BF Francis Ouellette

Empowering biological knowledgebases: advances in human-in-the-loop AI-driven literature curation Abstract. Biological knowledgebases facilitate discovery across the life sciences by structuring experimental findings into human-readable and computable f

From #OUP s @bioinfoadv.bsky.social journal | Empowering biological knowledgebases: advances in human-in-the-loop AI-driven literature #curation | #Bioinformatics #AI #LLM #OpenScience #Biocuration | 🧬 🖥️ 🧪 🔓
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academic.oup.com/bioinformati...

Démodé (2013) www.nature.com/articles/nph.... This short story imagines a future where AI systems designed to read and write scientific papers begin evolving on their own. At first, they help, running massive meta-analyses and accelerating discovery. Then they stop writing for us. 1/🧵

Later, in my NCBI life, I came across a slide from my mentor Mark Boguski:

//

What is true for _E. coli_ is also true for the elephant.
-- Jacques Monod

What is true for _yeast _is also true for human.
-- David Botstein

\\

Back then, and still today, I was a big fan of Jacques Monod:
"Je cherche à comprendre"

I loved this book: "Le Hasard et la Nécessité"

A good reductionist starting guide!
en.wikipedia.org/wiki/Chance_...

Wet Bags of Atoms Teaching Sand to Think On emergence, and the lazy dismissal of AI as "just next token prediction" as a thought-terminating reductive cliche that we need to give up.

This #PairedEnds post from @stephenturner.us, "Wet Bags of Atoms Teaching Sand to Think," reminded me of my younger self as a 1st- or 2nd-year biology undergraduate, telling my mother: "Love is just a chemical reaction." She did not like that ...
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blog.stephenturner.us/p/wet-bags-o...

Webinar at EMBL-EBI: Automatic annotation systems in UniProt. 12 March 2026, 15:00-16:00 GMT

Webinar speakers (with headshots): David CJ Carpentier, Scientific Database Curator; Pedro Raposo, Senior Curator/Bioinformatician. EMBL-EBI

If you are interested in knowing how #UniProt uses automatic annotation tools to enrich its data, join our #webinar on 12 March: we will discuss the two main tools currently in use in the database, ARBA and UniRule.

Registration is free but essential: www.ebi.ac.uk/training/eve...

🖥️🧬

Discover the new SIB learning paths 🧬 Structured #Bioinformatics training from beginner to advanced levels, including machine learning and omics data analysis. Plan your next learning step and share within your network

New GA4GH product establishes guidance to address genetic discrimination The GA4GH Regulatory & Ethics Work Stream has published a newly approved product: The Position Statement on Genetic Discrimination (GD). This Position statement outlines recommendations to monitor...

From @ga4gh.org | New #GA4GH product establishes guidance to address genetic discrimination | #GD #GeneticDiscrimination #Education #Genomics #Ethics #Law 🧬 🖥️ 🧪
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www.ga4gh.org/news_item/ne...

📣 Quick reminder:
The Call for Contributions for useR! 2026 conference in Warsaw 🇵🇱 is open. We are waiting for your application 😊

Info & submission here:
👉 user2026.r-project.org/call/

#RStats #useR2026 #DataScience #Poland

Hex logo sticker designs for Software Carpentry, Data Carpentry, Library Carpentry, and HPC Carpentry, arranged in a row.

From 1 September, The Carpentries will have four official Lesson Programs: Data Carpentry, Library Carpentry, Software Carpentry, and HPC Carpentry! 🎉

Blague a propos d'un migrant couvert des dossiers Epstein pour être incognito.

HPC Carpentry Approved as The Carpentries' Fourth Lesson Program On 5 February 2026, our Board of Directors voted unanimously to approve the adoption of HPC Carpentry as the fourth official lesson program of The Carpentries, alongside the Data Carpentry, Library Ca...

From The Carpentries @carpentries.carpentries.org | HPC Carpentry Approved as The Carpentries' Fourth Lesson Program | #HPC #OpenScience #Education 🖥️ 🧪 🔓
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carpentries.org/blog/2026/02...

Merci pour ces touchants témoignages!

YouTube video by ICI Québec Vendredi VIP avec Rémi Quirion

Sur #ICIQuébec @radiocanada.bsky.social | Très bon interview avec le scientifique en chef du Québec: Rémi Quirion @scichefqc.bsky.social | Bien triste de le voir partir, mais aussi curieux de voir la prochaine chef! | 🧪 #OpenScience #inFrench ⬇️

www.youtube.com/watch?v=Cfsk...

Diverse database and machine learning model to narrow the generalization gap in RNA structure prediction Length matters—secondary structures of long, diverse RNAs in RNAndria and deep learning model eFold improve prediction accuracy.

From #AAAS 's #scienceadvances journal | Diverse #database and machine learning model to narrow the generalization gap in #RNA structure prediction | #Bioinformatics #ML #Genomics #OpenScience #StructurePrediction #RNAStructurePrediction | 🧬 🖥️ 🧪 🔓
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www.science.org/doi/10.1126/...

Ten Common Misconceptions About Galaxy (And Why They're Wrong!) We are thrilled to announce that 'Ten Common Misconceptions About Galaxy (And Why They Are Wrong!)' has just been published in PLOS Computational Biology! This paper is the result of passionate discus

Whether you are a longtime Galaxy user or new to the platform, this paper challenges assumptions and highlights Galaxy's versatility, scalability, and impact across disciplines.
Read more about the paper, the story behind, and why it matters in our blog post: galaxyproject.org/news/2026-02...

