Travel award recipients for April 2017

We had a huge response to this round of the OBF travel award. After reviewing the applications, the OBF board selected four recipients. Three applicants accepted awards, and all plan to use the funds to attend this year’s BOSC, to take place July 22-23 in Prague.

Congratulations to our spring 2017 recipients:

  • Sourav Singh, who will participate in the Codefest and present the Biopython Project Update 2017 talk
  • Jonathan Sobel, presenting on a citizen science project named BeerDeCoded, carried out by members of the Swiss non-profit called the Hackuarium
  • Jiwen Xin, presenting the BioThings Explorer project, which integrates genomic data via public APIs

We encourage everyone at BOSC to come out and support our award winners! After BOSC, watch for blog posts from each of the awardees.

The next deadline for travel awards is August 15. You can apply to travel to participate at any event that develops or promotes open source development and open science in the biological research community. See the OBF travel award page for details and link to application.

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BOSC 2017 keynote speakers

We’re delighted to announce the keynote speakers for the Bioinformatics Open Source Conference, BOSC 2017, and our first sponsors.

But first a final reminder – today (Thursday 13 April 2017) is our deadline for submitting a full length talk abstract to BOSC 2017.

Dawn Field

Dawn Field is a Lamberg International Guest Professor at Göteborg University’s Department of Marine Sciences. Previously she was a senior research fellow at the NERC Centre for Ecology and Hydrology, Head of the Molecular Evolution and Bioinformatics Group at the Centre for Ecology and Hydrology in Wallingford, UK, and a research associate at the Smithsonian Institution. She is also a founder of the Genomic Standards Consortium, the Genomic Observatories Network and Ocean Sampling Day.

Dr. Field is credited with introducing the concept of a biological code, or “biocode” – the sum of all DNA on earth. In their book Biocode: The New Age of Genomics, she and coauthor Neil Davies describe the rapid rise of genomics, how it is revealing the scale and diversity of life on Earth, and future possibilities and implications.

Dr. Field’s advocacy for open data and interoperability is epitomized by her past leadership of the Genomics Standards Consortium (GSC), which aims to facilitate genomic data integration, discovery and comparison through international community-driven standards.

The title of Dr. Field’s keynote talk is “Understanding the Biocode: Global Sharing of Data.”

Nick Loman

Nick Loman is known as a vocal proponent of open genomic data in healthcare. A Professor of Microbial Genomics and Bioinformatics at the University of Birmingham, Dr. Loman explores the use of cutting-edge genomics and metagenomics approaches to human pathogens. He promotes the use of open data to facilitate the surveillance and treatment of infectious disease.

Dr. Loman helped establish real-time genomic surveillance of Ebola in Guinea and Zika in Brazil (via the ZiBRA project, which states that “Data will be subject to open release as it is generated”). In another recent project, real-time genomic data was used to analyze a small outbreak of Salmonella enteritidis in the UK. Through this sharing of genomic datasets, researchers were able to confirm that the cases were linked to a larger, national-scale outbreak. Dr. Loman is one of the authors of Poretools, and he regularly shares cutting-edge Nanopore data and protocols for using it. In collaboration with Lex Nederbragt, Dr. Loman is developing an open-source repository of sequencing and bioinformatics benchmarking datasets called Seqbench.

BOSC 2017 Sponsors

We are grateful to and welcome The Hyve (open source solutions for bioinformatics) and Mozilla Science Lab (a community of researchers, developers, and librarians making research open and accessible), as the first sponsors for BOSC 2017.

If you would like to be a sponsor of BOSC, please contact us at

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Biopython 1.69 released

Dear Biopythoneers,

Source distributions and Windows installers for Biopython 1.69 are now available from the downloads page on the official Biopython website, and the release is also on the Python Package Index (PyPI).

Continue reading

Posted in Biopython, Code, Development, OBF, OBF Projects, Uncategorized | Tagged , , , , , , | 1 Comment

OBF Travel Fellowship – CWL week in London

This is a guest blog post from Anton Khodak, who was supported by the ongoing Open Bioinformatics Foundation travel fellowship program to attend a week long Common Workflow Language (CWL) workshop in London, November 2016. This was a natural continuation of Anton’s work on porting tools to the CWL as one of the OBF’s Google Summer of Code 2016 students.

