Dear biopythoneers, We are pleased to announce the release of Biopython 1.42. This release includes a brand-new Genbank parser in Bio.GenBank by Peter Cock, numerous updates to Bio.Nexus by Frank Kauff and to Bio.Geo by Peter, lots of bug fixes by scores of contributors through BugZilla, and Bio.Cluster became object-oriented.

Raphaël Leplae has updated the Pdoc software to have an improved stylesheet and fix several bugs including problems rendering Bio::DB::Fasta. Thanks a lot Raphaël and Patrick Meidl for getting the bugs reported and fixed for this nice POD to HTML converter. You can see the Pdoc for Bioperl packages in action at the doc.bioperl.org site. See the bottom links which are for live code, the frozen version for releases remains, well, frozen.

Upgraded MW install for some bugfixes and security fixes.

Bioperl Network package documentation added to the Pdoc site and is automaticly updated daily.

Upgraded BioPerl mediawiki to 1.6.6.

We are announcing a new Sourceforge Project called Modware. It is an object-oriented API written in Perl that creates BioPerl object representations of biological features stored in a Chado database. It basically creates a Bio::Seq object for chromosomes in Chado and creates Bio::SeqFeature::Gene objects for protein coding transcripts stored in Chado. Things like contigs are represented as Bio::SeqFeature::Generic objects.

I’m glad to announce the availability of the Deobfuscator interface at the BioPerl website. You can use it at the following URL: http://bioperl.org/cgi-bin/deob_interface.cgi Many thanks to Laura Kavanaugh and David Messina for this great contribution to the BioPerl project!

ListSummaries for April 26-May 9 are up at the usual place: http://www.bioperl.org/wiki/Mailing_list_summaries Direct link: http://www.bioperl.org/wiki/ListSummary:April_26-May_9%2C2006 It’s a bit of a hurried one so don’t be surprised to find a few spelling errors here and there. I’m getting ready for a conference in a couple weeks so I may be off the radar a bit here and there. The next ListSummary won’t be posted until May 26. Enjoy!

It’s my great pleasure to announce the availability of the BioPerl-run packages (stable & developer releases) for the FreeBSD operating system. For instructions on how to install BioPerl ports in FreeBSD, please take a look into the Getting Bioperl section of the BioPerl Wiki.

I’ve added a page about RSS feeds in BioPerl. These include links to CVS commits as a RSS feed. This a bit of a hack using cvs2rss and cvs2cl and I have hardcoded it to show the last 30 commits only. In addition RSS news is now embedded on the main BioPerl and Tracking CVS commits webpages to make for better interlinking between the news and wiki site ( you might even be reading this there ).

The newest summary of the BioPerl mailing lists has been posted to the wiki: April 12-25 Post gripes, harrassments, and faint praises at the regular places.