BF Francis Ouellette
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bffo.bsky.social
BF Francis Ouellette
@bffo.bsky.social
3K followers 4.6K following 340 posts
Bioinformatics 🧬🖥️🧪
#PLOS Comp Biol Education Sect. Editor;
#DATABASE OUP Associate Editor;
#OpenScience #OpenAccess #OpenData;
friend of @jxtxfoundation.bsky.social,
@abinstitute.bsky.social
- I am 🇨🇦
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bffo.bsky.social
BF Francis Ouellette @bffo.bsky.social · Nov 29
Be Open so the world can see how great you are!

#OpenScience
#OpenAccess
#OpenData
#OpenSource
#OpenEducationalResources
bffo.bsky.social
From the @narjournal.bsky.social #NARDatabaseIssue | ProteomeXchange consortium in 2026: making proteomics data #FAIR | #Bioinformatics #Proteomics #OpenScience 🧪🔓
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academic.oup.com/nar/article/...
The ProteomeXchange consortium in 2026: making proteomics data FAIR
Abstract. The ProteomeXchange consortium of proteomics resources (http://www.proteomexchange.org) was established to standardize open data practices in the
academic.oup.com
November 10, 2025 at 4:21 PM
bffo.bsky.social
From @ngehlenborg.bsky.social & colleagues in @plos.org #Computational #Biology | Ten simple rules for making biomedical data resources accessible | I like Rule 10:Focus on progress over perfection | #Education #Bioinformatics #PLOSCBTSR #OpenScience 🧬 🖥️ 🧪 🔓
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journals.plos.org/ploscompbiol...
Ten simple rules for making biomedical data resources accessible
journals.plos.org
November 7, 2025 at 6:06 PM
Reposted by BF Francis Ouellette
scedmunds.bsky.social
Thank you Francis for all you've done for the journal. We put in a lot of effort to build up an excellent and very experienced Ed Board, and seeing so many of them resigning in this manner is sad but shows they've taken their responsibilities seriously.
November 7, 2025 at 12:38 PM
bffo.bsky.social
I was one of the Editorial Board Members at @gigascience.bsky.social who resigned from the Editorial Board.
🧪 🔓
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retractionwatch.com/2025/11/03/d...
Dozens of board members resign from big-data journal after mass staff firings
More than three-fifths of the editorial board of a biomedical sciences journal resigned after the publication’s operations moved from Hong Kong to Shenzhen, China, and the editors and software team…
retractionwatch.com
November 4, 2025 at 3:46 PM
Reposted by BF Francis Ouellette
atanas-g-atanasov.bsky.social
🤝 I’m forming a focus group to synergize and supercharge evidence‑based science communication on social media. Want to join? Drop a comment below or DM me. #SciComm
November 1, 2025 at 11:50 AM
bffo.bsky.social
From @plos.org #Computational #Biology | Ten rules for a structural bioinformatic analysis | i like Recommendation #10: Visualize everything! | #Bioinformatics #Education #Recommendations #NotSimpleRules 🧬 🖥️ 🧪 🔓 CC/ @ppalagi.bsky.social
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journals.plos.org/ploscompbiol...
Ten rules for a structural bioinformatic analysis
Author summary Here, we provide a roadmap for users to leverage the Protein Data Bank’s vast collection of protein structural models into reliable and valuable insights. It lays out 10 clear rules tha...
journals.plos.org
November 1, 2025 at 12:44 PM
Reposted by BF Francis Ouellette
matthewcobb.bsky.social
My article in tomorrow's @theobserveruk.bsky.social now online. But go and buy a copy!