The OBF’s Travel Fellowship program continues to help open source bioinformatics software developers with funding to attend conferences or workshops. The current call closes 15 April 2017 – if you’re planning to attend the OBF’s annual Bioinformatics Open Source Conference (BOSC) 2017 in Prague, you might want to apply? Continue reading

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OBF Public Board of Directors Meeting

The OBF has at least one public board meeting per year, in part to vote on important business issues, and in part to publicly discuss items relevant to the OBF community.  The latest public OBF Board of Director’s meeting took place October 4, 2016. It was attended by Board members Hilmar Lapp, Peter Cock, Nomi Harris, Chris Fields, and Karen Cranston, as well as guests Heather Wiencko (Board candidate), Michael Crusoe, Spencer Bliven, and Robert Gilmore.

The agenda, and tentative minutes (taken by then-secretary Peter Cock) are available from the OBF wiki.  The following is a summary: Continue reading

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BioPerl v1.7.0 released

We are happy to announce the long-awaited release of BioPerl v1.7.0.  The release is now available on CPAN and Github.

During this release series, we will move some extraneous code to separate repositories and CPAN releases, primarily to reduce the number of dependencies required for BioPerl installation (in many cases for modules that are never used) and also reduce maintenance overhead.

This may only impact you if your code incorrectly list the immediate downstream dependencies that you utilize.  For example, we have now moved Bio::Coordinate code to a separate repo and will release it as a separate distribution on CPAN.  If your tools require Bio::Coordinate::Result and list this module as a dependency, you should be fine: a separate Bio::Coordinate release should pull in the latest BioPerl, until then it would pull in the last BioPerl release with that module.  However, if you list Bio::Root::Root or Bio::Perl as a dependency to pull in Bio::Coordinate::Result, your installation will not work correctly (as Bio::Root::Root is not the proper code dependency).  We can work with distributions affected to help with this transition and will be more consistently evaluating reverse dependencies on CPAN for upcoming releases as we split out code.  Please post issues on Github if you see problems with your code and the latest release.

In addition to the above, modules relying on a remote web services that are no longer active or pose a security issue will be deprecated for use and (in some cases) immediately removed.  Normally these don’t affect normal tests, but we have noticed some remote services out of our control causing problems with network-requiring or release testing.

In addition, the following changes have been made since the last release:

  • NCBI HTTPS support [Mark Johnson (aka mjohnson) and others]
  • We have migrated to Github Pages. This was actually planned, but the
    recent OBF server compromise forced our hand. Brian Osborne [bosborne] took this under his wing to move docs and has done a tremendous amount of work formatting the site and working out some of the idiosyncracies with the new Jekyll-based design. Mark Jensen, Paul Cantalupo and Franscison Ossandon also helped. Kudos!!
  • Similarly, the official issue tracker is now Github Issues. This has been updated in the relevant documentation bits (we hope!)
  • Previously deprecated modules have been removed
    • Bio::Tools::Infernal, Bio::Tools::ERPIN, Bio::Tools::RNAMotif
    • Bio::DB::SeqHound has been removed due to the service no longer being available
    • Bio::Tools::Analysis::Protein::Mitoprot has been removed for security reasons due to the server no longer having a valid cert
    • Bio::EUtilities, Bio::Biblio are now separate releases on CPAN
    • Bio::Coordinate, Bio::SearchIO::blastxml, Bio::SearchIO::Writer::BSMLResultWriter are now separate releases to be released independently on CPAN
  • Docker instances of tagged releases are available! [hlapp]
  • Bio::SearchIO::infernal
    • Issue #131: added CMSEARCH parsing support for Infernal 1.1 [pcantalupo]
    • Bio::Search::HSP::ModelHSP: Added a ‘noncanonical_string’ method to retrieve the NC line from CMSEARCH reports [pcantalupo]
    • Bio::Search::Result::INFERNALResult – Added new module to represent features of Infernal reports [pcantalupo]
  • SQLite support for Bio::DB::Taxonomy – [cjfields]
  • WrapperBase quoted option values [majensen]
  • Various documentation fixes and updates [bosborne]

And many many bug fixes.  Please see the Changes file with the distribution.

