[Open-bio-l] OBF Newsletter February/March 2023

Thu Mar 16 14:41:44 EDT 2023

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 <https://github.com/OBF/newsletter/blob/master/newsletters/2023-02.md#obf-newsletter-february-march-2023>OBF
Newsletter February-March 2023

BOSC 2023 <https://www.open-bio.org/events/bosc-2023/> will be hybrid,
online + in person in Lyon (France), July 24-25, as a COSI of ISMB.
It's application season again for OBF Event Fellowships. The OBF Board
met in October and decided some things. People in the community are
doing cool things. Read on for full details.

Note these upcoming dates & deadlines:

   - March 30: Early poster acceptance
<https://www.open-bio.org/2023/03/09/bosc-early-poster-acceptance/>
submission deadline for BOSC 2023
   - April 1: Application deadline for OBF Event Fellowships
<https://www.open-bio.org/event-awards/>
   - April 20: Regular abstract submission deadline for BOSC 2023
<https://www.open-bio.org/events/bosc-2022/submit/>

In longer form:
 <https://github.com/OBF/newsletter/blob/master/newsletters/2023-02.md#obf-news>OBF
News <https://github.com/OBF/newsletter/blob/master/newsletters/2023-02.md#obf-event-fellowships-formerly-travel-fellowships>OBF
Event Fellowships (formerly "Travel Fellowships")

Previous round: October 1, 2022
Next round: April 1, 2023

Our call for applications is open again
<https://www.open-bio.org/2023/02/20/obf-event-fellowship-2023-1-call/>,
with a *deadline on April 1st*. We invite applications for financial
support to attend or host events taking place between May 2023 and
April 2024.

As described on the website <https://www.open-bio.org/event-awards/>,
the fellowship 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
childcare for the duration of the event, small hardware (e.g. a
headset or webcam), or high-speed internet.

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/>.
 <https://github.com/OBF/newsletter/blob/master/newsletters/2023-02.md#bosc-news>BOSC
News

Our annual get-together, the Bioinformatics Open Source Conference
(BOSC) 2023 <https://www.open-bio.org/events/bosc-2023/>, will take
place July 24-25 as a COSI of ISMB/ECCB 2023. It will once again be a
hybrid event; in-person in Lyon (France), and online. We hope that the
online component will offer the opportunity for many of you to
participate that otherwise could not.

Note that *the regular abstract submission deadline is April 20* and
you can request assistance for registration fees when submitting an
abstract.

*New this year*, BOSC is offering an "Early Poster Acceptance" option;
so submit your abstract
<https://www.open-bio.org/events/bosc-2023/submit/> by March 31 to
hear by April 6 whether it's been accepted for (at least) a poster!

For more detailed information, see the BOSC 2023 webpage
<https://www.open-bio.org/events/bosc-2023/>.
 <https://github.com/OBF/newsletter/blob/master/newsletters/2023-02.md#bosc-keynote-speaker-nomination-status-update>BOSC
keynote speaker nomination status update

We'd like to highlight that this year we are following a formal
process for selecting a keynote speaker. After having put out a public
call for nominations
<https://www.open-bio.org/2023/02/02/nominate-keynote-speaker-for-bosc-2023/>,
we held an open commenting period
<https://www.open-bio.org/2023/02/10/bosc-2023-keynote-comment-period/>
on the shorlist of nominated speakers. The BOSC organizing committee
has drawn on this list to extend invitations to potential keynote
speakers. We'd love to hear your feedback about this process at any
time.
 <https://github.com/OBF/newsletter/blob/master/newsletters/2023-02.md#bosc-sponsorships>BOSC
sponsorships

Interested in becoming a sponsor of BOSC 2023? Visit our sponsors page
<https://www.open-bio.org/events/bosc-2022/sponsors/> to see our 2022
sponsors and information about benefits of becoming a sponsor.
 <https://github.com/OBF/newsletter/blob/master/newsletters/2023-02.md#fall-2022-obf-board-meeting>Fall
2022 OBF Board Meeting

The Board met publicly on October 21, 2022
<https://www.open-bio.org/2022/09/29/obf-public-board-meeting-2022-10-21/>,
with the following outcomes:

   - Iddo Friedberg was elected as a new At-large Member.
   - Nomi Harris was elected as Secretary, replacing Chris Fields in that role.
   - Proposed updates to the bylaws were deferred to the next public
Board meeting (date TBD).