Francis Crick: The science genius with poetry in his DNA
He is celebrated for co‑discovering the double helix, but it was Crick’s poetic appreciation of the world that was key to how his mind worked
observer.co.uk
November 1, 2025 at 11:37 AM
bffo.bsky.social
From @mdpiopenaccess.bsky.social #Viruses | vvv2_align_[SE|PE|display]: Galaxy-Based Workflows & Tool Designed 2 Perform, Summarize & Visualize Variant Calling & Annotation in #Viral #Genome Assemblies | #UseGalaxy #Bioinformatics #OpenScience #NGS 🧬 🖥️ 🧪 🔓 🇫🇷
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www.mdpi.com/1999-4915/17...
www.mdpi.com
October 31, 2025 at 5:02 PM
bffo.bsky.social
From @plos.org #Computational #Biology | Nine quick tips for trustworthy machine learning in the biomedical sciences | #Bioinformatics #Education #ML #AI #PLOSCBQT 🧬 🖥️ 🧪 🔓 CC/ @ppalagi.bsky.social
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journals.plos.org/ploscompbiol...
Nine quick tips for trustworthy machine learning in the biomedical sciences
As machine learning (ML) becomes increasingly central to biomedical research, the need for trustworthy models is more pressing than ever. In this paper, we present nine concise and actionable tips to ...
journals.plos.org
October 31, 2025 at 1:32 PM
bffo.bsky.social
News you can use at your next dinner party!
The potato evolved from the tomato 9 million years ago
#RealScience #NotFakeNews #OpenScience 🧬 🖥️ 🧪 🔓
From @cellpress.bsky.social
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www.cell.com/news-do/pr-p...
The potato evolved from the tomato 9 million years ago
Recent Cell research covered by The Guardian, The New York Times, The Atlantic, and more.
www.cell.com
October 30, 2025 at 7:05 PM
bffo.bsky.social
@davidbujold.bsky.social speaking at #MonBUG tonight, full house! on Pan Canadian Genome Library
October 29, 2025 at 9:43 PM
bffo.bsky.social
From @drtamermansour.bsky.social & colleagues in @plos.org #Computational #Biology | Ten simple rules for optimal and careful use of generative AI in #science | #Education #Bioinformatics #GenAI #AI #PLOSCBTSR #OpenScience 🧬 🖥️ 🧪 🔓
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journals.plos.org/ploscompbiol...
Ten simple rules for optimal and careful use of generative AI in science
journals.plos.org
October 29, 2025 at 3:24 PM
bffo.bsky.social
The @nytimes.com "The Daily" podcast was excellent today |
How Trump Upended 60 Years of Civil Rights | #CivilRights
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overcast.fm/+AAoIe_kCGFQ
How Trump Upended 60 Years of Civil Rights — The Daily
During his second term, President Trump has upended 60 years of civil rights, largely under the guise of attacking diversity, equity and inclusion. Nikole Hannah-Jones, who covers racial injustice and...
overcast.fm
October 21, 2025 at 4:04 PM
bffo.bsky.social
From Lavrichenko and colleagues in @bmc.springernature.com #Genome #Medicine | Recommendations for #bioinformatics in clinical practice | #Education 🧬 🖥️ 🧪 🔓 🇳🇱 🇩🇰🇳🇴 🇫🇮  🇸🇪 
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genomemedicine.biomedcentral.com/articles/10....
Recommendations for bioinformatics in clinical practice - Genome Medicine
Background Next-generation sequencing (NGS) is well established in clinical diagnostics, and whole-genome sequencing (WGS) is increasingly becoming the method of choice, as a result of lower prices an...
genomemedicine.biomedcentral.com
October 18, 2025 at 10:58 PM
bffo.bsky.social
I do too, and you should too, if you can.

