BOSC 2015 Keynote Speakers

 Posted on March 26, 2015  |  peterc

Announcing the keynote speakers for the Bioinformatics Open Source Conference, BOSC 2015: Holly Bik Dr Holly Bik is a Birmingham Fellow (assistant professor) in the School of Biosciences at the University of Birmingham, UK. She obtained her Ph.D. in molecular phylogenetics at the University of Southampton, UK (working in conjunction with the Natural History Museum, London), followed by subsequent postdoctoral appointments at the Hubbard Center for Genome Studies at the University of New Hampshire and the UC Davis Genome Center. [Read More]

BOSC 2015 call for Abstracts

 Posted on March 5, 2015  |  peterc

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. [Read More]

Sadly OBF not accepted for GSoC 2015

 Posted on March 3, 2015  |  peterc

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. [Read More]

OBF Google Summer of Code 2014 Wrap-up

 Posted on February 23, 2015  |  hilmar

GoogleSummer_2014logo In 2014, OBF had six students in the Google Summer of Code 2014™ (GSoC) program mentored under its umbrella of Bio* and related open-source bioinformatics community projects: Loris Cro (Bioruby) with mentors Francesco Strozzi and Raoul Bonnal; Evan Parker (Biopython) with mentors Wibowo Arindrarto and Peter Cock; Sarah Berkemer (BioHaskell) with mentors Christian Höner zu Siederdissen and Ketil Malde; and three students contributed to JSBML: Victor Kofia (mentors: Alex Thomas and Sarah Keating), Ibrahim Vazirabad (mentors: Andreas Dräger and Alex Thomas), and Leandro Watanabe (mentors: Nicolas Rodriguez and Chris Myers).

As a change from earlier years in which OBF participated in GSoC as a mentoring organization, in 2014 we purposefully defined our umbrella as much more inclusive of the wider bioinformatics open-source community, bringing it more in line with the annual Bioinformatics Open-Source Conference (BOSC).  In part this was also motivated by " paying it forward", a concept central to growing healthy open-source communities, after the larger domain-agnostic language projects such as SciRuby and PSF had extended an open hand to OBF mentors when OBF did not get admitted as a GSoC mentoring organization in 2013. In the end, four out of the six succeeding student applications were for projects outside of the traditional core Bio* projects, a result with which everyone won: We had a terrific crop of students, our community grew larger and stronger, and open-source bioinformatics was advanced in a more diverse way than would have been possible otherwise.

[Read More]

Biopython 1.65 released

 Posted on December 17, 2014  |  peterc

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. [Read More]

BOSC 2015 will be in Dublin with ISMB/ECCB 2015

 Posted on September 18, 2014  |  peterc

We have asked you, and you have spoken! 59 past and/or future BOSC attendees participated in our survey, answering questions about what they liked at BOSC 2014, what changes they’d like to see, and — most importantly — what they thought about the proposal to possibly hold BOSC 2015 in Norwich (UK) rather than as an ISMB/ECCB SIG in Dublin (Ireland).. Under this plan, BOSC 2015 would have been shortly before ISMB/ECCB, but in Norwich. [Read More]

BOSC 2014 video recording

 Posted on June 19, 2014  |  peterc

We’re pleased to publicly announce that we aim to video record all the talks at BOSC 2014, and the panel discussion, to be made freely available online after the conference. This is on an opt-out basis, and thus far none of our speakers have declined to be filmed. Last year we managed to record many of the talks - including both keynotes, which you can watch via the YouTube links on the BOSC 2013 Schedule. [Read More]

OBF Mailing List Outage

 Posted on June 15, 2014  |  peterc

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. [Read More]

OBF Google Summer of Code students 2014

 Posted on April 26, 2014  |  etal

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! [Read More]

Catering at BOSC CodeFest 2014

 Posted on April 2, 2014  |  peterc

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. [Read More]