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Bérénice Batut

@bebatut.bsky.social

740 followers 1.3K following 77 posts

She/her. Bioinformatics. Microbiome 🦠. Open Science. Training. Mentoring. Galaxy. OLS. ELIXIR Microbiome Community. Mother

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Reposted by Bérénice Batut

Galaxy Project @galaxyproject.bsky.social · 10d

On Day 1 of European Galaxy Days, Mina Hojat Ansari presented FAIRYMAGS: A Galaxy Workflow for MAG Recovery Applied to Termite Microbiomes.
Read more: https://elixir-europe.org/how-we-work/scientific-programme/commissioned-services/science/bfsp/fairymags

##termite ##EGD2025 ##microbiomes (1/2)

FAIRYMAGS: A Galaxy Workflow for MAG Recovery Applied to Termite Microbiomes

Bérénice Batut @bebatut.bsky.social · 10d

Really happy to be back in Freiburg & at @uni-freiburg.de to present the Microbiology Galaxy Lab & the efforts of the microGalaxy community to build the first community-driven gateway for reproducible and FAIR analysis of microbial data.

Slides: f1000research.com/slides/14-1021

#EGD

Reposted by Bérénice Batut

Galaxy Project @galaxyproject.bsky.social · 10d

On Day 1 of European Galaxy Days, Bérénice Batut presented The Microbiology Galaxy Lab and the effort from the microGalaxy to build the first community-driven gateway for reproducible and FAIR analysis of microbial data.
Read more: https://doi.org/10.1101/2024.12.23.629682 (1/2)

The Microbiology Galaxy Lab and the effort from the microGalaxy to build the first community-driven gateway for reproducible and FAIR analysis of microbial data

Bérénice Batut @bebatut.bsky.social · 14d

Merci beaucoup @komo625.bsky.social !

Bérénice Batut @bebatut.bsky.social · 23d

Curious? Explore the full story here: galaxyproject.org/news/2025-09... and read our recently updated preprint: www.biorxiv.org/content/10.1...

Bérénice Batut @bebatut.bsky.social · 23d

Today is #InternationalMicroorganismDay, a chance to celebrate the invisible powerhouses shaping our health and ecosystems. With @galaxyproject.bsky.social, we're proud to support global research that decodes the secrets of microbes, from deadly pathogens to life-sustaining bacteria.

This image presents the Microbiology Galaxy Lab, a platform dedicated to One Health and ecological integrity, illustrating how it connects humans, animals, and the environment through the analysis of DNA, RNA, proteins, and metabolites using 315+ tool suites and 115+ workflows. On the left, it highlights ecosystem dynamics and biodiversity, covering areas such as microbial diversity, interactions, ecosystem modeling, strain discovery, pathway analysis, population omics, and temporal dynamics. On the right, it focuses on health and disease, addressing topics like clinical microbiota, antimicrobial resistance, pathogen profiling (viruses, bacteria, fungi, protozoa), virulence assessment, dysbiosis analysis, abundance quantification, outbreak modeling, biomarker correlation, and host interaction. The lab also emphasizes citizen science, education, and 35+ tutorials, promoting accessibility and knowledge sharing in microbiology research.

Bérénice Batut @bebatut.bsky.social · Sep 10

📢 Let’s spread the word! Share your thoughts, tag colleagues who might benefit, and help us bust these myths once and for all. Together, we can empower more researchers, educators, and decision-makers to leverage Galaxy's full potential.

Bérénice Batut @bebatut.bsky.social · Sep 10

🔬 Why does this matter? Galaxy isn't just for genomics or teaching. It's a robust tool for cutting-edge research, education, and even clinical workflows. This paper shines a light on its real-world applications, technical strengths, and the vibrant community driving its evolution.

Bérénice Batut @bebatut.bsky.social · Sep 10

These collective efforts help clarify Galaxy's true potential as a mature, open-source platform for accessible, reproducible, and scalable data analysis across the life sciences and beyond.

Bérénice Batut @bebatut.bsky.social · Sep 10

A huge thanks to Wendi Bacon, @hrhotz.bsky.social, & @beatrizserrano.bsky.social for leading this effort, to @elixir-europe.org, @ifb-elixir-fr.bsky.social, @denbi.bsky.social for the long-standing supporters, & to everyone who contributed their expertise, feedback, & enthusiasm to make this happen.

Bérénice Batut @bebatut.bsky.social · Sep 10

This preprint tackles persistent myths about Galaxy, from its perceived limitations in genomics to questions about scalability, usability, and its role in academia and industry. Spoiler alert: Galaxy is far more versatile, powerful, and impactful than many realize!

Bérénice Batut @bebatut.bsky.social · Sep 10

📄 New preprint!

After months/years of gathering insights and input from our incredible community, we're thrilled to share this important resource:
"Ten Common Misconceptions About Galaxy (and Why They Are Wrong!)" www.preprints.org/manuscript/2...

