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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.

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.

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 http://mmtf.rcsb.org), in addition to the mmCIF and PDB file formats (contributed by Anthony Bradley). This requires an optional external dependency on the mmtf-python library.

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!Dimitra

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 circle)

• 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.

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This was long over-due, but Biopython 1.67 was released earlier today. The most recent delay was due to migrating our website from MediaWiki to GitHub Pages earlier this year, following an OBF server failure.

Source distributions and Windows installers for Biopython 1.67 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 support for Python 2.6 is considered to be deprecated. It has also been tested on PyPy 5.0, PyPy3 version 2.4, and Jython 2.7.

Every year, BOSC includes a panel discussion that offers attendees the chance to engage in conversation with the panelists and each other. BOSC is all about community, so this year’s panel topic– Growing and Sustaining Open Source Communities–is right at the heart of what we do. Since the first BOSC in 2000, we have focused on bringing together open source bioinformatics developers and users to form and expand collaborations and grow the communities that use and improve their tools and resources.

The first round of the Open Bioinformatics Foundation travel fellowship program has granted funds to three open source bioinformatics software developers to help them attend the Bioinformatics Open Source Conference (BOSC) 2016 in Orlando, Florida, this July. The travel fellowship program ( announced 1 May 2016) aims to increase diverse participation at events promoting open source bioinformatics software development and open science in the biological research community. Applications for the first round in 2016 were due on April 15, with two more due dates this year on August 15 and December 15.

The Open Bioinformatics Foundation is participating in the Google Summer of Code 2016 program, and last Friday the selected students were announced. Congratulations to all of you, and welcome. I also want to use this opportunity to thank all students who applied. Resources are limited and your proposals did not make it easy to select our finalists. We wish you all the best for your future endeavours, and hope to be able to work with you in future. The field of bioinformatics is a small one after all.

The Open Bioinformatics Foundation is pleased to announce a gift of USD 18,125 from the Phyloinformatics Summer of Code toward the OBF travel fellowship program. The program, announced earlier this year on March 1, aims to increase diverse participation at events promoting open source bioinformatics software development and open science in the biological research community. The program includes but is not limited to the annual Bioinformatics Open Source Conference (BOSC), OBF’s flagship event.