The call for applications for the OBF Event Fellowship 2024, round 1, is now open. The deadline for this round is 1 April 2024. Applications should be submitted via this Google Form. We have provided a Word template to help you draft the application locally before filling out the form – make a copy of this template. The OBF Event Fellowship program aims to increase diverse participation at events that promote open-source bioinformatics and/or open science. We invite applications from candidates seeking financial support to attend relevant scientific events from May 2024 to December 2024. These ..read more

Gemma Turon, PhD (CEO and co-founder at Ersilia Open Source Initiative) will present on March 5 BOSC and the OBF will host an ISCBacademy webinar on March 5, 2024, at 8am PST (16:00 UTC). Gemma Turon (see bio below) will speak about “Ersilia, open source AI/ML for (antimicrobial) drug discovery”. Abstract The Ersilia Open-Source Initiative is a non-profit organisation whose mission is to equip laboratories, clinics and universities in lower and middle income countries (LMICs) with artificial intelligence (AI) tools for infectious disease research. The goal of our mission is to strengthen the ..read more

We asked our community to nominate potential BOSC keynote speakers, and we were pleased with the great suggestions! In the next phase of our process, we’re giving you a chance to let us know if there is anything that makes any of the nominated individuals NOT appropriate as BOSC keynote speakers. Our invited speaker process and rubric gives examples of some possible reasons for exclusion. If you have concerns about any of the people on our list, please let us know (with as much specificity as you feel comfortable providing) via this anonymous form no later than Thursday 2024-01-25. And the no ..read more

We are seeking a diverse list of potential BOSC keynote speakers. We invite you, our community, to nominate people you think would be appropriate (and at least somewhat likely to accept the invitation – for example, it is extremely unlikely that we would get a ‘yes’ from a recent Nobel Laureate). Please submit your nominations here (as many as you like; you can fill out the form more than once to submit additional suggestions) by the end of the day on Wednesday 2024-01-17. Keynote talks are a highlight at BOSC. BOSC typically bookends keynotes at the beginning and end of the conference. These ..read more

Dear Biopythoneers, Our first release of 2024 is now out, sooner than planned as this is purely to revert the removal of the .strand, .ref, and .ref_db attributes of the SeqFeature which was done in Biopython 1.82 without a deprecation period. They are again aliases for .location.strand etc, but now trigger deprecation warnings. See our deprecation policy. We apologize for any inconvenience, and thank you to those reporting this. This release of Biopython supports Python 3.8, 3.9, 3.10, 3.11 and 3.12. It has also been tested on PyPy3.9 v7.3.13. Python 3.8 is approaching end of life, our suppor ..read more

Biopython 1.82 has been released and is available from our website and PyPI. Our second release of 2023 is now out, albeit way later than we’d all intended. This contains about 10 months worth of updates, so the NEWS file information is denser than usual: https://github.com/biopython/biopython/blob/biopython-182/NEWS.rst Also, there have been more deprecations and removals of deprecated code than typical – see the DEPRECATED file too: https://github.com/biopython/biopython/blob/biopython-182/DEPRECATED.rst Many thanks to the Biopython developers and community for making this rel ..read more

The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Raquel Manzano Garcia, a PhD researcher at the University of Cambridge, was awarded an OBF Event Fellowship to attend the Nextflow Summit 2023 . This October, I had the incredible opportunity to attend the Nextflow Summit 2023 in Barcelona, thanks to the support of a generous travel grant from the Open Bioinformatics Foundation (OBF) and my supervisor Prof. Car ..read more

All are invited to join us (via Zoom) at the OBF’s upcoming public Board meeting. Date, Time, and How to Join Date and time: 2023-12-19, 16:00 UTC (8am PT / 11am ET / 4pm UK) Agenda Approve October 2022 Public Board Meeting minutes Review and approve minor changes to bylaws Remove one instance of gendered language, replacing “her” with “their” Change title of “Secretary” of Board to “Vice President” (with duties unchanged) Elections to the Board Three Board members are up for re-election: Peter Cock (President), Heather Wiencko (Treasurer), and Hilmar Lapp (Member at Large) This will be a ..read more

The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Dr Yvonne Joko Walburga, a Post-doc at the University of Cambridge, was awarded an OBF Event Fellowship to attend the African Organisation for Research and Training in Cancer (AORTIC) Cancer Conference. I initially applied for the OBF Travel Fellowship to attend the African Organisation for Research and Training in Cancer (AORTIC) Genomics Conference, and was a ..read more

As of November 21, 2023, the Open Bioinformatics Foundation and BOSC will no longer post on Twitter/X. Although in the past it was a useful social medium, it is no longer compatible with our values, as expressed in the OBF Code of Conduct: We are committed to creating a friendly and respectful place for learning, sharing and contributing. All participants in our events and communications are expected to show respect and courtesy to others. Currently, we are not planning to delete our X/Twitter accounts (@OBF_NEWS and @OBF_BOSC); we will leave them as archives. Even before recent events promp ..read more