O|B|F - Open Bioinformatics Foundation

(BOSC/ISMB) -- Julian Lombardi will present keynote at BOSC 2008

The BOSC 2008 Organizing Committee is pleased to announce that Julian Lombardi will be giving the keynote address this year. Dr. Lombardi is one of the original architects of the open-source, peer-to-peer OpenCroquet platform for creating and deploying deeply collaborative multi-user online applications and virtual worlds.

For further information about Dr. Lombardi, see the Wikipedia entry about him, his blog, and the OpenCroquet website.

(BioPython) -- Biopython release 1.45

We are pleased to announce the release of Biopython 1.45.

This release includes numerous code improvements and fixes, including in Bio.Seq, Bio.SeqIO, Bio.Entrez, Bio.PopGen, Bio.SwissProt, Bio.Cluster, Bio.SCOP, Bio.InterPro, Bio.GenBank, Bio.ExPASy, BioSQL, and the Biopython documentation. Too many to list them all here!

Source distributions and Windows installers are available from the Biopython website at http://biopython.org. My thanks to all code contributers who made this new release possible.

--Michiel on behalf of the Biopython developers

(OBDA / BioSQL) -- BioSQL v1.0.0 released

After a long wait and several earlier attempts, version 1.0.0 (code-named Tokyo, see below) of BioSQL has finally been released. The release can be downloaded at http://biosql.org/DIST/ as .tar.gz, .tar.bz, and Zip (which also has Windows-style end-of-line characters) archives. The full release announcement can be found in the BioSQL mailing list archives, and in the distribution itself.

(BOSC/ISMB) -- BOSC 2008 is on

Our application to hold BOSC as a two-day SIG (Special Interest Group) meeting in conjunction with ISMB has been accepted for this year. BOSC will take place July 18 and 19 in Toronto, Canada.

(BioPython) -- Biopython release 1.44

We are pleased to announce the release of Biopython 1.44.

This release includes lots of code improvements and fixes in the Blast interface and parsers, sequence input/output, the SwissProt parser, the clustering routines, as well as a brand new module for population genetics. For reasons of compatibility, some radical changes were necessary in some parts of the code; please let us know if you find some functionality missing.

Source distributions and Windows installers are available from the Biopython website at http://biopython.org. My thanks to all code contributers who made this new release possible.

--Michiel on behalf of the Biopython developers

(BioPython) -- Biopython release 1.43

We are pleased to announce the release of Biopython 1.43.

This release includes a brand-new set of parsers in Bio.SeqIO by Peter Cock for reading biological sequence files in various formats, an updated Blast XML parser in Bio.Blast.NCBIXML, a new UniGene flat-file parser by Sean Davis, and numerous improvements and bug fixes in Bio.PDB, Bio.SwissProt, Bio.Nexus, BioSQL, and others. Believe it or not, even the documentation was updated.

Source distributions and Windows installers are available from the Biopython website at http://biopython.org. My thanks to all code contributers who made this new release possible.

--Michiel on behalf of the Biopython developers

(BioPerl) -- Bioperl 1.5.2 Release

I'm proud to announce the final release of Bioperl 1.5.2. Full details are available at http://www.bioperl.org/wiki/Release_1.5.2

(BioPython) -- Biopython release 1.42

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 contributers 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 contributers who made this new release possible.

--Michiel on behalf of the Biopython developers

(General) -- CVS server move

The CVS repository is migrating from 'pub' to a new host called 'dev' and requires us to re-issue accounts. This will be a good opportunity to verify email addresses and remove unused accounts.

You should have received an email from Chris D requesting specific information and you will get a new password in the response. If not you will need to send a note to the helpdesk at support_AT_open-bio.org. The changover will happen around March 25th.

(General) -- Gallery updated

The BOSC 2002 pictures have been migrated to the O|B|F gallery site hackathon2002.

(BioPerl) -- new Bioperl website

I am pleased to announce the release of a new website for BioPerl. The site is based on the mediawiki software that was developed for the wikipedia project. We intend the site to be a place for community input on documentation and design for the BioPerl project. There is also a fair amount of documentation started surrounding bioinformatics tools and techniques applicable to using BioPerl and some of the authors who created these resources.

The website continues to be at the URL http://www.bioperl.org. The DNS updates may take up to 24 hours to reach everyone.

