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TL;DR: In this newsletter we provide a summary of BOSC 2023 in Lyon; share news about the OBF event fellowship; and announce an opening for an OBF admin for the 2024 Google Summer of Code.
In longer form:
The OBF will hold its next public board meeting some time this fall (date TBD). When the date is determined, we will announce it on the OBF Blog and in social media, as well as email to OBF members.
The 24th annual Bioinformatics Open Source Conference (BOSC 2023) took place in July as part of ISMB/ECCB 2023 in Lyon, France, and online. As in prior years, BOSC was preceded by a CollaborationFest, a collaborative work event (including but not limited to hacking). This year CoFest was hosted by Jérémy Just at the nearby École Normale Supérieure de Lyon, which provided space and infrastructure for the 29 in-person participants as well as the numerous online participants. Those two days saw intense moments of collaboration and exchange around 10 projects submitted by the attendees, and enjoyable breaks for lunches, thanks to funding from the Complex Systems Institute.
In addition to 43 talks and nearly 50 posters, BOSC itself included two keynotes – by Sara El-Gebali, who spoke about "A New Odyssey: Pioneering the Future of Scientific Progress Through Open Collaboration – and by Joseph Yracheta – who spoke about "The Dissonance between Scientific Altruism & Capitalist Extraction: The Zero Trust and Federated Data Sovereignty Solution”. The conference closed out with a panel on Open & Ethical Data Sharing.
You can read the full report about the conference on the OBF blog.
For those who like to plan ahead, BOSC 2024 will take place between July 12-16, 2024, as part of ISMB 2024 in Montréal, Québec, Canada.
Next round: December 1, 2023 Last round: August 1, 2023
The current application period for the OBF Event Fellowship lasts until December 1, 2023. So there is still some time to get your application submitted.
These fellowships can be used to cover registration fees for relevant events related to open source bioinformatics or open science (in-person or virtual), and potentially additional expenses such as travel, lodging, childcare for the duration of the event, small hardware (e.g. a headset or webcam), or high-speed internet. You can read more about applying for an OBF Event Fellowship, and the experiences of past awardees.
We are looking for a motivated person who would like to volunteer as the organisation admin to enable the OBF to participate in the 2024 Google Summer of Code, as we have in previous summers. As an organisation we have been providing an umbrella project for various open source bioinformatics projects – including non-member projects – since 2010. In 2023 we sat out one round, as we did not find someone with the time to volunteer as GSoC admin.
If you are interested in filling that role, please get in touch with us via email at board@open-bio.org.
On March 14, 2023, the OBF hosted an ISCBacademy webinar in which Hannah Wei – co-founder of the Patient-Led Research Collaborative – gave a talk on "Re-Thinking the Patient’s Role in a Learning Health System: Lessons from the Patient-Led Research Collaborative". The recording of the talk is now on YouTube.
Our next ISCBacademy webinar on October 3 will be jointly sponsored with the Bio-Ontologies COSI. Sierra Moxon will speak about "LinkML: an open data modeling framework, grounded with ontologies". Free registration at https://www.iscb.org/iscbacademy.
The 2024 Common Workflow Language (CWL) Conference will be the week of May 13th, 2024 in the Netherlands. More details to follow.
During CoFest 2023, the iCn3D viewer was updated to include two new features: It can now show isoforms and exons as tracks and users can also predict structures from sequences using ESMFold directly in iCn3D. You can learn more about it on the project's GitHub page.
Tell us about the things that catch your attention in the open source bioinformatics world! If you have an exciting project update, request for feedback, or interesting link, feel free to share it with us on GitHub, or contact Bastian Greshake Tzovaras (Mastodon: @gedankenstuecke@scholar.social, Email: bgreshake@gmail.com) if you're not sure whether or not your content is suitable for our newsletter. We're looking for content that's primarily open source / science related.