Posts

Biopython 1.76 has been released and is available from our website and PyPI. Coming relatively soon after our last release, the timing is linked to the official end of life for Python 2, and a focus hereafter on Python 3. We intend this to be our final release supporting Python 2.7 and 3.5. Focusing on Python 3.6 or later will let us take advantage of new functionality and syntax, and simplify our code base and testing. [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. Arunav Konwar’s participation at Global Community Biosummit (GCBS), 2019 was supported by this fellowship. Find more information here. I recently had the opportunity to attend the Global Community Biosummit (GCBS), which took place between October 11-13 at the Massachusetts Institute of Technology (MIT) in Cambridge, MA, USA. [Read More]

Among the core values shared across the OBF community are inclusiveness and welcoming newcomers to contribute, without discrimination. Every year at BOSC, when we ask who is at BOSC for the first time, about half of the audience’s hands go up. To signify the importance of this, both to existing and prospective community members, BOSC successfully advocated several years ago for ISMB to adopt a Code of Conduct by ISMB (which applies to BOSC when it is held as part of ISMB). [Read More]

The call for OBF travel fellowship to select the next round of awardees is officially open! Please submit your application by filling out this form. Deadline for this round is 1 December 2019. This fellowship aims to support our community members in attending events that promote open source software development and/or open science in the biological research fields. As the organiser of Bioinformatics Open Source Conference (BOSC) since 2000, OBF understands the role of such conferences and wants to support people who can benefit from showcasing their work, learn from each other and promote open science at BOSC or similar events. [Read More]

The OBF Travel Fellowship program, which was started in 2016, will be making some changes to the schedule. Until now, there have been three application rounds per year, with deadlines April 15, August 15 and December 15. For the next round, we are moving our December deadline two weeks earlier, to December 1, 2019. Starting in 2020, we will move to two application deadlines per year, on March 1 and September 1. [Read More]

This post is co-authored by Bérénice Batut, Malvika Sharan, Emmy Tsang, and Yo Yehudi. In 2016, Mozilla launched a program to help grow the skills of people interested in working openly and empower a generation of open-inspired leaders. The program has been through several stages of evolution, from early Working Open Workshops, and eventually to regular twice-yearly cohorts, mentoring project leads from all around the globe. Projects spanned a broad number of domains, but included a large number of research/science and tech-oriented projects, including PREreview, an initiative to get people involved in scientific preprint journal clubs; Outbreak science, a nonprofit using technology to support disease outbreaks; MBac, a computer vision tool for bacterial motility assays; and DuraCloud, an open-source digital preservation storage service. [Read More]

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]

This is a guest blog post from Aziz Khan, who was supported by the ongoing Open Bioinformatics Foundation travel fellowship program to attend the ISMB/ECCB and BOSC 2019 meeting in Basel, July 2019. The OBF’s Travel Fellowship program aimed at increasing diverse participation at events promoting open source bioinformatics software development and open science in the biological research community. Find more information here. Computational tools and software are now becoming the core of scientific discovery, and making it open source and sharing it freely with the community helps to take scientific discoveries to the next level. [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]