An Application Note describing Biopython has recently been accepted for publication in the Oxford Journal Bioinformatics. An advance copy of the Open Access article is available online:
P.J.A. Cock, T. Antao, J.T. Chang, B.A. Chapman, C.J. Cox, A. Dalke, I. Friedberg, T. Hamelryck, F. Kauff, B. Wilczynski and M.J.L. de Hoon (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics, doi:10.1093/bioinformatics/btp163
Initially for evaluation purposes only, Giovanni and Bartek have setup a mirror of Biopython on GitHub, which is automatically updated from the OBF hosted Biopython CVS repository. See our git migration wiki page for details. If this is favorably received, then moving Biopython from CVS to git seems likely at some point this year.
Originally, all the OBF hosted projects used CVS for their source code repositories. At the start of 2008, BioPerl and BioJava moved over to Subversion (SVN), followed by BioSQL. Biopython was originally going to do the same, but this didn’t actually happen. Having all the Bio* projects using the same version control system would have simplified server administration for the OBF, but using SVN wouldn’t really have made that much difference to Biopython development. Discussion on the Biopython development mailing list has since shifted towards next-generation distributed version control systems like git or Bazaar.
[Read More]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:
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.
[Read More]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.
[Read More]The OBF Conference call is scheduled for 12:30PM to 2PM PST on Wednesday Nov 19, 2008. Members of the Open Bioinformatics Foundation and those interested in the decisions are invited to listen in and participate. A brief agenda is available here.
Please email Hilmar Lapp at hlapp _AT_ gmx.net for call in number and codes if you wish to participate or listen to the discussion. Those official members should have gotten an email via the OBF members email list.
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If you’ll be at BOSC or ISMB - please see this page and sign your name if you would like to try and meet up. We’ll do a developer’s dinner as well as have a BoF.
I’ve added a page about RSS feeds in BioPerl. These include links to CVS commits as a RSS feed. This a bit of a hack using cvs2rss and cvs2cl and I have hardcoded it to show the last 30 commits only.
In addition RSS news is now embedded on the main BioPerl and Tracking CVS commits webpages to make for better interlinking between the news and wiki site ( you might even be reading this there).
[Read More]The newest summary of the BioPerl mailing lists has been posted to the wiki:
Post gripes, harrassments, and faint praises at the regular places.