The Wikimedia Foundation is a non-profit organisation that supports and operates Wikipedia.

Here is more info on how to "give":

donate.wikimedia.org/wiki/Ways_to...:
October 17, 2025 at 2:24 PM
bffo.bsky.social
From #OUP 's @bioinfoadv.bsky.social journal | Competencies for #bioinformatics core facility scientists: extension of the ISCB competency framework for bioinformatics | #OpenScience #Education CC/ @iscb.bsky.social 🧬 🖥️ 🧪 🔓
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academic.oup.com/bioinformati...
Competencies for bioinformatics core facility scientists: extension of the ISCB competency framework for bioinformatics
AbstractMotivation. The competency framework of the International Society of Computational Biology (ISCB) provides a benchmark for capturing the knowledge,
academic.oup.com
October 16, 2025 at 4:50 PM
bffo.bsky.social
From @gonzaparra.bsky.social et al., in @plos.org #Computational #Biology | Impact of the #COVID-19 pandemic on computational biology early career researchers: A global retrospective study | #Bioinformatics #Education #OpenScience CC/ @iscb.bsky.social 🧬 🖥️ 🧪🔓
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journals.plos.org/ploscompbiol...
Impact of the COVID-19 pandemic on computational biology early career researchers: A global retrospective study
The COVID-19 pandemic led to devastating physical, psychological, and financial impacts on millions of people across the world. Amidst a rapidly evolving research landscape, the global scientific comm...
journals.plos.org
October 16, 2025 at 4:43 PM
bffo.bsky.social
From @plos.org #Computational #Biology | Ten quick tips for developing a reproducible #Shiny application | #Bioinformatics #Education #PLOSCBQT #OpenScience #OpenSource 🧬 🖥️ 🧪🔓
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journals.plos.org/ploscompbiol...
Ten quick tips for developing a reproducible Shiny application
journals.plos.org
October 14, 2025 at 12:12 PM
Reposted by BF Francis Ouellette
scedmunds.bsky.social
Thank you OBF (and especially Taz) for this lovely post about the GigaScience team. I've been going to your #BOSC meetings since 2011 and will miss catching up with you all each summer, but hopefully it's not goodbye!
openbio.bsky.social Open Bioinformatics Foundation @openbio.bsky.social · Sep 30
An open letter about the recent cuts at GigaScience: www.open-bio.org/2025/09/30/2...
(open for signatures until the end of October)

#OpenScience #OpenData #GigaScience
Scott Edmunds cuts the cake at the 2025 GigaScience birthday party at ISMB/ECCB 2025
October 1, 2025 at 8:48 AM
bffo.bsky.social
From #OUP 's #DATABASE journal | Navigating #OpenSource waters: the pharmaceutical #industry's role in #bioontology development | #Bioinformatics #Genomics #Ontology #OpenScience 🧬 🖥️ 🧪 🔓 🇩🇰
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academic.oup.com/database/art...
Navigating open-source waters: the pharmaceutical industry’s role in bioontology development
Abstract. Bioontologies are core to many data management strategies, artificial intelligence and machine learning initiatives, and search functionality wit
academic.oup.com
October 1, 2025 at 6:26 PM
Reposted by BF Francis Ouellette
openbio.bsky.social
An open letter about the recent cuts at GigaScience: www.open-bio.org/2025/09/30/2...
(open for signatures until the end of October)

#OpenScience #OpenData #GigaScience
Scott Edmunds cuts the cake at the 2025 GigaScience birthday party at ISMB/ECCB 2025
September 30, 2025 at 9:02 PM
Reposted by BF Francis Ouellette
maniagnosis.bsky.social
These are all valuable suggestions for handling the (sudden) end of a project.

Keep in mind that code which is not actively being used and maintained is dead and will quickly become useless.

Also few projects will be adopted by an active open source community.
September 29, 2025 at 8:43 PM
bffo.bsky.social
From @richlitt.bsky.social and colleagues in @arxiv-cs-cl.bsky.social | 10 quick tips for making your software outlive your job | 🧪 🔓 #ProfessionalDevelopment #Education #OpenSource #OpenScience
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arxiv.org/abs/2505.06484
10 quick tips for making your software outlive your job
Loss of key personnel has always been a risk for research software projects. Key members of the team may have to step away due to illness or burnout, to care for a family member, from a loss of financ...
arxiv.org
September 29, 2025 at 8:16 PM
Reposted by BF Francis Ouellette
genetics-gsa.bsky.social
📢 NEW GENOME ALERT

In #G3journal, Frandsen et al. present a chromosome-scale assembly of the tetraploid epazote, a perennial plant growing in tropical climates in the Americas with regional culinary and medicinal importance. buff.ly/Vbp0rde
September 26, 2025 at 8:01 PM
Reposted by BF Francis Ouellette
bioinfoadv.bsky.social
🧰 Now published in Bioinformatics Advances: "Atlantool: A command line tool to retrieve DNA and RNA sequencing reads from BAM files by the read identifier"   

Read the full paper here: https://doi.org/10.1093/bioadv/vbaf226 

Authors include: @nibor.org, @egiannoulatou.bsky.social
September 26, 2025 at 9:02 AM