Bérénice Batut
Tenure Track Researcher at LMGE
Clermont-Ferrand, Auvergne-Rhône-Alpes, France
Summary
🤩
Rockstar🎓
Top School
Top expert inComputational Genomics and Bioinformatics Workflow Development
Bérénice Batut is a tenure-track researcher and senior scientist specializing in microbiome data analysis with 11 years of experience building FAIR, open, and sustainable bioinformatics infrastructure. She combines hands-on tool and workflow development (notably extensive contributions to the Galaxy training-material and tools ecosystems) with curriculum design and capacity building, having led training programs and co-founded Open Life Science. Her work spans back-end automation, packaging and CI for bioconda, and data manager development for key bioinformatics tools, reflecting strong DevOps and reproducible-research skills. Based in Clermont-Ferrand, she has helped coordinate ELIXIR training efforts and co-leads multiple community initiatives like microGalaxy and the Galaxy Training Network. Beyond research and engineering, she brings a talent for improving user experience in technical documentation and training material—reorganizing and enriching tutorials to make complex analyses accessible.
10 years of coding experience
14 years of employment as a software developer
Doctor of Philosophy (PhD), Bioinformatics, Doctor of Philosophy (PhD), Bioinformatics at INSA Lyon - Institut National des Sciences Appliquées de LyonMaster's degree, Theoretical computer science, option Complex system modelling, Master's degree, Theoretical computer science, option Complex system modelling at École normale supérieure de Lyon
French, English, German
Github Skills (25)
markdown10
biom10
python10
package-management10
scripting10
conda10
bash10
data-management10
automation10
markdown-it10
build-automation10
bioinformatics10
galaxy10
automations10
documentation10
Programming languages (20)
Github contributions (5)
galaxyproject/tools-iuc
Dec 2015 - Oct 2022
Tool Shed repositories maintained by the Intergalactic Utilities Commission
Role in this project:
Back-end Developer & Automation Engineer
Back-end Developer & Automation EngineerContributions:192 reviews, 809 commits, 209 PRs in 6 years 11 months
Contributions summary:Bérénice primarily contributed to the development of tools within the repository, adding wrappers for various bioinformatics programs such as `jackknifed_beta_diversity_through_plots_html_generation.py` and scripts for EBI-related tools, including `ebeye_urllib3.py` and macro generation using `generate_macros.py`. Their work also involved script development for test data generation and report formatting, indicating an emphasis on both the functionality and the automation of bioinformatics analysis pipelines. These contributions improved both the analytical capabilities and the robustness of the tool.
intergalacticrepositoriesusegalaxywrapperscommission
galaxyproject/training-material
Aug 2016 - Jan 2023
A collection of Galaxy-related training material
Role in this project:Technical Writer
Technical WriterContributions:267 reviews, 1853 commits, 656 PRs in 6 years 6 months
Contributions summary:Bérénice primarily focused on reorganizing and improving the structure of the existing Exome-Seq training materials. Their contributions included moving tutorial files, adding and formatting introductory slides, and integrating custom CSS and JavaScript scripts to enhance the presentation and user experience. They also began the creation of a README file to consolidate essential information about the tutorials.
chip-seqmetagenomicsrnaseqtraining-materialusegalaxy
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