This paper started as an exchange here in late 2024 and evolved over the next year into a tidy set of recommendations for labs hoping to build more collaborative coding communities. 🎉

Would love to hear if any of these (really not so "simple") rules resonate with you, and what else you've tried.

Ten simple rules for building a collaborative coding culture

This was such a fun collaboration with @analog-ashley.bsky.social and team, including some of our own @sciencebanshee.bsky.social and @shen4brains.bsky.social And h/t to Alana McPherson for the infographic!

dx.plos.org/10.1371/jour...

Great lab to go learn #bioinformatics, in the great city of #Montréal! #summerJob #summerintern

Ten simple rules for building a collaborative coding culture

From @sciencebanshee.bsky.social @shen4brains.bsky.social @analog-ashley.bsky.social & colleagues in @plos.org #Computational #Biology | Ten simple rules for building a collaborative #coding #culture | #Education #Bioinformatics #PLOSCBTSR #OpenScience 🧬 🖥️ 🧪🔓
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journals.plos.org/ploscompbiol...

Ten simple rules for coordinating a large digital health project: Perspectives from EU and implications for global contexts Coordinating a large-scale digital health project requires a unique mix of scientific leadership, administrative skill, and human sensitivity. Drawing from our experience leading CAPABLE, a European H...

From @plos.org #Computational #Biology | Ten simple rules for coordinating a large #digital #health project: Perspectives from EU and implications for global contexts | #Education #Bioinformatics #Research #Healthcare #PLOSCBTSR 🧬 🖥️ 🧪 🔓
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journals.plos.org/ploscompbiol...

AI is helping individual scientists, study suggests — but not science Artificial intelligence is helping researchers advance their careers and drill deeper into specific questions, but it is not necessarily benefiting science on the whole.

#ShortWave #Podcast on @npr.org | AI is helping individual scientists, study suggests -- but not science | #Bioinformatics #Proteomics #Genomics #Science #AI 🧬 🖥️ 🧪 CC/ @stevensalzberg.bsky.social
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www.npr.org/2026/02/17/n...

We are thrilled to announce that "Ten Common Misconceptions About Galaxy (And Why They Are Wrong!)" has just been published! This is the result of passionate discussions, collaborative debates, and a shared commitment to clarifying what Galaxy @galaxyproject.bsky.social truly is and what it can do.

Now Available: RefSeq Release 233 - NCBI Insights RefSeq release 233 is now available online and from the FTP site! You can access RefSeq data through NCBI Datasets. The release is provided in several directories as a complete dataset and also as div...

#NCBI has released ver 233 of #RefSeq which includes 442,943,508 proteins, 76,278,418 RNAs, and sequences from 174,157 organisms. One is the Rhesus macaque T2T assembly | #OpenScience #OpenData #Genomics #Proteomics #Bioinformatics 🧬 🖥️ 🧪
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ncbiinsights.ncbi.nlm.nih.gov/2026/02/19/r...

The CDC is the only .gov that is not run from within the Washington DC beltway … Atlanta is not next door to Bethesda!

New collaborative work our team in @plos.org Plos Computational Bio. Our goal was to demystify the annotation process and make it more accessible. Give it a try! @terryfoxresearch.bsky.social @bhcri.bsky.social

Rubrics, Not Vibes: Consistency as a Feature in Peer Review with AI Responsibly using AI for a structured first pass manuscript / grant proposal review can reduce reviewer variance while keeping human judgment central. Bonus: a prompt I use for my own draft proposals.

From @stephenturner.us | Rubrics, Not Vibes: Consistency as a Feature in Peer Review with AI | 🧪 #AI #OpenScience #PeerReview #Grants #Publications #PairedEnds
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blog.stephenturner.us/p/rubrics-no...

Staying Current in Data Science and Computational Biology: 2026 Edition Part 3 in a series of posts going back 14 years

Staying Current in Data Science and Computational Biology: 2026 Edition. Part 3 in a series of posts going back 14 years. doi.org/10.59350/2na...

Tutorial for variant interrogation in tumor samples The increasing accessibility of next-generation sequencing has empowered researchers to investigate somatic mutations in cancer. The complexity of variant analysis pipelines, terminology, and tool sel...

From @jeanetteeb.bsky.social & colleagues in @plos.org #Computational #Biology | Tutorial for variant interrogation in tumor samples | #Bioinformatics #Education #NGS #Cancer #Genomics #OpenEducationalResources #OpenScience 🧬 🖥️ 🧪 🔓 CC/ @ppalagi.bsky.social
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journals.plos.org/ploscompbiol...

Ten common misconceptions about Galaxy (and why they are wrong!) Author summary Galaxy is a free, community-built web interface that helps scientists analyse data in a way that’s easy to use, transparent and reproducible. While it is widely used in biology and othe...

From @bebatut.bsky.social @abretaud.bsky.social @hrhotz.bsky.social et al. in @plos.org #Computational #Biology | Ten common misconceptions about Galaxy (and why they are wrong!) | #Bioinformatics #Education #UseGalaxy 🧬 🖥️ 🧪 🔓 CC/ @galaxyproject.bsky.social
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journals.plos.org/ploscompbiol...