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A wiki page for collecting ideas, possible projects, prerequisites, possible solution approaches, mentors, other people or channels to contact for more information or to bounce ideas off of, etc. has been setup:

http://open-bio.org/wiki/Google_Summer_Code_2009

All,

I am proud to announce that the 1.6 release for BioPerl-run, BioPerl- db, and BioPerl-network are now available by direct download and via CPAN. These are designated as 1.006000, with a requirement for BioPerl 1.6 and higher (1.006000).

FIXED:

1. Bio::Tools::Run::Primer3 now accepts primer3 or primer3_core as executable names
2. Bio::Tools::Run::Vista tests now pass if Vista.jar is installed.
3. bug fix in bioperl-network

What remains for the 1.6 release series:

\* Documentation, Documentation, and Documentation. I haven’t had much time unfortunately to work on documentation, primarily for BUGS/ INSTALL/README etc within db/run/network (the latter has been mainly updated by Brian O.) I will attempt to update these for the next point release, tentatively scheduled for mid-April.

Please forward as appropriate and forgive multiple postings.

Call for Abstracts for the 2009 Bioinformatics Open Source Conference (BOSC) 2009

An ISMB 2009 Special Interest Group (SIG) Date: June 27-28, 2009 Location: Stockholm, Sweden URL: /wiki/BOSC_2009 Abstract submission via EasyChair: https://www.easychair.org/login.cgi?conf=bosc2009

Important Dates Monday, April 13: Abstract deadline May 1, 2009: Notification of accepted abstracts May 15, 2009: Early Registration Discount Cut-off date June 27-28, 2009: BOSC 2009

The Bioinformatics Open Source Conference (BOSC) is sponsored by the Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development within the biological research community. To be considered for acceptance, software systems representing the central topic in a presentation submitted to BOSC must be licensed with a recognized Open Source License, and be freely available for download in source code form.

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:

[Read More]

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.