Bérénice Batut
@bebatut.bsky.social
She/her. Bioinformatics. Microbiome 🦠. Open Science. Training. Mentoring. Galaxy. OLS. ELIXIR Microbiome Community. Mother
Reposted by Bérénice Batut
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...
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...
docs.google.com
November 10, 2025 at 6:24 PM
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 👏
November 7, 2025 at 3:16 PM
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!
Reposted by Bérénice Batut
🚀👩💻🧑💻 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 👏
November 7, 2025 at 12:29 PM
🚀👩💻🧑💻 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 👏
Reposted by Bérénice Batut
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)
Read more: https://elixir-europe.org/how-we-work/scientific-programme/commissioned-services/science/bfsp/fairymags
##termite ##EGD2025 ##microbiomes (1/2)
October 1, 2025 at 10:32 AM
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)
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
Slides: f1000research.com/slides/14-1021
#EGD
October 1, 2025 at 10:14 AM
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
Slides: f1000research.com/slides/14-1021
#EGD
Reposted by Bérénice Batut
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)
Read more: https://doi.org/10.1101/2024.12.23.629682 (1/2)
October 1, 2025 at 10:05 AM
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)
Read more: https://doi.org/10.1101/2024.12.23.629682 (1/2)
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.
September 17, 2025 at 2:17 PM
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.
📄 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...
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...
September 10, 2025 at 1:46 PM
📄 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...
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
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 !
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 !
September 10, 2025 at 10:22 AM
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 !
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 !
Reposted by Bérénice Batut
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
September 7, 2025 at 9:40 AM
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...
Reposted by Bérénice Batut
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
August 8, 2025 at 2:19 PM
taxburst v0.3.0 is now released - this is an update of the Krona visualization system for microbiome/metagenome taxonomy analyses. Enjoy!
Reposted by Bérénice Batut
✨ 📹 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
July 25, 2025 at 12:16 PM
✨ 📹 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...
Reposted by Bérénice Batut
@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 !
July 10, 2025 at 8:00 AM
@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 !
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
#Training @galaxyproject.bsky.social
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
Read more at https://training.galaxyproject.org/training-material/news/2025/07/01/gtn-elixir-life-cycle.html
@galaxyproject.bsky.social
July 7, 2025 at 2:13 PM
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
#Training @galaxyproject.bsky.social
Reposted by Bérénice Batut
@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
- 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
July 4, 2025 at 7:52 AM
@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
- 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
📢 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 !
July 1, 2025 at 2:28 PM
📢 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 !
Exciting news! We're leading a project at the ELIXIR BioHackathon Europe to make microbiome research more accessible!
🤝 We're creating a comprehensive catalog of microbiome-related bioinformatics resources, and we want YOU to join us! #Microbiome #Bioinformatics
🤝 We're creating a comprehensive catalog of microbiome-related bioinformatics resources, and we want YOU to join us! #Microbiome #Bioinformatics
📆 Save the date for BioHackathon registration!
Register your interest to join #BioHackEU25 in person from 30 June to 15 July. All expressions of interest will be reviewed, and accepted attendees will be notified by the end of July.
More information: https://loom.ly/UfwZREk
Register your interest to join #BioHackEU25 in person from 30 June to 15 July. All expressions of interest will be reviewed, and accepted attendees will be notified by the end of July.
More information: https://loom.ly/UfwZREk
June 26, 2025 at 12:29 PM
Exciting news! We're leading a project at the ELIXIR BioHackathon Europe to make microbiome research more accessible!
🤝 We're creating a comprehensive catalog of microbiome-related bioinformatics resources, and we want YOU to join us! #Microbiome #Bioinformatics
🤝 We're creating a comprehensive catalog of microbiome-related bioinformatics resources, and we want YOU to join us! #Microbiome #Bioinformatics
Reposted by Bérénice Batut
@jobim2025.bsky.social - Épisode 6/13
🚀 Pour en savoir plus, venez découvrir notre poster « Exploring the Richness of the French Galaxy Ecosystem », qui sera présenté par @bebatut.bsky.social , le GT Galxy, Gildas et Anthony Bretaudeau !
🚀 Pour en savoir plus, venez découvrir notre poster « Exploring the Richness of the French Galaxy Ecosystem », qui sera présenté par @bebatut.bsky.social , le GT Galxy, Gildas et Anthony Bretaudeau !
June 20, 2025 at 11:43 AM
@jobim2025.bsky.social - Épisode 6/13
🚀 Pour en savoir plus, venez découvrir notre poster « Exploring the Richness of the French Galaxy Ecosystem », qui sera présenté par @bebatut.bsky.social , le GT Galxy, Gildas et Anthony Bretaudeau !
🚀 Pour en savoir plus, venez découvrir notre poster « Exploring the Richness of the French Galaxy Ecosystem », qui sera présenté par @bebatut.bsky.social , le GT Galxy, Gildas et Anthony Bretaudeau !
