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.

Brian Osborne and James Thompson have written a Bioperl HOWTO for beginners, for those who are interested in learning about Bioperl but have done very little programmming. Topics include creating a Sequence object, I/O and files, retrieving from Genbank, and using the Sequence object. All HOWTOs are published on the bioperl website.

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.

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.

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.

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!