Obf-Projects

Dear Biopythoneers, Biopython 1.74 has been released and is available from our website and PyPI. This release of Biopython supports Python 2.7, 3.4, 3.5, 3.6 and 3.7. However, it will be the last release to support Python 3.4 which is now at end-of-life. It has also been tested on PyPy2.7 v6.0.0 and PyPy3.5 v6.0.0. (Please note we will be dropping support for Python 2.7 in early 2020.) Over half our code is now explicitly available under either our original “Biopython License Agreement”, or the very similar but more commonly used “3-Clause BSD License”. [Read More]

Dear Biopythoneers, Biopython 1.73 has been released and is available from our website and PyPI. This release of Biopython supports Python 2.7, 3.4, 3.5 and 3.6. It has also been tested on PyPy2.7 v6.0.0 and PyPy3.5 v6.0.0. As in recent releases, more of our code is now explicitly available under either our original " Biopython License Agreement", or the very similar but more commonly used “3-Clause BSD License”. See the LICENSE. [Read More]

Dear Biopythoneers, I’m writing this in Portland at the GCC BOSC 2018 conference, where I will present the Biopython Project Update 2018 talk tomorrow. Yesterday during my airport layover in Iceland, I published the Biopython 1.72 release to our website and PyPI: https://biopython.org/wiki/Download https://pypi.python.org/pypi/biopython/1.72 This release of Biopython supports Python 2.7, 3.4, 3.5 and 3.6. It has also been tested on PyPy2.7 v6.0.0 and PyPy3.5 v6.0.0. Internal changes to Bio.SeqIO have sped up the SeqRecord . [Read More]

BioJava 5.0.0 was released on the 23rd of March 2018. This represents a major milestone that brings more consolidation and reorganisation of modules. This is the first release to be based on Java 8, bring in your lambdas and stream API calls! The release represents work done in the last 2 years, alpha releases were available for quite some time and now this makes all the changes officially public. Some major refactoring occurred in the biojava-structure module. [Read More]

Dear Biopythoneers, Source distributions of Biopython 1.71 are now available from the downloads page on the official Biopython website, and the release is also on the Python Package Index (PyPI) including pre-compiled Wheel Packages 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 PyPy2.7 v5.10.0 and PyPy3.5 v5. [Read More]

The Open Bioinformatics Foundation has been accepted as a mentoring organisation for the 2018 instance of the Google Summer of Code. OBF is acting as an umbrella for ten bioinformatics Open Source projects, making it possible to offer a very diverse set of student projects. Are you a student and interested in applying for any of the projects? The student application period is open from March 12th through 27th from the official GSoC website. [Read More]

The OBF’s self-hosted mailman server is still struggling right now, so we are looking at migrating the active mailing lists to paid hosting, and as part of this consolidating down to ideally about a dozen mailing lists. Currently we have a lot of mailing lists, but many are dormant or redundant. [Read More]

TL;DR: The OBF isn’t doing enough in public policy and advocacy around Open Science, and we are looking to recruit a new board member who is interested in this role. Is that you? If yes, then contact us. At our October meeting, the OBF board took some time to think broadly about the OBF, current and future. We tried to answer the questions: What do we say we do? What do we actually do? [Read More]

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: [Read More]

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. [Read More]