We are pleased to announce the release of Biopython 1.40 beta. It has been nine months since the last official release (1.30), and there are numerous changes, bugfixes, enhancements, goodies and new contributors. Most notable are the addition of the Nexus parser (Frank Kauff w/ Cymon Cox), the CAPS module (Jonathan Taylor), the Restriction enzyme package (Frederic Sohm), hefty improvements to Bio.PDB (Thomas Hamelryck), MutableSeq (Michiel de Hoon), and more. The delay in the release was caused by day jobs creeping into the lives of most core developers. So we are very happy with this release finally out, and we hope to have the non-beta out soon.

BOSC 2005 website /bosc/

The 6th annual Bioinformatics Open Source Conference (BOSC'2005) is organized by the not-for-profit Open Bioinformatics Foundation. The meeting will take place June 23-24, 2005 in Detroit, Michigan, USA, and is one of several Special Interest Group (SIG) meetings occurring in conjunction with the 13th International Conference on Intelligent Systems for Molecular Biology.

see http://www.iscb.org/ismb2005 for more information.

Because of the power of many Open Source bioinformatics packages in use by the Research Community today, it is not too presumptuous to say that the work of the Open Source Bioinformatics Community represents the cutting edge of Bioinformatics in general. This has been repeatedly demonstrated by the quality of presentations at previous BOSC conferences. This year, at BOSC 2005, we want to continue this tradition of excellence, while presenting this message to a wider part of the Research Community.

Bioperl 1.5.0 Developer’s release is available for download.

• http://bioperl.org/DIST/bioperl-1.5.0.tar.bz2 425ac55ecbb4339b7b532ba6d429bb40

• http://bioperl.org/DIST/bioperl-1.5.0.tar.gz 172472f0675de9a583432e21c9b1b5fc

• http://bioperl.org/DIST/bioperl-1.5.0.zip 3febcd2445a7393c65981a6f9f13a9ed

We’ll update the website to reflect this new release.

The odd-numbered releases are called developer releases and are not deposited on CPAN. Please note that the API in 1.5.0 may change before the 1.6.0 release. which will be consider a stable API. We may do another developer release before 1.6.0 goes out.

Lots of people have contributed to this release, I apologize for not naming them all. I’ll try to cover some: thanks to Aaron Mackey for getting this release started, Brian Osborne for extensive documentation improvements, Nathan Haigh for volunteering to make a PPM of the release and Barry Moore and Nathan answering many of the windows related questions, Allen Day & Scott Cain & Steffen Grossmann for the work on FeatureIO, GFF3, and SeqFeature::Annotated, Chris Mungall for the work with Unflattener to merge GenBank annotations into GFF3 objects.

Please see the AUTHORS file for a complete list of contributors.

Jason Stajich on behalf of the Bioperl developers.

http://portal.open-bio.org/pipermail/bioperl-l/2005-January/018031.html

Release candidate 2 of Bioperl 1.5.0 is ready for downloading and testing. Please report back to the bioperl list with any problems. We would like to make a developer release by the end of January 2005.

• http://bioperl.org/DIST/bioperl-1.5.0-RC2.tar.gz
• http://bioperl.org/DIST/bioperl-1.5.0-RC2.tar.bz2
• http://bioperl.org/DIST/bioperl-1.5.0-RC2.zip

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. Please do download, test with your code, and report any bugs or problems to the normal lists (biopython at biopython.org or biopython-dev at biopython.org). For the full details about changes, please see: http://portal.open-bio.org/pipermail/biopython/2004-May/002078.html

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.

The invited speakers are leaders in the use of Perl in bioinformatics and development of BioPerl:

Aaron Mackey (U. of Pennsylvania) Jason Stajich (Duke University) Lincoln Stein (Cold Spring Harbor Labs)

Seminars and exercise sessions will be in a Linux computer lab for a total hands-on experience.

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