Community

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.

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.

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.

[Read More]

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