Reposted by Bérénice Batut
JOBIM 2025 - Épisode 5/13
🚀 Venez découvrir notre poster « Galaxy Training: A powerful framework for teaching! », qui sera présenté par Helena Rasche, @shiltemann.bsky.social , Björn Grüning, Galaxy Training Network et @bebatut.bsky.social
#ScienceOuverte #Galaxy #Bioinformatique #Formation #FAIR
🚀 Venez découvrir notre poster « Galaxy Training: A powerful framework for teaching! », qui sera présenté par Helena Rasche, @shiltemann.bsky.social , Björn Grüning, Galaxy Training Network et @bebatut.bsky.social
#ScienceOuverte #Galaxy #Bioinformatique #Formation #FAIR
June 18, 2025 at 12:36 PM
JOBIM 2025 - Épisode 5/13
🚀 Venez découvrir notre poster « Galaxy Training: A powerful framework for teaching! », qui sera présenté par Helena Rasche, @shiltemann.bsky.social , Björn Grüning, Galaxy Training Network et @bebatut.bsky.social
#ScienceOuverte #Galaxy #Bioinformatique #Formation #FAIR
🚀 Venez découvrir notre poster « Galaxy Training: A powerful framework for teaching! », qui sera présenté par Helena Rasche, @shiltemann.bsky.social , Björn Grüning, Galaxy Training Network et @bebatut.bsky.social
#ScienceOuverte #Galaxy #Bioinformatique #Formation #FAIR
Reposted by Bérénice Batut
🚀🦠 Lancement de la #formation #Metagenomics and #Metatranscriptomics Initiation - 2025 autour de l’analyse de ces données sous #Galaxy !
June 17, 2025 at 9:54 AM
🚀🦠 Lancement de la #formation #Metagenomics and #Metatranscriptomics Initiation - 2025 autour de l’analyse de ces données sous #Galaxy !
Reposted by Bérénice Batut
JOBIM 2025 - Épisode 4/13
🚀 Venez découvrir notre poster « Breaking Myths: The Reality of Galaxy’s Capabilities and Impact », qui sera présenté par Gildas Le Corguillé , Anthony Bretaudeau, Björn Grüning , le GT Galaxy et @bebatut.bsky.social !
🚀 Venez découvrir notre poster « Breaking Myths: The Reality of Galaxy’s Capabilities and Impact », qui sera présenté par Gildas Le Corguillé , Anthony Bretaudeau, Björn Grüning , le GT Galaxy et @bebatut.bsky.social !
June 16, 2025 at 11:45 AM
JOBIM 2025 - Épisode 4/13
🚀 Venez découvrir notre poster « Breaking Myths: The Reality of Galaxy’s Capabilities and Impact », qui sera présenté par Gildas Le Corguillé , Anthony Bretaudeau, Björn Grüning , le GT Galaxy et @bebatut.bsky.social !
🚀 Venez découvrir notre poster « Breaking Myths: The Reality of Galaxy’s Capabilities and Impact », qui sera présenté par Gildas Le Corguillé , Anthony Bretaudeau, Björn Grüning , le GT Galaxy et @bebatut.bsky.social !
Reposted by Bérénice Batut
✨📰🗓️Thank you @elixir-europe.org , we look forward to welcoming you to the next All Hands Meeting in 2026! #ELIXIR26 ✨
@cnrs-idf-villejuif.bsky.social @cnrsbiologie.bsky.social @cea.fr @inserm.fr @inrae-france.bsky.social
@cnrs-idf-villejuif.bsky.social @cnrsbiologie.bsky.social @cea.fr @inserm.fr @inrae-france.bsky.social
🎊 2025 ELIXIR All Hands Meeting #ELIXIR25 has come to an end! 👏 Thank you all for joining us in Thessaloniki 🇬🇷 and we look forward to seeing you again next year in Lyon, France 🇫🇷 for #ELIXIR26! @ifb-elixir-fr.bsky.social
June 5, 2025 at 11:47 AM
✨📰🗓️Thank you @elixir-europe.org , we look forward to welcoming you to the next All Hands Meeting in 2026! #ELIXIR26 ✨
@cnrs-idf-villejuif.bsky.social @cnrsbiologie.bsky.social @cea.fr @inserm.fr @inrae-france.bsky.social
@cnrs-idf-villejuif.bsky.social @cnrsbiologie.bsky.social @cea.fr @inserm.fr @inrae-france.bsky.social
Reposted by Bérénice Batut
Today (June 1) marks the 20th anniversary of Galaxy! Thanks to all the developers, admins, researchers, trainers, educators, students and more that have made up this amazing community. Here is to the next 20 years! @galaxyproject.bsky.social @jxtxfoundation.bsky.social galaxyproject.org
June 2, 2025 at 2:55 AM
Today (June 1) marks the 20th anniversary of Galaxy! Thanks to all the developers, admins, researchers, trainers, educators, students and more that have made up this amazing community. Here is to the next 20 years! @galaxyproject.bsky.social @jxtxfoundation.bsky.social galaxyproject.org
Reposted by Bérénice Batut
Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler that I've been working on during my postdoc in the Heng Li lab (@lh3lh3.bsky.social).
myloasm-docs.github.io
myloasm-docs.github.io
myloasm - metagenomic assembly with (noisy) long reads
myloasm-docs.github.io
May 28, 2025 at 5:54 PM
Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler that I've been working on during my postdoc in the Heng Li lab (@lh3lh3.bsky.social).
myloasm-docs.github.io
myloasm-docs.github.io
Reposted by Bérénice Batut
