Bérénice Batut

@bebatut.bsky.social

882 Followers 1529 Following

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

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.
The image features a vibrant and engaging graphic promoting the FAIRyMAGs Hybrid Hackathon 2025. At the top, the title 'FAIRyMAGs Hybrid Hackathon 2025: Optimising Metagenomics Assembled Genomes building' is prominently displayed, accompanied by a rocket icon. Below the title, the event dates 'October 06-10th, 2025' are highlighted with a flag icon. In the center, there are illustrations of three individuals collaborating on a project. One person is standing and pointing at a large screen displaying a graph, another person is sitting on a desk with a coffee mug, and the third person is sitting on the desk with a laptop. The background is minimalistic, focusing attention on the collaborative scene. At the bottom, logos of the supporting organizations are displayed: de.NBI (German Network for Bioinformatics Infrastructure), IFB (Institut Français de Bioinformatique), and ELIXIR.
2 women smiling in front of tables with men and slide
A smiling woman holding a sign for Stand up for Science
Heatmap illustrating the presence of microGalaxy tool suites within the available microGalaxy training materials, grouped by EDAM topics. The tool suites are organized based on their corresponding EDAM operations, highlighting the breadth of tools utilized for different training contexts.
Heatmap illustrating the presence of microGalaxy tool suites within the available microGalaxy workflows, grouped by three levels of development. The tool suites are organized based on their corresponding EDAM operations, highlighting the breadth of tools utilized for different workflows.
Heatmap illustrating the availability of microGalaxy tool suites (x-axis) across various Galaxy servers (y-axis), grouped by EDAM topics. Tool suites may appear in multiple clusters, as they can be annotated with several topics. A logarithmic scale is applied for improved visualization.
Barplots with anonymous responses highlighting the main research targets, techniques, and analyses used or desired by microbial researchers. The figure also reports challenges faced by users who rarely or never use Galaxy, survey responses by continent, and preferences regarding tool deployment in Galaxy.
Barplot showing the annual publication trends with the total number of citations (blue) alongside those specific to microbial research (brown)
Overview of microbial isolate data analysis tasks with corresponding tool suites and potential workflows available on microGalaxy. This figure illustrates the diverse range of microbial isolate analysis tasks, grouped by data types (e.g., genomics, transcriptomics, proteomics, and multi-omics approaches). Each task is linked to intermediate and final outputs, with annotations indicating the tool suites that could be used for these analyses.
Overview of microGalaxy's applications across Environment, Health, and Agri-Food domains, supporting DNA, RNA, protein, and metabolite analysis. Key topics include biogeochemical cycles, antimicrobial resistance, and pathogen monitoring. Centered on One Health, the platform integrates 220+ tool suites, 65+ workflows, and 45+ tutorials, promoting FAIR principles, citizen science, and education.