperl 1.2.3. This is the set of Core libraries which constitutes Bioperl and covers areas like Sequence file parsing, Sequence Feature representations, Database access to flatfile web-based sequence databases, Alignment parsing and manipulation, parsing of and data representation of output from a majority of standard bioinformatics tools, and many

Hi Everyone, Apologies for the mass cross-posting but this email is about server and IP changes that will affect all of our projects and servers. Simply put – Wyeth, the company that provides us with our hosting and wonderful T3 connection to the internet is cutting their internet connection circuits over from one ISP to a different Tier 1 internet backbone.

Jason has summarized a significant amount of work he has done on the CVS tree. Major work done on Bio::PopGen, Bio::Matrix and bug fixes to Bio::Tree and Bio::SeqIO.

Available now at http://biopython.org/download/ Changes include: added Andrew Dalke’s EUtils library added Michiel de Hoon’s gene expression analysis package updates to setup code, now smarter about dependencies updates to test suite, now smarter about code that is imported Michael Hoffman’s fixes to DocSQL syntax fixes in triemodule.c to compile on SGI, Python 2.1 compatible updates in NCBIStandalone, short query error Sebastian Bassi

The “Biojava in Anger: A Tutorial and Recipe Book for Those in a Hurry” posted online at http://www.biojava.org/docs/bj_in_anger/index.htm has been translated into French and Japanese

Rob Edwards and Heikki Lehvaslaiho have been writing new restriction analysis classes. These will eventually replace the long serving Bio::Tools::RestrictionEnzyme by Steve Chervitz. The first working versions are in CVS. A UML graph shows the class relationships. A more verbose overview is below. Bio::Restriction::Enzyme class knows (almost) everything there to know about restriction enzymes.

This is a bug fix release from the stable branch. The Bioperl release 1.2.2 is available at http://www.bioperl.org/DIST/bioperl-1.2.2.tar.gz and is propagating around CPAN now. Bioperl-run is a collection of modules that wrap bioinformatics applications to allow running them from bioperl. The release cycle of bioperl-run follows the core.

Our “Bioinformatics Open Source Conference” was held in Brisbane, Australia in conjunction with the larger ISMB'2003 meeting. It was quite successful — 96 attendees, wireless internet, BOF rooms and 30+ presentations over 2 days.

A possible release candidate for BioPerl 1.2.2 is now available for download: http://bioperl.org/DIST/bioperl-1.2.2rc1.tar.gz Please download and give it a test. New aditions, features and fixes are in the “Changes” file.

BOSC always comes and goes so fast. I am a melancholy kind of guy so whenever things finish up I get a little misty eyed with regrets at the things I could have done and the people I could have met. But it was all so great it makes me smile with the understanding of the entire world. Plus weeping really gets you the women – makes you look quite sensitive. And I am all about sensitivity.

If you are not lucky enough to be here in wonderfully beautiful Brisbane with beaches next to the river and where every man and woman is a perfect physical specimen, then you can read all about BOSC colored through my mind. Enjoy.