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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 support for it is now deprecated.

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 release possible, especially the following contributors:

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. Carlos Caldas. The eent wasn’t just a conference; it was a confluence of ideas, coding, and camaraderie, set against the vibrant backdrop of one of Spain’s most iconic cities.

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 accepted, but the timing was too tight. Happily, the board agreed to defer my funding to the next AORTIC Conference in November 2023 instead. So, I could make it for the AORTIC conference in Dakar, Senegal from November 2nd – 6th 2023 with support from the OBF Travel Fellowship and the African Cancer Registry Network.

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 an electronic ballot of the current board members

After the meeting, the meeting minutes will be made available in the obf-docs GitHub repository as a pull request.

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:

The call for applications for the OBF Event Fellowship 2023, round 3, is now open. The deadline for this round is 1 December 2023. 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 January 2024 to August 2024. These events include conferences, workshops, code fests, hackathons, training courses, collaborative sprints, informal meet-ups or other skill-building and networking events. For more details, please read our OBF Event Fellowship policy document.

CollaborationFest, CoFest for short, is a collaborative work event that has been held each of the past 13 years as a satellite event of BOSC. At these free events, held right before or after BOSC, participants  gather in small groups to exchange ideas and work together on projects including but not limited to hacking. Participants were encouraged to submit their project ideas in advance to facilitate collaboration.

CoFest 2023 took place during the two days just before BOSC, which was part of ISMB/ECCB 2023 in Lyon and online. It was the first in-person edition after several online-only CoFests, due to Covid pandemics. It was hosted by Jérémy Just at the nearby École Normale Supérieure de Lyon, which provided space and infrastructure, with funding from Complex Systems Institute for lunches and coffee breaks. Free virtual machines were made available by the French Institute for Bioinformatics and the Pôle scientifique de modélisation numérique.

Sierra Moxon to speak about “LinkML: an open data modeling framework, grounded with ontologies”

[If you missed the webinar, the video is here and the slides are here.]

ISCBacademy is a series of free webinars sponsored by the International Society for Computational Biology. They are open to all, including those who are not ISCB members. ISCB members can access the webinars via the ISCB Nucleus platform: https://iscb.junolive.co/. Non-members need to register for Nucleus: https://iscb.swoogo.com/ISCBnucleus-registration

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. Michell Salcan, an undergraduate at the Universidad Regional Amazonica Ikiami, was awarded an OBF Event Fellowship to atten d The 3rd Latin American Conference on Complex Networks in Cusco, Peru.

The week of August 21 to 25 has been one of the most beautiful and satisfying experiences of my personal life and the beginning of my professional life because I had the opportunity to attend and present my undergraduate thesis at the LANET 2023 event.