Thanks, and enjoy!


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BioRuby 1.5.1 released

We are pleased to announce the release of BioRuby 1.5.1.

In this new release, NCBI Entrez web client classes, Bio::NCBI::REST and Bio::PubMed, are changed to use HTTPS instead of HTTP, to prepare NCBI website transitioning to HTTPS.

Continue reading

Posted in BioRuby, Code, Development, OBF, OBF Projects | Tagged | 2 Comments

Biopython 1.68 released

Dear Biopythoneers,

Source distributions and Windows installers for Biopython 1.68 are now available from the downloads page on the official Biopython website, and the release is also on the Python Package Index (PyPI).

This release of Biopython supports Python 2.6, 2.7, 3.3, 3.4 and 3.5, but this will be our final release to run on Python 2.6. It has also been tested on PyPy 5.0, PyPy3 version 2.4, and Jython 2.7.

Bio.PDB has been extended to parse the RSSB’s new binary Macromolecular Transmission Format (MMTF, see, in addition to the mmCIF and PDB file formats (contributed by Anthony Bradley). This requires an optional external dependency on the mmtf-python library.

Module Bio.pairwise2 has been re-written (contributed by Markus Piotrowski). It is now faster, addresses some problems with local alignments, and also now allows gap insertions after deletions, and vice versa, inspired by the preprint from Flouri et al.

The two sample graphical tools SeqGui (Sequence Graphical User Interface) and xbbtools were rewritten (SeqGui) or updated (xbbtools) using the tkinter library (contributed by Markus Piotrowski). SeqGui allows simple nucleotide transcription, back-transcription and translation into amino acids using Bio.Seq internally, offering of the NCBI genetic codes supported in Biopython. xbbtools is able to open Fasta formatted files, does simple nucleotide operations and translations in any reading frame using one of the NCBI genetic codes. In addition, it supports standalone Blast installations to do local Blast searches.

New NCBI genetic code table 26 (Pachysolen tannophilus Nuclear Code) has been added to Bio.Data (and the translation functionality), and table 11 is now also available under the alias Archaeal.

In line with NCBI website HTTPS changes, Biopython now uses HTTPS rather than HTTP to connect to the NCBI Entrez and QBLAST API.

Additionally, a number of small bugs have been fixed with further additions to the test suite, and there has been further work to follow the Python PEP8 and best practice standard coding style.

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

  • Anthony Bradley (first contribution)
  • Ben Fulton
  • Carlos Pena
  • Connor T. Skennerton
  • Iddo Friedberg
  • Kai Blin
  • Kristian Davidsen (first contribution)
  • Markus Piotrowski
  • Olivier Morelle (first contribution)
  • Peter Cock
  • Tiago Antao
  • Travis Wrightsman
  • Uwe Schmitt (first contribution)
  • Xiaoyu Zhuo (first contribution)

Thank you all.