The full meeting minutes are available in this pull request
<https://github.com/OBF/obf-docs/pull/106> (to be merged at the next
public Board meeting).
 <https://github.com/OBF/newsletter/blob/master/newsletters/2023-02.md#community-updates>Community
updates <https://github.com/OBF/newsletter/blob/master/newsletters/2023-02.md#online-webinar-on-patient-led-research-hosted-by-iscbacademy>Online
webinar on patient-led research hosted by ISCBacademy

On March 14, we held a webinar about "Re-Thinking the Patient’s Role
in a Learning Health System: Lessons from the Patient-Led Research
Collaborative" presented by Hannah Wei, co-founder and technologist at
the Patient-Led Research Collaborative, hosted by ISCBacademy
<https://www.iscb.org/iscbacademy>. See the webinar announcement
<https://www.open-bio.org/2023/02/09/iscbacademy-webinar-on-patient-led-research/>
for a full description. The webinar recording is available on YouTube
at https://youtu.be/M2vAotWKd_Q.

*If you're not familiar with ISCBacademy
<https://www.iscb.org/iscbacademy>, it's a series of free webinars
offered by the ISCB <https://www.iscb.org/>, which runs the annual
ISMB conference, through the ISCB Communities of Special Interest
(COSIs), which include BOSC/OBF.*
 <https://github.com/OBF/newsletter/blob/master/newsletters/2023-02.md#google-summer-of-code>Google
Summer of Code

Google Summer of Code <https://summerofcode.withgoogle.com/> is a
global, online program focused on bringing new contributors into open
source software development.

The OBF is not participating as a host organization this year, but our
friends at the Global Alliance for Genomics and Health (GA4GH) are, so
we encourage you to check out their call for applications
<https://summerofcode.withgoogle.com/programs/2023/organizations/global-alliance-for-genomics-and-health>.
 <https://github.com/OBF/newsletter/blob/master/newsletters/2023-02.md#reads2map-a-collection-of-workflows-to-build-linkage-maps-from-sequencing-data>Reads2Map:
A collection of workflows to build linkage maps from sequencing data

As part of the Tools for Polyploids <https://www.polyploids.org/>
project, the Reads2Map
<https://github.com/Cristianetaniguti/Reads2Map> package integrates
diverse computational tools for diploid and polyploid species genetic
data analysis. It uses the reproducible and scalable structure of WDL
<https://openwdl.org/> to run SNP and dosage calling software and
compare their performance using linkage maps as benchmarks. The main
workflows' results can be easily evaluated in a Shiny app
<https://github.com/Cristianetaniguti/Reads2MapApp>. The group already
released a preprint
<https://www.biorxiv.org/content/10.1101/2022.11.24.517847v2> with
results for diploid analysis. The repository is being expanded and it
has room for improvements and implementations of other software. The
group is open for feedback or contributions through the GitHub issues
<https://github.com/Cristianetaniguti/Reads2Map/issues> page or the
email chtaniguti at tamu.edu.
 <https://github.com/OBF/newsletter/blob/master/newsletters/2023-02.md#interesting-links>Interesting
links <https://github.com/OBF/newsletter/blob/master/newsletters/2023-02.md#follow-obf-and-bosc-on-mastodon>Follow
OBF and BOSC on Mastodon

For more up to the minute news and announcements about the OBF and
BOSC, join the genomic.social community on Mastodon and follow us at
@OpenBio <https://genomic.social/@OpenBio> and @BOSC
<https://genomic.social/@BOSC>. Mastodon is the leading
community-friendly alternative to Twitter. We hope to see you there!
 <https://github.com/OBF/newsletter/blob/master/newsletters/2023-02.md#your-content-needed-for-the-next-issue>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/29>, or contact
Geraldine Van der Auwera (Twitter: @VdaGeraldine
<https://twitter.com/VdaGeraldine>, Email:
geraldinevdauwera 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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