Blogroll

Dear Biopythoneers, Biopython 1.75 has been released and is available from our website and PyPI. This release of Biopython supports Python 2.7, 3.5, 3.6, 3.7 and is expected to work on the soon to be released Python 3.8. It has also been tested on PyPy2.7.13 v7.1.1 and PyPy3.6.1 v7.1.1-beta0. Note we intend to drop Python 2.7 support in early 2020. The restriction enzyme list in Bio.Restriction has been updated to the August 2019 release of REBASE. [Read More]

A record number of people applied for the latest round of the OBF Travel Fellowship, which closed on August 15, 2019. Out of this great set of applicants, we offered travel awards to three who epitomize the goal of the awards: to promote diversity in the world of open source bioinformatics / open science. The awardees are Arunav Konwar, Fernanda Troyner and Nicolás Palopoli. Arunav has contributed to open source projects including Deep Learning Indaba (an African Machine Learning community), Wikimedia, and Metafluidics. [Read More]

The Open Bioinformatics Foundation (OBF) sponsors a Travel Fellowship program aimed at increasing diverse participation at events promoting open source bioinformatics software development and open science in the biological research community. Malvika’s participation at Bioinformatics Open Source Conference 2019 was supported by this fellowship granted to her in January 2019. Find more information here. The phrase ‘water cooler effect’ is derived from informal gatherings and connections made around water coolers (or vending machines these days! [Read More]

Thanks to OBF support with a travel grant, I was able to attend the first European CarpentryConnect event in Manchester CCMcr19 organized by The Software Sustainability Institute. Colourful Manchester days post Pride weekend The Carpentries is a global community with a mission to teach essential data and foundational computational skills to researchers for conducting efficient, open, and reproducible research. The community includes instructors, trainers, maintainers and many more helpers and supporters on a global scale. [Read More]

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]

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]

This is a guest blog post from Tendai Mutangadura, who was supported by the ongoing Open Bioinformatics Foundation travel fellowship program to attend the GCCBOSC 2018 meeting in Portland, June 2018. The OBF’s Travel Fellowship program continues to help open source bioinformatics software developers with funding to attend conferences or workshops. This was one of three awards from our April 2018 travel fellowships call. Our August call recently closed, the current call closes 15 December 2018, you might want to apply? [Read More]

BOSC 2019 will be part of ISMB 2019 Every year until 2018, BOSC was part of the annual ISMB conference as a community of special interest (COSI, formerly known as a SIG, Special Interest Group). As part of our continuing quest to broaden and deepen the BOSC community, we decided to perform an experiment this year by partnering with the Galaxy Community Conference rather than with ISMB. As we reported, the experiment was a success–participants were overwhelmingly positive about the experience, and the conference did attract a somewhat different mix of attendees than in past years. [Read More]