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Google is committed to run the Summer of Code program again this year. It will be for the 5th time.

In broad strokes, the program funds what you might call remote summer internships for students to contribute to an open-source software project. Projects (or umbrella organizations) wishing to participate in the program apply during the organization application period (March 9-13 in 2009). Those accepted into the program provide project ideas and supply mentors that guide the work on those. Students apply to a project within the program with specific project ideas, based on those suggested or based on their own idea, get ranked by the mentors of the project, and those accepted into the program get paired up with mentors. Projects are chiefly about programming, the coding period is 3 months (Jun-Aug), and there is no travel required by either student or mentor. The program is global; other than the US trade restrictions that Google is under, there are no restrictions as to where student or mentor reside. The main motivations behind the program are to recruit new contributors to open-source projects, and to produce more open-source code. See the program FAQs for more information.

O|B|F News feed is now available in Twitter! You are welcome to follow us.

Cheers, The O|B|F Admins.

Release Pumpkin Chris Fields has announced the release of BioPerl 1.6 - the first stable release in a several years containing many significant improvements and bug fixes.

I am proud to announce, on behalf of the BioPerl core developers, that BioPerl 1.6.0 is now available.  This is the first BioPerl core release in the 1.6 series and is considered a ‘stable’ (non-developer) release.  The distribution has been uploaded to CPAN and is available under author name CJFIELDS; it should be hitting the various CPAN nodes over the next 24 hours.  A direct CPAN link is here:

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RC4 is up, we are days away from final release…

Belated, and probably most of you knew already, but just in case you didn’t, the 2009 Bioinformatics Open Source Conference (BOSC) was accepted on Dec 16 as a Special Interest Group (SIG) meeting by the respective ISMB 2009 review committee. Special thanks and congratulations to Kam Dahlquist, who agreed again this year to chair the conference, and who pulled the proposal together.

You can follow the organization and the conference taking shape at the BOSC 2009 wiki page. Ideas, preliminary schedules, etc are discussed  on the associated talk page. You are welcome and encouraged to join us there. The blurb for publicizing the event on the ISMB website is due on January 16, in a little more than 1 week. If you have ideas or would like to help, do let us know.

The minutes of the November 2008 O|B|F Board of Directors meeting have been posted. The most important result of that meeting is that Kam Dahlquist was elected to the Board, bringing the number of Board members back to four. Please join us in extending a warm welcome to Kam!

We aim to elect additional Directors this year, please contact the Nominating Committee if you are interested in serving, or if you know people who might be. Suggestions of people we should tap to serve are also welcome and appreciated.

BioPerl has branched for 1.6 and the RC1 is up for testing as Chris announced.

BioPerl is preparing for version 1.6 release in the coming months. As part of this some restructuring and simplification of the packaging is occurring.

• Bio-Graphics has been split off into its own package back on Sourceforge to allow for a separate release schedule. It will be uploaded to CPAN as a separate package. In the future other small groups of modules will also be split off from the Core.  Eventually the Core will constitute components that will be the main parsers and data objects while less-common use cases or tightly related modules (like bioperl-network) will be released to CPAN on their own.
• Tests have been split off into smaller chunks.
• Anyone who has contributed to the code and feels their name should be included in the authors’ list needs to either add it or email the mailing list or Chris Fields.
• S endu has moved ModuleBuildBioperl and BioperlTest into Bio::Root
• Bugs are being triaged at bugzilla so if you have any opinions you can vote on the bugs in the queue.

We are pleased to announce the release of Biopython 1.49. There have been some significant changes since Biopython 1.48 was released a few months ago, which is why we initially released a beta for wider testing. Thank you to all those who tried this and reported the minor problems uncovered.

As previously announced, the big news is that Biopython now uses NumPy rather than its precursor Numeric (the original Numerical Python library).

Scheduled for Nov 19, 12:30 - 2PM PST via Conference call. Please email board@open-bio.org to receive call-in information so we will know how many callers there will be.

Agenda

Old Business

1. Approve minutes from BOSC 2008 Meeting

New Business

1. To vote on a new member to the board, Kam Dahlquist
2. Discuss leadership changes and plan how Board membership will be expanded in the next year
3. BOSC 2009: planning is underway by BOSC committee, will discuss any input needed by BoD
4. Treasurer’s financial report from summer 2008, with accounts updated to be current for
5. Any purchase or server hosting decisions
   • I put some thoughts regarding the OSC hosting offer on my talk page: User:Dag – Dag 20:34, 19 November 2008 (UTC)

Minutes

Venue: held by conference call, starting 12.30pm Pacific Time (US).