OBF News | Open Source Bioinformatics news
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The Open Bioinformatics Foundation or OBF is a non profit, volunteer run organization focused on supporting open source programming in bioinformatics.
OBF News | Open Source Bioinformatics news
1M ago
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
OBF News | Open Source Bioinformatics news
1M ago
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
OBF News | Open Source Bioinformatics news
1M ago
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
OBF News | Open Source Bioinformatics news
2M ago
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
OBF News | Open Source Bioinformatics news
2M ago
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
OBF News | Open Source Bioinformatics news
2M ago
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
OBF News | Open Source Bioinformatics news
3M ago
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
OBF News | Open Source Bioinformatics news
3M ago
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
OBF News | Open Source Bioinformatics news
5M ago
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 ..read more
OBF News | Open Source Bioinformatics news
5M ago
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
BOSC and Bio-Ontologies are pleased to co-host an ISCBacademy talk on Octob ..read more