Blogroll

This time of year we’d normally be having a public board meeting as part of our commitment to communication with our member projects and the wider OBF community. As per our bylaws we notify the community at least 10 days in advance, and we’d also handle election of new board members and leadership changes where appropriate. For a couple of reasons, we’re going to postpone that until early 2018.

Our mailing list server (which hosts many of our member project lists) has been overwhelmed in the past few days, leading to delayed or blocked communication not just to our members but for our member projects who rely on it. We’re looking into options for solving this problem, which might include migrating to a hosted solution.

Podcast.__init__ describes itself as “The Podcast About Python and the People Who Make It Great”, and the most recent episode is " Biopython with Peter Cock, Wibowo Arindrarto, and Tiago Antão (Episode 125)".

Listening to the finished podcast, interviewer Tobias Macey did a great job. There are things I would have liked to have said - but it turned out pretty well. I hope you’ll agree:

Its worth looking back over the podcast archives, here are a few that caught my eye:

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.

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.

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.

  [Read More]

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.

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.