Bérénice Batut

Affiliations

Gallantries: Bridging Training Communities in Life Science, Environment and Health avatar GallantriesInstitut Français de Bioinformatique avatar IFBELIXIR Europe avatar ELIXIR Europe

Former Affiliations

University of Freiburg avatar UFRGerman Network for Bioinformatics Infrastructure Service, Training, Cooperations & Cloud Computing avatar de.NBI

Contributions

The following list includes only slides and tutorials where the individual or organisation has been added to the contributor list. This may not include the sum total of their contributions to the training materials (e.g. GTN css or design, tutorial datasets, workflow development, etc.) unless described by a news post.

19 Editorial Roles

This contributor has taken on additional responsibilities as an editor for the following topics. They are responsible for ensuring that the content is up to date, accurate, and follows GTN best practices.

307 Tutorials

65 Slides

96 FAQs

18 Video Recordings

6 Events



Your Contributor Card

Bérénice Batut avatar
Bérénice Batut

Editorial board member for Contributing to the Galaxy Training Material, Foundations of Data Science, Development in Galaxy, ELIXIR, Microbiome, Sequence analysis, Teaching and Hosting Galaxy training, Transcriptomics, Variant Analysis

307 Tutorials 96 FAQs 65 Slides Editorial Board 18 Videos 15 News 6 Events

GTN contributor since 2017-09

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GitHub Activity

Issues Reported

318 Merged Pull Requests

See all of the Pull Requests and Commits by Bérénice Batut.

Reviewed 435 PRs

We love our community reviewing each other's work!

