Sadly OBF not accepted for GSoC 2015

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.

Other organizations with bioinformatics as keyword are Ruby Science Foundation, Department of Biomedical Informatics, Stony Brook University, OncoBlocks, University of Nebraska – Helikar Lab. Other organizations related to sciences are ASCEND , BRL-CAD, Debian Project, HPCC Systems®International Neuroinformatics Coordinating Facility , lmonade: scientific software distribution, OSGeo – Open Source Geospatial Foundation, The Concord Consortium, The Visualization Toolkit. Languages: Python, Scala, Apache Foundation. Last but not least : Global Alliance for Genomics & Health.

On behalf of the OBF, we would like to thank our volunteer GSoC Administrators, Raoul Bonnal and Francesco Strozzi, for organising our application – and all our potential mentors across the Bio* projects who put forward potential project suggestions.

Posted in BioJava, BioLib, BioPerl, Biopython, BioRuby, Blogroll, Community, Development, General, Google Summer of Code, OBF, OBF Projects | Tagged , , , , | 3 Comments

OBF Google Summer of Code 2014 Wrap-up

GoogleSummer_2014logoIn 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. Continue reading

Posted in Biopython, BioRuby, Community, Google Summer of Code, OBF | Tagged , , , , | 8 Comments

BOSC welcomes Sarah Hird as Outreach Coordinator

sarah-hirdThe BOSC 2015 Organizing Committee is pleased to welcome Sarah Hird as our new Outreach Coordinator. BOSC is eager to increase the participation of individuals and groups that have been historically underrepresented at our conferences, and Sarah will be spearheading this effort.

Sarah is currently a UC Davis Chancellor’s Postdoctoral Fellow with Jonathan Eisen in the UC Davis Genome Center, where her research interests lie at the intersection of phylogeography, bioinformatics and microbial diversity.  She earned her PhD in biology and bioinformatics at LSU. Sarah is also known for her focus on promoting diversity in STEM. “I am personally and professionally interested in how we can make “the Academy” a more representative sample of the world around us,” she says.

Please join us in welcoming Sarah to the BOSC organizing committee, and stay tuned for more information about BOSC 2015 (which will take place July 10-11, 2015, in Dublin).

Posted in BOSC/ISMB, Community | 12 Comments

Biopython 1.65 released

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).

The Bio.KEGG and Bio.Graphics modules have been expanded with support for the online KEGG REST API, and parsing, representing and drawing KGML pathways.

The Pterobranchia Mitochondrial genetic code has been added to Bio.Data (and the translation functionality), which is the new NCBI genetic code table 24.

The Bio.SeqIO parser for the ABI capillary file format now exposes all the raw data in the SeqRecord’s annotation as a dictionary. This allows further in-depth analysis by advanced users.

Bio.SearchIO QueryResult objects now allow Hit retrieval using its alternative IDs (any IDs listed after the first one, for example as used with the NCBI BLAST NR database).

Bio.SeqUtils.MeltingTemp has been rewritten with new functionality.

The new experimental module Bio.CodonAlign has been renamed Bio.codonalign (and similar lower case PEP8 style module names have been used for the sub-modules within this).

Bio.SeqIO.index_db(…) and Bio.SearchIO.index_db(…) now store any relative filenames relative to the index file, rather than (as before) relative to the current directory at the time the index was built. This makes the indexes less fragile, so that they can be used from other working directories. NOTE: This change is backward compatible (old index files work as before), however relative paths in new indexes will not work on older versions of Biopython!

Behind the scenes, we have done a lot of work applying PEP8 coding styles to Biopython, and improving the formatting of the source code documentation (PEP257 docstrings).

Many thanks to the Biopython developers and community for making this release possible, especially the following contributors:

  • Alan Du (first contribution)
  • Carlos Pena (first contribution)
  • Colin Lappala (first contribution)
  • Christian Brueffer
  • David Bulger (first contribution)
  • Eric Talevich
  • Evan Parker (first contribution)
  • Hongbo Zhu
  • Kai Blin
  • Kevin Wu (first contribution)
  • Leighton Pritchard
  • Leszek Pryszcz (first contribution)
  • Markus Piotrowski
  • Matt Shirley (first contribution)
  • Mike Cariaso (first contribution)
  • Peter Cock
  • Seth Sims (first contribution)
  • Tiago Antao
  • Travis Wrightsman (first contribution)
  • Tyghe Vallard (first contribution)
  • Vincent Davis
  • Wibowo ‘Bow’ Arindrarto
  • Zheng Ruan

This is a longer list of contributors and changes than usual, but it was also a longer gap since our last release.

Posted in Biopython, Blogroll, Code, Development, OBF, OBF Projects | Tagged , , , | 2 Comments

BOSC 2015 will be in Dublin with ISMB/ECCB 2015

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. We would have been hosted by The Genome Analysis Centre (TGAC) just after and co-located with the Galaxy Community Conference 2015 (GCC 2015, hosted by The Sainsbury Laboratory). Although some survey participants indicated that they would be more likely to attend BOSC 2015 if it were co-located with GCC, the majority preferred BOSC to remain an ISMB SIG, so we will hold BOSC 2015 in Dublin right before ISMB/ECCB 2015.

Here is the summary of responses to the questions about the location of BOSC 2015:



Although the survey is now closed, we are always happy to hear your suggestions for BOSC 2015. (We are particularly interested in increasing diversity at BOSC, and welcome suggestions of people to invite.) You can reach us at

Nomi Harris and Peter Cock
Co-Chairs, BOSC 2015

Posted in Blogroll, BOSC/ISMB, Community, OBF | Tagged , , , | 9 Comments

BOSC 2014 video recording

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.YouTubeLast 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. This year we are hiring a professional from Next Day Video (@NextDayVideo on Twitter).

Google LogoThis is thanks to very generous support from Google’s Open Source Programs Office (who also run the amazing Google Summer of Code program which the OBF and its member projects have regularly taken part in), a new sponsor for BOSC this year.

Posted in OBF | Tagged , , | 7 Comments

OBF Mailing List Outage

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.

Update (Monday 16 June 2014): The replacement mailman server is now live, but our apologies for the inconvenience. Some delayed emails should now be delivered, but unfortunately older emails where you received a failure message will have to be resent.

Posted in OBF | 4 Comments