[Open-bio-l] OBF Newsletter September/October

[Bastian Greshake]

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OBF Newsletter October 2023
<https://github.com/OBF/newsletter/blob/master/newsletters/2023-09.md#obf-newsletter-october-2023>

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:
OBF News
<https://github.com/OBF/newsletter/blob/master/newsletters/2023-09.md#obf-news>Upcoming
public board meeting
<https://github.com/OBF/newsletter/blob/master/newsletters/2023-09.md#upcoming-public-board-meeting>

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
<https://www.open-bio.org/blog/> and in social media, as well as email to
OBF members.
BOSC news
<https://github.com/OBF/newsletter/blob/master/newsletters/2023-09.md#bosc-news>

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
<https://www.open-bio.org/2023/09/29/bosc-collaborationfest-2023-report/>,
and enjoyable breaks for lunches, thanks to funding from the *Complex
Systems Institute <https://www.ixxi.fr/?set_language=en>*.

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
<https://www.open-bio.org/2023/08/14/bosc-2023-report/>.

For those who like to plan ahead, BOSC 2024 will take place between July
12-16, 2024, as part of ISMB 2024 <https://www.iscb.org/ismb2024> in
Montréal, Québec, Canada.
OBF Event Fellowships
<https://github.com/OBF/newsletter/blob/master/newsletters/2023-09.md#obf-event-fellowships>

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
<https://docs.google.com/forms/d/e/1FAIpQLScMayX_XwTLxc8MiYgQOHIILJNjxF0gL75TUsbaO17h5UuUeA/viewform>
.

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
<https://www.open-bio.org/event-awards/#fellowships-applications>, and the
experiences of past awardees
<https://www.open-bio.org/category/travel-fellowship/event-fellowship/>.
Google Summer of Code
<https://github.com/OBF/newsletter/blob/master/newsletters/2023-09.md#google-summer-of-code>

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 at open-bio.org.
ISCBacademy recording
<https://github.com/OBF/newsletter/blob/master/newsletters/2023-09.md#iscbacademy-recording>

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 <https://www.youtube.com/watch?v=M2vAotWKd_Q&feature=youtu.be>.

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.
Community updates
<https://github.com/OBF/newsletter/blob/master/newsletters/2023-09.md#community-updates>Save
the date: CWL Conference 2024
<https://github.com/OBF/newsletter/blob/master/newsletters/2023-09.md#save-the-date-cwl-conference-2024>

The 2024 Common Workflow Language (CWL) Conference will be the week of May
13th, 2024 in the Netherlands. More details to follow.
iCn3D received updates at CoFest
<https://github.com/OBF/newsletter/blob/master/newsletters/2023-09.md#icn3d-received-updates-at-cofest>

During CoFest 2023, the iCn3D viewer
<https://www.ncbi.nlm.nih.gov/Structure/icn3d/> 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
<https://github.com/ncbi/icn3d>.
Your content needed for the next issue!
<https://github.com/OBF/newsletter/blob/master/newsletters/2023-09.md#your-content-needed-for-the-next-issue>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
<https://github.com/OBF/newsletter/issues/37>, or contact Bastian Greshake
Tzovaras (Mastodon: @gedankenstuecke at scholar.social
<https://scholar.social/@gedankenstuecke>, Email: bgreshake at 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.
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