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This is a belated notice that the OBF mailing lists are down due to a server failure. Posting a tweet is easier than writing a blog post, please follow @OBF_news for updates.

We have a complete back up and running as a virtual machine hosted on Amazon Web Services (AWS), which should become live by Monday pending DNS updates etc.

Back in later 2012 we previously migrated the OBF websites AWS, and this has proved very reliable and saves us worrying about looking after physical hardware.

Source distributions and Windows installers for Biopython 1.64 are now available from the downloads page on the official Biopython website and from the Python Package Index (PyPI).

This release of Biopython supports Python 2.6 and 2.7, 3.3 and also the new 3.4 version. It is also tested on PyPy 2.0 to 2.3, and Jython 2.7b2.

The new experimental module Bio.CodonAlign facilitates building codon alignment and further analysis upon it. This work is from the Google Summer of Code (GSoC) project by Zheng Ruan.

Hi all, I’m pleased to announce the acceptance of OBF’s Google Summer of Code 2014 (GSoC) students:

• Sarah Berkemer - " Open source high-performance BioHaskell" (Mentors: Christian Höner zu Siederdissen, Ketil Malde) ( blog)
• Loris Cro - " An ultra-fast scalable RESTful API to query large numbers of VCF datapoints" (Mentors: Francesco Strozzi, Raoul Bonnal & the BioRuby team) ( blog)
• Victor Kofia - " JSBML: Redesign the implementation of mathematical formulas" (Mentors: Alex Thomas, Sarah Keating & the JSBML team) ( blog)
• Evan Parker - " Addition of a lazy loading sequence parser to Biopython’s SeqIO package" (Mentors: Wibowo Arindrarto, Peter Cock & the Biopython team) ( blog)
• Ibrahim Vazirabad - " Improving the Plug-in interface for CellDesigner" (Mentors: Andreas Dräger, Alex Thomas & the JSBML team) ( blog)
• Leandro Watanabe - " Dynamic Modeling of Cellular Populations within JSBML" (Mentors: Nicolas Rodriguez, Chris Myers & the JSBML team) ( blog)

Congratulations to our accepted students!

Bioinformatics Open Source Codefest, July 9 and 10th in Boston, now with sponsored food and drinks!

The OBF will be holding the fifth annual BOSC Codefest, an informal two day “hackathon” or “coding festival” preceding the Bioinformatics Open Source Conference (BOSC 2014) in Boston (USA).

This year, the BOSC Codefest 2014 is being hosted by hack/reduce (a wonderful hackerspace in Cambridge, Boston) and has also been kindly sponsored by Curoverse (the team behind the open source platform Arvados) and Harbinger Partners, Inc. Thanks to this sponsorship, this year the organisers will able to include catering for the participants - I’m expecting at least coffee and pizza, plus what ever caffeine rich drinks or local pastries are in fashion with the Boston programmers? I checked on wikipedia and Jolt Cola doesn’t exist in the USA any more… so I’m waiting to see what our local organisers Brad Chapman & Michael Heuer have planned.

To encourage more student presentations at the Bioinformatics Open Source Conference (BOSC), this year we’re waiving the registration fee for accepted student presenters. When you submit your abstract ( BOSC abstract call open until 4th April), you must tick the student box:

Student submissions must have a full-time student as the first named and presenting author, and be mostly written by students.

Please note that because BOSC registration is via the ISCB as one of the ISCM SIG meetings, eligible students must contact us before filling in their ISCB registration to ensure the BOSC SIG fee is waived.

Are you a university student and interested in spending the summer developing open-source bioinformatics software?

(Good! Keep reading.)

On Monday, March 10, Google Summer of Code 2014 (GSoC) will begin accepting student applications to work with mentoring organizations like OBF.

Here are the steps for you to prepare an application and apply for GSOC 2014 with OBF:

1. Check the OBF ideas page for potential projects you’d like to work on, and identify one or a few that you’re most interested in doing.
2. Read our guide for prospective GSoC students on the OBF wiki. Also see Google’s GSoC FAQ and GSoC student guide, if you’re with us so far.
3. Introduce yourself on the OBF GSoC mailing list. Tell us which project(s) you like, any modifications to them you’d like to make, or propose your own idea.
4. Once you’ve settled on a project or two and contacted your potential mentors, begin preparing a detailed project timeline for the summer. This timeline should cover each week of the summer, as far as you can plan it, describing the week’s specific goals, coding tasks, anticipated problems and open questions. ( Example 1, Example 2)
5. Submit your application to Google early. You can keep revising it on the Melange website until the deadline on March 21, but once you’ve submitted your basic information we can begin giving you feedback and suggestions to improve your application. In addition to your weekly timeline, you can link to examples of code you’ve written (e.g. on GitHub); a small contribution of code (e.g. a bug fix) to the project you’re applying to work with would really impress us.

Feel free to contact us on the mailing list or Google Plus if you have any questions.

Call for Abstracts for the 15th Annual Bioinformatics Open Source Conference (BOSC 2014), a Special Interest Group (SIG) of ISMB 2014.

• Dates: July 11-12, 2014
• Location: Boston, MA, USA
• Web site: /wiki/BOSC_2014
• Email: bosc@open-bio.org
• BOSC announcements mailing list
• Twitter: @OBF_BOSC and @OBF_News

Important Dates:

• March 24, 2014: Registration opens for ISMB and BOSC
• April 4, 2014: Deadline for submitting BOSC abstracts
• May 1, 204: Notification of accepted talk abstracts emailed to authors
• July 9-10, 2014: BOSC Codefest 2014, Boston
• July 11-12, 2014: BOSC 2014, Boston
• July 11-15, 2014: ISMB 2014, Boston

The Bioinformatics Open Source Conference (BOSC) covers the wide range of open source bioinformatics software being developed, and encompasses the growing movement of Open Science, with its focus on transparency, reproducibility, and data provenance. We welcome submissions relating to all aspects of bioinformatics and open science software, including new computational methods, reusable software components, visualization, interoperability, and other approaches that help to advance research in the biomolecular sciences. Two full days of talks, posters, panel discussions, and informal discussion groups will enable BOSC attendees to interact with other developers and share ideas and code, as well as learning about some of the latest developments in the field of open source bioinformatics.

Open Bio is officially a mentoring organization for Google Summer of Code 2014! See Google’s official announcement for more details on what this means in general.

What’s next? Google’s GSoC timeline lays out what we need to do as a mentoring organization during the coming weeks. Students can apply March 10–21 through the official GSoC 2014 website to work with OBF. Up to that point, we’ll be reaching out to potential students and mentors, and contining to develop potential project ideas. If you’d like to get involved, introduce yourself on our Google Plus community or on the mailing lists.

On Friday, OBF applied to be a mentoring organization for Google Summer of Code 2014. The core of our application to Google is our list of project ideas and our team of mentors supporting them. (We also have a separate page for general information about GSoC and OBF’s involvement.) As another way to interact with potential GSoC students, we’ve created a Google Plus page for OBF and a G+ community for OBF’s GSoC activities.

Highlights of this year’s Ideas list:

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.