P.S. You can follow @Biopython on Twitter


$ md5sum biopython-1.68.*
078e915185485a5327937029b7577ddc biopython-1.68.tar.gz
362e964543a424a2f7585ea4008ea834 biopython-1.68.win32-py2.6.exe
772d07d9a6490d674688d00ede2bdfe9 biopython-1.68.win32-py2.7.exe
fda2d1c8d4a7862f6af85122c86fcd0f biopython-1.68.win32-py2.7.msi
8de95a90704f15f4c22d5359dbc54b75 biopython-1.68.win32-py3.3.exe
92f40105761520daeeb9128254a8bc94 biopython-1.68.win32-py3.3.msi
b1cd3f6b4ad1096347d5019c68128dac biopython-1.68.win32-py3.4.exe
9403b9b0d01c22b49edb34e2164c31de biopython-1.68.win32-py3.4.msi
72202792fc387376c07e28997ece181f biopython-1.68.win32-py3.5.exe
ff0cfc6c835ddf890b69ba872fb46b39 biopython-1.68.win32-py3.5.msi
$ shasum -a 256 biopython-1.68.*
d1dc09d1ddc8e90833f507cf09f80fa9ee1537d319058d1c44fe9c09be3d0c1f  biopython-1.68.tar.gz
09449d7204c65e6010545092f2bc1dc662a0b5f6a873e52a08e19392f935fdb7  biopython-1.68.win32-py2.6.exe
a7c2fe52ce8dcf503a492e4ee006dd8bc62faa77078d04c92abdbf7713bf2166  biopython-1.68.win32-py2.7.exe
f92dfefc9a4ee61dda838a61d73a38b55552a1771ce411505009a48702aefd41  biopython-1.68.win32-py2.7.msi
bce6a4cece7b75650d6a478f4ed9d7d1a5351df42a1820866a0cbd74c254565d  biopython-1.68.win32-py3.3.exe
85bd5d499400e594f77d297966f56c139499711513b9cd24b87fece5a0463fbe  biopython-1.68.win32-py3.3.msi
05c1f59933ef35ecb838649f6fabacb823f2a48c2498ed57ac59a6b3629b5369  biopython-1.68.win32-py3.4.exe
10928347029bc6b0b76567d5f6026a8a002bd3502a7ceeaded7d566938db4bef  biopython-1.68.win32-py3.4.msi
5d08e4de11f920ec5207e10d264fceb837e2000843a56fd684e0ee2dfb948fe5  biopython-1.68.win32-py3.5.exe
299888c32b36f32542775952e7b863bd9c3d362f61a69b7d8a136a63aeabec36  biopython-1.68.win32-py3.5.msi

Updated 29 August 2016 to include the Python 3.5 installer checksums.

Posted in Biopython, Blogroll, Code, Development, OBF, OBF Projects | Tagged | 30 Comments

BOSC 2016 in Disney World with Donald Docker!

First I would like to congratulate OBF that supports diversity in the community with its travel awards initiative. I was very pleased to be one of the three travel fellowship awardees. Thank you OBF! Ιt was great to attend BOSC 2016 and meet remarkable people and know their work.

It was one of the most welcoming meetings I have attended and Ι liked that is was active on the social media and the conference materials and speaker presentations were available online. It made it fun and useful and we could focus less on our notebooks and more on the speakers. Τhis also attracted a lot of positive comments from the other Special Interest Groups. So “Bravo” to the organizers!

On the scientific part, it was nice to see Docker making an impression on the bioinformatics community. Everyone was talking about it. It is an awesome way to package bioinformatics applications and the fact that it received so much attention got me pretty excited. I am planning to use it to package CollOS, an open source web application I presented at the conference, that tracks, annotates and barcodes biological samples to facilitate wet lab scientists to locate and identify biological samples.

Last but definitely not least, I would like to congratulate Mónica Muñoz-Torres and the organizers for their reference to the recent tragic shooting incident in Orlando.

Hope to see you next year in Prague!


Posted in BOSC/ISMB, Community, OBF, Travel Fellowship | Tagged , , , | 7 Comments

New BioJava Logo Design Competition

BioJava is organizing a design competition to come up with a new logo.
Anybody can participate:

  • The logo should look modern and be better than the current one (yellow

  • The logo should be able to be rendered as a favicon, as well as large
    (e.g. on a t-shirt). Designs that come in two (or multiple) sizes are ok.

  • Logos shall not look similar in any way to the trademarked Java
    programming language logo. This means no coffee cups in any way.

Deadline for submissions is July 4th.

Announcement of Winner:
The winner of the new logo competition will be announced during BOSC 2016.

We will print t-shirts with the new logo and the designer will get a free

If the designer of the winning new logo will be attending ISMB 2016, the
attending BioJava developers will take the winner out for dinner.

BioJava will carry the new logo on its homepage and GitHub Profile

For full details of the competition and how to make a submission please
view here:

Result Update:

As announced via the mailing list and at BOSC 2016, the winning logo was by Aleix Latifa:

Posted in BioJava, Blogroll, BOSC/ISMB, Community, Development, OBF, OBF Projects, Website | Tagged , , , , , , | 7 Comments