The initial content of the site is result of the work of myself, Mauricio Herrera Cuadra, Brian Osborne, and Torsten Seemann. We encourage you to contribute to the site's content by signing up for an account.

There are several guides for style of the site. One in particular is how to link to Modules which can contain additional information from the POD http://bioperl.org/wiki/Module:Bio::SeqIO

You'll notice that many of the paths have changed but the DIST and SRC continues to be available at http://bioperl.org/DIST and http://bioperl.org/SRC. The HOWTOs are now available from http://bioperl.org/wiki/HOWTOs.

The FAQ is available at http://bioperl.org/wiki/FAQ and I encourage you to add your questions to it so they can be properly archived and addressed.

We also have initiated a News site for Bioperl for posting announcements regarding development and software. I would like to see if there are volunteers to post weekly or monthly summaries of mailing list traffic and development. http://www.bioperl.org/news/

Jason Stajich on behalf of Mauricio Herrera Cuadra, Brian Osborne, Torsten Seemann.

(BioPython) -- BIOPYTHON 1.41 RELEASED

We are pleased to announce the release of Biopython 1.41. Many improvements were made in Biopython during the eight months since the previous release, and the new release contains lots of bugfixes, improvements, new functionalities, and better documentation. To pick a few, there's the new Bio.MEME module by Jason Hackney, updates to the Blast parser using Bertrand Frottier's NCBIXML code, a BLAT parser by Yair Benita, numerous updates in Bio.PDB, CompareACE support in AlignAce, and improved user-friendliness in Bio.Seq.

Lots of people of contributed to this release, in particular Frank Kauff (Bio.Nexus), Jason Hackney (Bio.MEME), Thomas Hamelryck (Bio.PDB), Frederic Sohm (Bio.Restriction), James Casbon (Bio.SCOP) for bug fixes and updates, Peter (Bio.Blast.NCBIXML test cases), and of course Jeff Chang, Brad Chapman, Andrew Dalke, and Iddo Friedberg for Biopython and the fool-proof instructions on how to roll a release, which made this a lot easier than I anticipated. My apologies if I forgot to thank somebody.

Michiel de Hoon on behalf of the Biopython development team.

(BioPerl) -- Bioperl 1.5.1

I am pleased to announce the 1.5.1 developer release of Bioperl.

Essential links here
Core
http://bioperl.org/DIST/bioperl-1.5.1.tar.gz
http://bioperl.org/DIST/bioperl-1.5.1.zip
http://bioperl.org/DIST/bioperl-1.5.1.tar.bz2

Run
http://bioperl.org/DIST/bioperl-run-1.5.1.tar.gz
http://bioperl.org/DIST/bioperl-run-1.5.1.zip
http://bioperl.org/DIST/bioperl-run-1.5.1.tar.bz2

Ext
http://bioperl.org/DIST/bioperl-ext-1.5.1.tar.gz
http://bioperl.org/DIST/bioperl-ext-1.5.1.zip
http://bioperl.org/DIST/bioperl-ext-1.5.1.tar.bz2

MD5 sum
http://bioperl.org/DIST/SIGNATURES.md5

Please see my mailing list postfor more information.

(BioPerl) -- Bioperl 1.5.1 RC4

Release Candidate 4 for bioperl 1.5.1 (Developer release) core, run, and ext packages is available.

Several bug fixes went in last week so I've made what I hope to be
the last release candidate before 1.5.1 goes out.

More Info:
http://portal.open-bio.org/pipermail/bioperl-l/2005-October/019904.html

(General) -- O|B|F Board of Directors Meeting

The 2005 Board of Directors meeting for the Open Bioinformatics Foundation was held on Thursday, June 24th 2005 in Detroit, MI USA at the site of the BOSC2005 meeting.

This was a major meeting and represents the first attempt to build a governance platform for the organization as well as set up the mechanism for building a voting membership. The O|B|F members will be able to direct the operation of the organization and will also be able to join the Board.

Other major news from the meeting:
- Ewan Birney steps down as president; joins Board as at-large member
- Jason Stajich joins board and is elected President
- Hilmar Lapp is elected to a new position of 'Parlimentarian'
- Determined efforts to build a voting membership body

Links to meeting minutes and Election Bylaws follow are below ...