Development

We are pleased to announce the release of BioRuby 1.5.0. This new release includes support of recent Ruby versions (Ruby 2.0.0, 2.1 and 2.2),  improvement of codes, and bug fixes.

Here is a brief summary of changes.

• Ruby 2.0.0, 2.1, 2.2 support.
• Some features are removed because of remote service discontinuance or difficulty of code maintenance.
• Refactoring of code.
• Bio::SPTR is renamed as Bio::UniProtKB.
• Bug fixes.

In addition, many changes have been made, including incompatible changes. For more information, see RELEASE_NOTES.rdoc and ChangeLog.

Call for Abstracts for the 16th Annual Bioinformatics Open Source Conference (BOSC 2015), a Special Interest Group (SIG) of ISMB/ECCB 2015.

• Dates: 10-11 July, 2015
• Location: Dublin, Ireland
• Web site: /wiki/BOSC_2015
• Email: bosc@open-bio.org
• BOSC announcements mailing list
• Twitter: @OBF_BOSC and @OBF_News

Important Dates:

• March 24, 2015: Registration opens for ISMB and BOSC ( https://www.iscb.org/ismbeccb2015-registration)
• April 3, 2015: Deadline for submitting BOSC abstracts
• May 3, 2015: Notification of accepted talk abstracts emailed to authors
• July 8-9, 2015: BOSC Codefest 2015, Dublin
• July 10-11, 2015: BOSC 2015, Dublin
• July 10-14, 2015: ISMB/ECCB 2015, Dublin

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. We particularly wish to invite those who have not participated in previous BOSCs to join us this year!

Last year’s Google Summer of Code 2014 was very productive for the OBF with six students working on Bio* and related bioinformatics projects. We applied to be part of GSoC 2015, but unfortunately this year were not accepted.

Google’s program is enormously popular, and over-subscribed, meaning Google has had to rotate organisation membership. The OBF is grateful to have been accepted in 2010, 2011, 2012 and 2014. This year any participation will be down to individual projects to find a willing umbrella group from the organisations accepted for GSoC 2015. For example, a Biopython project was included under NESCent for GSoC 2013.

Dear Biopythoneers,

Source distributions and Windows installers for Biopython 1.65 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, 2.7, 3.3 and 3.4. It is also tested on PyPy 2.0 to 2.4, PyPy3 version 2,4, and Jython 2.7b2.

The most visible change is that the Biopython sequence objects now use string comparison, rather than Python’s object comparison. This has been planned for a long time with warning messages in place (under Python 2, the warnings were sadly missing under Python 3).

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.

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.