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.

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 post for more information.

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

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 …

The backend MovableType software powering this site was upgraded and the backend storage was switched from berkelyDB to SQL. These preparations are being done to ease the transition of http://news.open-bio.org to a new server. The primary purpose of this news entry is to confirm that the posting system still works after the upgrade!

Venue: Renaissance Center in Detroit, on the first floor next to the Starbucks.  Date: June 23, 2005, 16:15.

Call to order:

• Board members present: Chris, Hilmar, Ewan, Andrew
• Others: Jason Stajich

Chris / Treasurer’s Report

• Review of the accounts / passing the statements around
• Summary of response to the fraud attempt
• Request to activate the debit card. Granted.
• The account got a $9,000 deposit but we don’t know who it comes from. Chris will investigate.
• We have not yet received our money from the Glasgow BOSC. Chris will follow up on that.
• Chris will pull the current credit report for Open Bio.
• Develop a succession / “hit by the bus” plan for hardware and people. Eg, can we get access to the account if Chris decides to be a beach bum in the S. Pacific?
• We did not pay Delaware to renew our corporate registration. Chris will look into getting the right person to fix that and pay any penalties.
• Some discussion about letting Chris make minor (<$1,000) payments without a counter-signature. Hilmar pointed out that’s in the new bylaws

New Bylaws, Membership

Hilmar presentation of the new OBF bylaws. We reviewed it and made comments. Some time later he finished.

The BOSC 2005 schedule has been posted. Lightning talks are still being accepted.

A PopGen HOWTO added to the website for using the population genetics modules in Bioperl.

The PAML HOWTO is in-process of being updated to describe the new functionalilty.

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.