Development

This is a guest blog post from Lindsay Rutter, who was supported by the ongoing Open Bioinformatics Foundation travel fellowship program to attend a National Center for Biotechnology Information (NCBI) hackathon and the Plant and Animal Genome Conference (PAG). 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 on 15 April 2019. If you are hoping to attend an open source / open science bioinformatics even and travel costs are a barrier, we encourage you to apply for one of our $1000 travel fellowships. [Read More]

We have recently applied to Google for the OBF to be part of the Google Summer of Code 2019 programme, again with Kai Blin and Michael Crusoe as joint administrators. Last year, OBF GSoC 2018, was another good year with five students successfully completing their projects: Synchon Mandal (mentor Moritz Beber) “Adding methods to cobrapy for improved constraint-based metabolic modelling.” ( first blog bost; final report) Sophia Mersmann (mentors Oliver Alka, Julianus Pfeuffer, and Timo Sachsenberg) “Improve Posterior Error Probability Estimation For Peptide Search Engine Results” (blog posts; final report) Edgar Garriga Nogales (mentors Paolo Di Tommaso, Michael R. [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]

The Open Bioinformatics Foundation is again participating in the Google Summer of Code program this year. Last Monday the selected students were announced. Congratulations to all of you, and a heartfelt welcome. I also want to use this opportunity to thank all students who applied. Resources were limited, we did not get all the slots that we asked for, and so we had to make some tough choices. We wish you all the best for your future endeavours, and hope to be able to work with you in future. [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]

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]