Reposted by Bérénice Batut

Galaxy Project @galaxyproject.bsky.social · Sep 10

after a long effort, gathering a lot of input from many people, we finaly put it all together:
Ten Common Misconceptions About Galaxy (and Why They Are Wrong!)
https://www.preprints.org/manuscript/202509.0823
Thank you very much to all people involved !

overview

Reposted by Bérénice Batut

Rob Waterhouse @rmwaterhouse.bsky.social · Sep 7

TDM & NLP 💻 applied to #taxonomy & #biodiversity literature 📚 will facilitate #data synthesis studies & #literature reviews, identification of knowledge gaps & biases, & data-informed investigation of #ecological & #evolutionary trends & patterns bdj.pensoft.net/article/1530...

From literature to biodiversity data: mining arthropod organismal traits with machine learning

The fields of taxonomy and biodiversity research have witnessed an exponential growth in published literature. This vast corpus of articles holds information on the diverse biological traits of organi...

bdj.pensoft.net

Reposted by Bérénice Batut

Titus Brown @titus.idyll.org · Aug 8

taxburst v0.3.0 is now released - this is an update of the Krona visualization system for microbiome/metagenome taxonomy analyses. Enjoy!

Announcing taxburst, an update of the Krona software for taxonomy exploration

Announcing taxburst for metagenome taxonomy!

ivory.idyll.org

Reposted by Bérénice Batut

IFB/ELIXIR-Fr @ifb-elixir-fr.bsky.social · Jul 25

✨ 📹 Pour se replonger encore un peu dans cette belle édition de JOBIM Bordeaux qui s'est déroulée début juillet, découvrez notre vidéo ! www.youtube.com/shorts/U2sPu...

L'IFB/ELIXIR-FR à JOBIM Bordeaux - Juillet 2025

YouTube video by French Institute of Bioinformatics

www.youtube.com

Reposted by Bérénice Batut

GenOuest @genouest.bsky.social · Jul 10

@abretaud.bsky.social and @bebatut.bsky.social presenting @galaxyproject.bsky.social France during the @ifb-elixir-fr.bsky.social network presentation at @jobim2025.bsky.social !

Bérénice Batut @bebatut.bsky.social · Jul 7

Read the full blog post here: gxy.io/GTN:N00115

Bérénice Batut @bebatut.bsky.social · Jul 7

Aligning with SPLASH recommendations, the GTN offers robust resources that enhance the training experience, including defining learning objectives, developing diverse learning materials, ensuring accessibility, and gathering feedback.

Bérénice Batut @bebatut.bsky.social · Jul 7

The GTN contributes significantly to each phase of the training life-cycle, from planning and designing to delivering and evaluating training programs. This ensures that scientists worldwide have access to high-quality, sustainable training resources.

Bérénice Batut @bebatut.bsky.social · Jul 7

To guide trainers through the Life-Cycle, the ELIXIR Training Platform developed and maintains the SPLASH framework: elixir-europe-training.github.io/ELIXIR-Train.... It supports the various stages of the Life-Cycle by providing recommendations and linking to services and tools supported by ELIXIR.

ELIXIR Training SPLASH

elixir-europe-training.github.io

Bérénice Batut @bebatut.bsky.social · Jul 7

In today's rapidly evolving data science landscape, continuous learning and skill development are more crucial than ever. The ELIXIR Training Platform formalized the Training Life-Cycle, a structured path from identifying needs to evaluating impact, ensuring high-quality and sustainable training.

Bérénice Batut @bebatut.bsky.social · Jul 7

As a follow-up to our poster at the @elixir-europe.org All Hands Meeting in June, Lisanna Paladin and I wrote the following blog post on how the Galaxy Training Network aligns with the Training Life-Cycle and @elixir-europe.org SPLASH recommendations.

#Training @galaxyproject.bsky.social

GTN @galaxytraining.bsky.social · Jul 2

Enhancing Scientific Training: The Galaxy Training Network’s Role in the ELIXIR Training Life-Cycle

Read more at https://training.galaxyproject.org/training-material/news/2025/07/01/gtn-elixir-life-cycle.html

@galaxyproject.bsky.social

Reposted by Bérénice Batut

IFB/ELIXIR-Fr @ifb-elixir-fr.bsky.social · Jul 4

@jobim2025.bsky.social
- Épisode 13/13
🚀 Enfin, venez découvrir notre démonstration « ABRomics-analysis: a web service for the analysis of Antibiotic Resistance in bacterial genomes »

➡️ analysis.abromics.fr

Reposted by Bérénice Batut

IFB/ELIXIR-Fr @ifb-elixir-fr.bsky.social · Jul 1

📢 Inscription - L’IFB & le réseau MERIT organisent 2 jours de formation du 25 au 27 novembre 2025 pour maîtriser les langages de #workflows #Snakemake & #Nextflow 🧬💻. Optimisez vos analyses bioinformatiques et assurez leur reproductibilité !