Bioperl wiki is now running Mediawiki 1.8.2. nothing too different under the hood at this point, the mediawiki people probably have more to say in the release-notes.

We are currently planning a timetable for the next few Bioperl releases, including the next developer release (v1.5.2), the next stable release (1.6) and beyond. Users are welcome to add requests (within reason!), donate code, etc. Lots of changes in store!

The release schedule can be found here. In order to add comments, you will be required to sign up for an account on the BioPerl wiki.

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.

Source distributions and Windows installers are available from our spiffy new Wiki-based website at http://biopython.org. My thanks to all code contributors who made this new release possible.

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. We also provide many methods for manipulating these objects once they are in memory.

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!