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Google Summer of Code is on again for 2014, and OBF is once again applying as a mentoring organization. Participating in GSoC as an organization is very competitive, and we will need your help in gathering a good set of ideas and potential mentors.

Since OBF is an umbrella organization covering several member projects, most of these GSoC ideas will likely be associated with a specific Bio* community. For our GSoC application, and for the convenience of students, we aggregate each Bio* project’s ideas on the GSoC page of the OBF wiki, but the details of each idea are posted on the specific Bio* project’s own wiki. So, if you have an idea for a Summer of Code project, please post your idea on your Bio* project mailing list for discussion and start an outline on the corresponding wiki page. Feel free to reuse or adapt ideas from 2013 or previous years that were not taken on by a student already, if you feel the idea is still viable.

Update: The deadline for responding has been extended to January 25. The 2014 Google Summer of Code (GSoC) is coming up soon. The published timeline puts the mentoring organization applications from Feb 3 to 14.

OBF participated on behalf of our member projects in 2010, 2011, and 2012. Those participations were both important and successful. Through them, our projects gained new contributors, new features, and new community members. The mentors involved from our projects learned as much from the experience as the students, and formed bonds. The mentoring organization payment allowed OBF to sponsor community events and infrastructure.

Thanks to those who participated in the BOSC 2014 Keynote Competition! Our winner is Manuel Corpas, who correctly surmised Philip Bourne:

https://twitter.com/manuelcorpas/status/412520369044463616

(In fact, we had already confirmed Philip Bourne as our second keynote speaker before his new job at NIH was announced.) Congratulations, Manuel, on winning free admission to BOSC 2014!

Dr. Bourne’s keynote talk will be entitled “Biomedical Research as an Open Digital Enterprise”:

The biomedical research lifecycle is fast becoming completely digital and increasingly open to the point that publishing could simply become changing the access control on given research objects comprising ideas, hypotheses, data, software, results, conclusions, reviews, grants and so on. This offers immense opportunities for software developers to enable the enterprise. I will describe a vision for the digital enterprise and what the NIH and others are doing to support the notion with the intent to accelerate scientific discovery.

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The latest BioPerl release (v1.6.923) is now available on CPAN. This is a point release to address a few bugs, as well as push out the recent code updates that Francisco Ossandón has made to improve Windows support and improve Bio::Location (among other bits and pieces).

Contributing to the release:

• Francisco Ossandón
• Brian Osborne
• Dave Messina
• Carnë Draug
• Chris Fields
• Benjamin Warren

Enjoy!

chris

We’re pleased to officially confirm that one of the two keynote speakers for the 15th annual Bioinformatics Open Source Conference ( BOSC 2014) will be C. Titus Brown, as he announced on Twitter recently:

Titus Brown (@ctitusbrown):
Excited to be a keynote speaker at BOSC 2014! My title: “A History of Bioinformatics (in the year 2039)” - plenty of room for mischief ;)
https://twitter.com/ctitusbrown/status/410934403565490176

In recognition of the growing use of Twitter and social media within science as a way of connecting across geographical divides, we’re announcing a Twitter competition to guess who is scheduled to give the second keynote at BOSC 2014 in Boston.

Agenda

Venue: to be held by conference call on Dec 12, 2013, 12pm EDT (17:00 UTC) 
Dial-in Number: 1-605-475-5950 (US Midwest) 
Participant Access Code: 279610

1. Old business
   • Apr 2013 BoD meeting minutes
2. New business
   1. Board elections (by secret electronic ballot):
      • Hilmar Lapp, running for a 2nd term as President
      • Peter Cock, running for office of Secretary
      • Nomi Harris, running for a 2nd term on the Board, as at-large member
   2. To the extent available, review of 2013 financials (Hilmar)
   3. BOSC 2014: update from and vote of confidence for the 2014 chairs (Nomi, Peter)
   4. Does OBF and/or BOSC want to be listed as an ISCB “Community of Special Interest” (COSI) along side other SIGs and communities? See NetBio and RegSys examples. (Peter)

Minutes

Attending:

Agenda

Venue: to be held by conference call on April 9, 2013, 1.30pm EDT (17:30 UTC) 
Dial-in Number: 1-605-475-5950 (Midwest) 
Participant Access Code: 279610

1. Old business
   • Nov 2012 BoD meeting minutes
   • Treasurer’s 2012 report (Chris Dagdigian)
2. New business
   1. Administration of O|B|F’s 2013 Google Summer of Code participation (Pjotr Prins)

Minutes

Venue: held by conference call on April 9, 2013, 1.30pm EDT (17:30 UTC)

Attending:

• Directors: Hilmar Lapp, Nomi Harris, Chris Dagdigian, Chris Fields, Peter Cock; Jason Stajich joined for the last 15 minutes.
• Guests: none

Minutes:

Source distributions and Windows installers for Biopython 1.63 are now available from the downloads page on the official Biopython website and ( soon) from the Python Package Index (PyPI).

The current version removed the requirement of the 2to3 library. This was made possible by dropping Python 2.5 (and Jython 2.5).

This release of Biopython supports Python 2.6 and 2.7, and also Python 3.3.

The Biopython Tutorial & Cookbook, and the docstring examples in the source code, now use the Python 3 style print function in place of the Python 2 style print statement. This language feature is available under Python 2.6 and 2.7 via:

Note: I’m reposting here the original announcement from Florent Angly on the BioPerl mail list.

Dear all,

Some time ago, I announced that I was working on a set of BioPerl modules collectively forming the Bio-Community distribution. These Moose-based modules provide objects to represent communities, metacommunities and their members, and they also provide many methods to interact with them, perform various ecological operations (e.g. rarefaction, taxonomic summary, subsampling), and to read/write them to file in multiple formats.

Source distributions and Windows installers for Biopython 1.63 beta are now available from the downloads page on the official Biopython website.

This is a beta release for testing purposes, the main reason for a beta version is the large amount of changes imposed by the removal of the 2to3 library previously required for the support of Python 3.X. This was made possible by dropping Python 2.5 (and Jython 2.5).