News

CoFest logo with two generic people shapes conversing next to the GTN logo and text 'gtn cofest'
Next GTN CoFest May 20, 2021
Saskia Hiltemann avatar Helena Rasche avatar Bérénice Batut avatar Jennifer Hillman-Jackson avatar Delphine Lariviere avatar Anna Syme avatar Maria Doyle avatar
18 March 2021
Every 3 months we organise one day dedicated to the GTN community! Thursday, May 20th is the next GTN CoFest. We will be working on the training materials, have discussions with the global Galaxy traning community. Do you teach with Galaxy? Want to learn how to add your tutorial to the GTN? New to the community and just want to learn more? Everybody is welcome!
cofest contributing
GTN logo with a multi-coloured star and the words Galaxy Training Network
New Feature: FAQs
Saskia Hiltemann avatar Helena Rasche avatar Bérénice Batut avatar
24 March 2021
Snippets have received an major overhaul! Snippets/FAQs are small reusable bits of training, often answering a single question. In addition to the general Galaxy snippets, we now also support topic-level and tutorial-level FAQs. This will allow contributors to add common questions and answers to their tutorials, which not only can be included in the tutorial text itself, but are also used to autogenerate an FAQ page for the tutorial or topic listing all common questions (and answers).This will be useful both to participants following tutorials via self-study, and also to instructors preparing for a training event.
gtn infrastructure contributors instructors new feature contributing
Analysis flow in the 'Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data' tutorial. It teaches how to obtain, run and combine workflows appropriately for 4 different types of input data. Image adapted from covid19.galaxyproject.org
New Tutorial: Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data
Bérénice Batut avatar Wolfgang Maier avatar
30 June 2021
Effectively monitoring global infectious disease crises, such as the COVID-19 pandemic, requires capacity to generate and analyze large volumes of sequencing data in near real time. These data have proven essential for monitoring the emergence and spread of new variants, and for understanding the evolutionary dynamics of the virus.
new tutorial variant-analysis covid-19 one-health
Screenshot of the top of the feedback page with the titles and 2 graphs: the cumulative number of feedback answers over month for all topics, and a barplot with number of answers for different scores
New Feature: a feedback page to aggregate and display feedback answers
Bérénice Batut avatar
28 July 2021
As you have probably already seen, a feedback form is embedded on the bottom of each tutorial.
new feature contributing
Adversitement for the survey. Written: Got a minute? Did you use Galaxy for training / teaching? Have your say... Take our survey. We appreciate your feedback. Logos: Galaxy Project and Galaxy Training Network
Got a minute? Take our survey about Galaxy for training and have your say!
Bérénice Batut avatar
29 September 2021
Do you use Galaxy for Training? Have your say! Please take a few minutes to let us know about your training experiences.
feedback contributing
GTN logo with a multi-coloured star and the words Galaxy Training Network
New Topic: Data Science Survival Kit
Saskia Hiltemann avatar Helena Rasche avatar Bérénice Batut avatar Anthony Bretaudeau avatar Yvan Le Bras avatar Fotis E. Psomopoulos avatar The Carpentries avatar
12 October 2021
As part of our work under the Gallantries Grant we are establishing a new topic within the GTN specifically focused on Data Science skills. This topic will include tutorials covering things such as:
gtn infrastructure new topic data-science
Content of material available on the GTN and feedback from learners. (A) Evolution of number of topics, tutorials, and contributors over the months between 2017 and 2022. (B) Number and type of tutorials per topics available on the GTN on April 2022. The latest statistics are publicly available from https://training.galaxyproject.org/stats. (C) Type of supporting materials for tutorials per topics available on the GTN on April 2022. (D) Score of the embedded feedback in the tutorials per topics. Three questions are asked in the form: 'How much did you like this tutorial?' (from 1 (bad) to 5 (great)), 'What did you like?', 'What could be improved?'. The latest feedback results are publicly available from https://training.galaxyproject.org/feedback.
New GTN paper: "Galaxy Training: A powerful framework for teaching!"
Bérénice Batut avatar Saskia Hiltemann avatar Helena Rasche avatar
10 January 2023
Our new paper about the Galaxy Training Network has been published this week in Plos Computational Biology: “Galaxy Training: A powerful framework for teaching!”
paper contributing
screenshot from the data manipulation tutorial
New Tutorial: Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
Bérénice Batut avatar Engy Nasr avatar
26 January 2023
Food contamination with pathogens are a major burden on our society. Globally, they affect an estimated 600 million people a year and impact socioeconomic development at different levels. These outbreaks are mainly due to Salmonella spp. followed by Campylobacter spp. and Noroviruses.
new tutorial microbiome
GTN logo with a multi-coloured star and the words Galaxy Training Network
Lost in a topic? Try a Learning Pathway!
Helena Rasche avatar Bérénice Batut avatar
4 March 2024
We know the GTN has a lot of learning materials (400 and counting!) which can make it quite difficult to figure out where to start in some topics.
gtn infrastructure new feature
A screenshot of a radar plot visibly from fair-checker's site showing a perfect score.
Perfectly FAIR Training!
Helena Rasche avatar
13 May 2024
We are happy to report that over the years of our fruitful collaboration with ELIXIR TeSS, all GTN materials should receive a perfect score on the FAIR-Checker.
gtn infrastructure fair contributing
400 tutorials
Celebrating the Milestone: 400 Tutorials on the Galaxy Training Network!
Bérénice Batut avatar Helena Rasche avatar Saskia Hiltemann avatar
6 June 2024
The Galaxy Training Network (GTN) has reached an exciting milestone: our 400th tutorial! This achievement is a testament to the dedication and hard work of our community of educators, researchers, and developers over the last 9 years.
gtn contributing community
GTN logo with a multi-coloured star and the words Galaxy Training Network
New Galaxy training: Building an amplicon sequence variant (ASV) table from 16S data using DADA2
Bérénice Batut avatar
6 June 2024
The GTN hosts its 400th tutorial: Building an amplicon sequence variant (ASV) table from 16S data using DADA2
new tutorial microbiome
the title slide of the presentation titled Updates from the GTN , Galaxy Community Conference 2024 Brno, Saskia and Helena. The background consists of paper pieced flowers and a butterfly. a CC-BY-SA logo is in the top right corner.
So many new features! GTN 2023-2024 Updates
Saskia Hiltemann avatar Helena Rasche avatar
9 July 2024
We recently presented the GTN at the 2024 Galaxy Community Conference. This presentation was a summary of the updates and new features that were added to the GTN in the past year.
gcc gtn infrastructure contributing
The image illustrates the training life cycle through a circular diagram featuring five interconnected stages. Starting with the Plan stage, depicted by a checklist icon, it involves identifying and assessing training needs to ensure they align with desired outcomes. The Design stage, represented by a pencil and ruler icon, focuses on creating effective training methods and determining the best delivery approach. In the Develop stage, shown with a computer screen displaying code, training materials such as job aids, activities, presentations, and assessments are created. The Deliver stage, illustrated with a document and folder icon, covers logistical aspects of training delivery, including registration, advertisement, and course execution. Finally, the Evaluate stage, represented by a checklist with checkmarks, involves assessing the training's effectiveness and integrating findings for continuous improvement. The circular arrangement of these stages emphasizes the continuous and iterative nature of the training life cycle.
Enhancing Scientific Training: The Galaxy Training Network's Role in the ELIXIR Training Life-Cycle
Bérénice Batut avatar Lisanna Paladin avatar
1 July 2025
In the rapidly evolving landscape of data science, continuous learning and skill development are crucial. The Galaxy Training Network (GTN) plays a pivotal role in this educational ecosystem, particularly within the ELIXIR Training Life-Cycle. This blog post explores how the GTN contributes to each phase of the life-cycle and aligns with the SPLASH recommendations, ensuring high-quality training for researchers worldwide.
gtn
graphic showing the 10 misconceptions and their rebuttals
New Paper! Ten common misconceptions about Galaxy (and why they are wrong!)
Wendi Bacon avatar Bérénice Batut avatar Sanjay Kumar Srikakulam avatar Paul Zierep avatar Anthony Bretaudeau avatar Björn Grüning avatar Gildas Le Corguillé avatar Helge Hecht avatar John Davis avatar Hans-Rudolf Hotz avatar Beatriz Serrano-Solano avatar
23 February 2026
This is an external post, please follow the link to read it.
paper
Bérénice Batut avatar
GTN contributor since 2017-09

External Links

Training Philosophy
bebatut
berenice.batut@gmail.com
bebatut:matrix.org
https://piaille.fr/@bebatut
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berenicebatut
0000-0001-9852-1987
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Stats for materials contributed to by Bérénice Batut