OBF Travel Fellowship – IGC Bioinformatics Training

This blog post is syndicated from a post on Vitalina Kirgizova’s blog, originally published June 6, 2017. Vitalina was supported by the ongoing OBF travel fellowship program to attend bioinformatics training course held at the Instituto Gulbenkian de Ciência, Oeiras, Portugal, in November 2016.

The OBF’s Travel Fellowship program continues to help open source bioinformatics software developers with funding to attend conferences, workshops, or training events. The next call closes 15 December 2017. Continue reading

Posted in Blogroll, Community, Travel Fellowship | Tagged , | Leave a comment

Travel fellowships: deadline August 15

The next deadline for the OBF travel fellowship is coming up soon on August 15, 2017. If you are attending any event that develops / promotes open source software or open science, and you are willing to write a blog post about the event, we welcome your application. See the travel fellowship page for more details and link to the application form.

Posted in Community, OBF, Travel Fellowship | Tagged | Leave a comment

Biopython 1.70 released

Dear Biopythoneers,

Source distributions of Biopython 1.70 are now available from the downloads page on the official Biopython website, and the release is also on the Python Package Index (PyPI). Windows installers and/or wheels should be available later. (Update: Compiled wheel packages now available for Linux, Mac OS X and Windows).

This release of Biopython supports Python 2.7, 3.4, 3.5 and 3.6 (we have now dropped support for Python 3.3). It has also been tested on PyPy v5.7, PyPy3.5 v5.8 beta, and Jython 2.7 (although we are deprecating support for Jython).

New Logo:

Biopython now has a new logo, contributed by Patrick Kunzmann. Drawing on our original logo (with two yellow snakes) and the current Python logo, this shows a yellow and blue snake forming a double helix.

[Biopython Logo]

Setup changes:

We now explicitly recommend installation using pip, rather than the classic “python setup.py install” approach. In a related change, we now depend on the Python package setuptools (rather than the older package distutils in the Python standard library) and have made the dependency on NumPy explicit and automatic (except on Jython).

License changes:

As of Biopython 1.69, we have started to dual-license Biopython under both our original liberal “Biopython License Agreement”, and the very similar but more commonly used “3-Clause BSD License”. A growing number of the Python files are explicitly available under either license, but most of the code remains under the “Biopython License Agreement” only. See the LICENSE file for more details.

Code changes:

Bio.AlignIO now supports Mauve’s eXtended Multi-FastA (XMFA) file format under the format name “mauve” (contributed by Eric Rasche).

Bio.ExPASy was updated to fix fetching PROSITE and PRODOC records, and return text-mode handles for use under Python 3.

Two new arguments for reading and writing blast-xml files have been added to the Bio.SearchIO functions (read/parse and write, respectively). They are use_raw_hit_ids and use_raw_query_ids. Check out the relevant SearchIO.BlastIO documentation for a complete description of what these arguments do.

Bio.motifs was updated to support changes in MEME v4.11.4 output.

The Bio.Seq sequence objects now have a .count_overlap() method to supplement the Python string like non-overlap based .count() method.

The Bio.SeqFeature location objects can now be compared for equality.

In Bio.Phylo.TreeConstruction, the DistanceMatrix class (previously _DistanceMatrix) has a new method .format_phylip() to write Phylip-compatible distance matrix files (contributed by Jordan Willis).

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, PEP257 and best practice standard coding style.


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

  • Aaron Kitzmiller (first contribution)
  • Adil Iqbal (first contribution)
  • Allis Tauri
  • Andrew Guy
  • Ariel Aptekmann (first contribution)
  • Ben Fulton
  • Bertrand Caron (first contribution)
  • Chris Rands
  • Connor T. Skennerton
  • Eric Rasche
  • Eric Talevich
  • Francesco Gastaldello
  • François Coste (first contribution)
  • Frederic Sapet (first contribution)
  • Jimmy O’Donnell (first contribution)
  • Jared Andrews (first contribution)
  • John Kern (first contribution)
  • Jordan Willis (first contribution)
  • João Rodrigues
  • Kai Blin
  • Markus Piotrowski
  • Mateusz Korycinski (first contribution)
  • Maximilian Greil
  • Michiel de Hoon
  • morrme (first contribution)
  • Noam Kremen (first contribution)
  • Patrick Kunzmann
  • Peter Cock
  • Rasmus Fonseca (first contribution)
  • Rodrigo Dorantes-Gilardi (first contribution)
  • Sacha Laurent (first contribution)
  • Sourav Singh
  • Ted Cybulski (first contribution)
  • Tiago Antao
  • Wibowo ‘Bow’ Arindrarto
  • Zheng Ruan

Thank you all.

P.S. You can follow @Biopython on Twitter



$ md5sum biopython-1.70.*
feff7a3e2777e43f9b13039b344e06ff  biopython-1.70.tar.gz
6307ab27c257fe69b9dae4bfc3052f49  biopython-1.70.zip
$ shasum -a 256 biopython-1.70.*
4a7c5298f03d1a45523f32bae1fffcff323ea9dce007fb1241af092f5ab2e45b  biopython-1.70.tar.gz
34312ce899f6c3fc9dea77ca997f9a8c228043d05284a0653577594aeb119d4f  biopython-1.70.zip


Posted in Biopython, Code, Community, Development, OBF, OBF Projects | Tagged , , , , , , , , | Leave a comment

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.

Posted in BOSC/ISMB, Community, OBF, Travel Fellowship | Tagged , , , , | Comments Off on Travel award recipients for April 2017

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 bosc@open-bio.org.

Posted in Blogroll, BOSC/ISMB, Community | Tagged , , , | Comments Off on BOSC 2017 keynote speakers

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

Posted in Blogroll, Code, Community, Development, Google Summer of Code, Travel Fellowship | Tagged , , , , | Comments Off on OBF Travel Fellowship – CWL week in London

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

Posted in Board, Community, OBF | Tagged , , , | 4 Comments

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!


Posted in BioPerl | Tagged , , | 17 Comments

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