Bérénice Batut

The Galaxy Community Conference is coming to my hometown this year! 🎉
Mark your calendars & register by the end of February for early bird rates. It’s a fantastic opportunity to connect with the global Galaxy Community.
Looking forward to seeing you there!
@ifb-elixir-fr.bsky.social

🔬 C'est la Journée des femmes et filles de science ! #FemmesEnSciences #11février

Envie de découvrir (ou faire découvrir) des femmes scientifiques ? J'ai rassemblé plein de ressources ici ⬇️
www.linkedin.com/pulse/envie-...

Et mon starter pack de chercheuses sur bluesky go.bsky.app/TBEzKC

F1000Research Article: Fostering and sustaining collaborative innovation: Insights from ELIXIR Europe's life science Communities. Read the latest article version by Clare Garrard, Katharina F Heil, Maria Cristina Aspromonte, Bérénice Batut, Magda Chegkazi, John M Hancock, Elaine Harrison, Naveed Ishaque, Giselle Ke...

#Communities of experts collaborating on #scientific or technical projects are drivers of innovation across the life #sciences f1000research.com/articles/14-... @elixir-europe.org @sib.swiss @ergabiodiv.bsky.social #biodiversity #genomics

Connexion directe de Galaxy à Recherche Data Gouv

My team at @cbitoulouse.bsky.social is recruiting a postdoc #bioinformatics with solid experience in metagenomic analyses.
Interest in evolution, ecology & MGEs is important.
The offer stands until the perfect candidate is found, and it could be you 🫵

🔁 🙏

#microSky #phagesky #UTIsky
@cnrs.fr

2026 Galaxy Community Conference (GCC2026) The annual gathering of the Galaxy Community with opportunities to hear latest developments, get training, and meet everyone involved.

Get ready for GCC2026!
Join the Galaxy community June 22–24, 2026, in Clermont-Ferrand, France, to learn new tools, share your work, and connect with researchers and developers from around the world. Followed by CoFest on June 25–26.

galaxyproject.org/events/gcc20...

Data visualization is a critical step in data analysis. 8 links to bookmark for better data visualization:🧵

As 2025 wraps up, we’re looking back at some of the most intriguing microbes that made their scientific debut this year. This blog highlights standout bacterial species that caught our eye. Read the full #FEMSmicroBlog: buff.ly/2wz7k16

#NewMicrobes

How effective are AI assistants like Claude and ChatGPT for literature reviews? Anton Nekrutenko ran a systematic experiment using multiple AI-assisted approaches to survey RNA-seq studies on Candida auris, a multidrug-resistant fungal pathogen. Summary here:
galaxyproject.org/news/2025-12...

Life Identification Numbers: A bacterial strain nomenclature approach Unified strain taxonomies are needed for the epidemiological surveillance of bacterial pathogens and international communication in microbiological research. Core genome multilocus sequence typing (cg...

Huge preprint if you are interested in bacterial strain taxonomy! The why and how of cgMLST LIN codes: An extensively revised and expanded version doi.org/10.1101/2024... I will summarize it for you in this thread 👇

Proud to have contributed to this important work!

STREAMS guidelines: standards for technical reporting in environmental and host-associated #microbiome studies. www.nature.com/articles/s41... @natmicrobiol.nature.com

LorMe: a streamlined and interoperable R framework for end-to-end microbiome analysis www.biorxiv.org/content/10.1... #Rstats 🧬🖥️🧪 github.com/wangnq111/Lo...

📢🚀💻Le nouveau site internet de l’IFB/ELIXIR-FR est en ligne !!!
Lancé début 2025, le projet de refonte/création du nouveau site internet de l’IFB/ELIXIR-FR atteint aujourd’hui l’une de ses étapes cruciales : sa publication ! www.ifb-elixir.fr

GlobDB: a comprehensive species-dereplicated microbial genome resource AbstractMotivation. Over the past years, substantial numbers of microbial species’ genomes have been deposited outside of conventional INSDC databases.Resu

Our paper describing the GlobDB is now published in @bioinfoadv.bsky.social
doi.org/10.1093/bioa...

The GlobDB is the largest species dereplicated genome database currently available, containing 306,260 species representatives.
More information on globdb.org 1/5
🖥️🧬🦠

🧬 🔎 Ce 17 novembre a eu lieu la journée du consortium ABRomics à l’Institut Pasteur. L’occasion de présenter aux différents représentants de nos parties prenantes l’avancement du projet et les développements en cours !

YouTube video by Radio Nova Le beurre, l’argent du beurre et le c*l des chercheurs- La chronique de Tania Louis dans La dernière

De mon côté on m'a confié le micro pour la chronique sciences.

Cette fois j'ai décidé de parler du fonctionnement scandaleux de l'édition scientifique, peu connu en dehors des labos : www.youtube.com/watch?v=Yg2C...

Mais 4 minutes c'est court, alors j'ajoute quelques ressources ci-dessous !

L'intégrale : "La dernière" du 9 novembre 2025 avec Audrey Dussutour Sur Radio Nova ce dimanche : Audrey Dussutour (biologiste), Doully, Florence Mendez et Tania Louis. La dernière, le dimanche à 18h en direct sur Radio Nova et ...

Dimanche dernier @ladernierenova.bsky.social était de retour à Toulouse.
L'invitée de l'émission était @docteur-drey.bsky.social donc je recommande chaudement d'écouter le podcast entier : podcasts.nova.fr/radio-nova-l...

@laradionova.bsky.social

...

Metagenomic classification survey Background: We're seeking the views of researchers on the possibility of a repository for metagenomic classification data, which we're hoping to build. The rationale is that people are familiar with t...

Know metagenomics and could spare 2 mins? I'm applying for funding to build a visual repository for metagenomic classification data (not sequence data). To support the application, I have a short 2 minute survey and it would be a big help if you could fill it in: docs.google.com/forms/d/e/1F...

It was a really nice week working on building MiCoReCa, a catalogue of resources (tools, workflows, etc) for microbiome research, and more importantly networking with the large @elixir-europe.org community. Thank you all! See next year!

🚀👩‍💻🧑‍💻 End of this week of #BioHackEU25, organised by @elixir-europe.org , to advance all projects in synergy! Thank you to the IFB/ELIXIR-FR team (on-site and remotely), and to our colleagues at @genouest.bsky.social 👏

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

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)

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

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

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)

Merci beaucoup @komo625.bsky.social !

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

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.

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.

📢 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.

🔬 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.

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.

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.