Favourite Topics
Favourite Formats
Bérénice Batut
Contributions
The following list includes only slides and tutorials where the individual 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.
GitHub Activity
Tutorials
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Genome Annotation
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Essential genes detection with Transposon insertion sequencing
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Epigenetics
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Formation of the Super-Structures on the Inactive X
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Epigenetics
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Identification of the binding sites of the Estrogen receptor
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Foundations of Data Science
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R basics in Galaxy
📝
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Foundations of Data Science
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Advanced R in Galaxy
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Teaching and Hosting Galaxy training
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Assessment and feedback in training and teachings
✍️
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Teaching and Hosting Galaxy training
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Live Coding is a Skill
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Teaching and Hosting Galaxy training
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Teaching online
✍️
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Teaching and Hosting Galaxy training
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Teaching experiences
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Teaching and Hosting Galaxy training
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Running a workshop as instructor
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Teaching and Hosting Galaxy training
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Hybrid training
✍️
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Teaching and Hosting Galaxy training
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Organizing a workshop
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Teaching and Hosting Galaxy training
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Training techniques to enhance learner participation and engagement
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Teaching and Hosting Galaxy training
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Set up a Galaxy for Training
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Teaching and Hosting Galaxy training
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Motivation and Demotivation
✍️
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Assembly
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Assembly of metagenomic sequencing data
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Contributing to the Galaxy Training Material
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Tools, Data, and Workflows for tutorials
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Contributing to the Galaxy Training Material
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Generating PDF artefacts of the website
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Contributing to the Galaxy Training Material
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Principles of learning and how they apply to training and teaching
✍️
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Contributing to the Galaxy Training Material
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Running the GTN website locally
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Contributing to the Galaxy Training Material
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Design and plan session, course, materials
✍️
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Contributing to the Galaxy Training Material
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Contributing with GitHub via its interface
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Contributing to the Galaxy Training Material
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Creating a new tutorial
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Contributing to the Galaxy Training Material
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Contributing with GitHub via command-line
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Contributing to the Galaxy Training Material
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Including a new topic
✍️
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Contributing to the Galaxy Training Material
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Creating content in Markdown
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Contributing to the Galaxy Training Material
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Creating Interactive Galaxy Tours
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Sequence analysis
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Mapping
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Sequence analysis
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Quality Control
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Single Cell
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Pre-processing of Single-Cell RNA Data
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Single Cell
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Clustering 3K PBMCs with Scanpy
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Ecology
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Regional GAM
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Ecology
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Species distribution modeling
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Development in Galaxy
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Data source integration
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Statistics and machine learning
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Machine learning: classification and regression
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Metagenomics
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Assembly of metagenomic sequencing data
✍️
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Metagenomics
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Metatranscriptomics analysis using microbiome RNA-seq data
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Metagenomics
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Identification of the micro-organisms in a beer using Nanopore sequencing
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Metagenomics
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Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
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Metagenomics
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16S Microbial Analysis with mothur (short)
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Metagenomics
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Analyses of metagenomics data - The global picture
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Metagenomics
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Metatranscriptomics analysis using microbiome RNA-seq data (short)
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Metagenomics
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16S Microbial Analysis with mothur (extended)
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Transcriptomics
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RNA Seq Counts to Viz in R
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Transcriptomics
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CLIP-Seq data analysis from pre-processing to motif detection
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Transcriptomics
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Reference-based RNA-Seq data analysis
✍️
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Using Galaxy and Managing your Data
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Understanding Galaxy history system
📝
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Using Galaxy and Managing your Data
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RStudio in Galaxy
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Introduction to Galaxy Analyses
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A short introduction to Galaxy
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Introduction to Galaxy Analyses
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From peaks to genes
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Introduction to Galaxy Analyses
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Upload data to Galaxy
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Variant Analysis
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Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data
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Variant Analysis
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Exome sequencing data analysis for diagnosing a genetic disease
Slides
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Development in Galaxy
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Galaxy from a developer point of view
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Epigenetics
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Introduction to ChIP-Seq data analysis
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Epigenetics
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ChIP-seq data analysis
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Contributing to the Galaxy Training Material
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Contributing with GitHub via command-line
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Contributing to the Galaxy Training Material
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Creating Slides
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Contributing to the Galaxy Training Material
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Overview of the Galaxy Training Material
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Sequence analysis
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Quality Control
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Development in Galaxy
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Galaxy Interactive Tours
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Development in Galaxy
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Tool Shed: sharing Galaxy tools
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Development in Galaxy
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Tool development and integration into Galaxy
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Metagenomics
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Introduction to metagenomics
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Transcriptomics
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Introduction to Transcriptomics
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Galaxy Server administration
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Docker and Galaxy
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Introduction to Galaxy Analyses
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Introduction to Galaxy
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Variant Analysis
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Introduction to Variant analysis
News
26 January 2023
Authors: 
Bérénice Batut
Engy Nasr
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.
Full Story
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!”
Full Story
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:
Full Story
29 September 2021
Authors: Bérénice Batut
Do you use Galaxy for Training? Have your say! Please take a few minutes to let us know about your training experiences.
Full Story
28 July 2021
Authors: Bérénice Batut
As you have probably already seen, a feedback form is embedded on the bottom of each tutorial.
Full Story
30 June 2021
Authors: Bérénice Batut
Wolfgang Maier
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.
Full Story
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.
Full Story
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!
Full Story
Bérénice BatutEngy Nasr
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.
Full Story
Saskia Hiltemann
Helena RascheOur new paper about the Galaxy Training Network has been published this week in Plos Computational Biology: “Galaxy Training: A powerful framework for teaching!”
Full Story
Anthony Bretaudeau
Yvan Le Bras
Fotis E. Psomopoulos
The CarpentriesAs 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:
Full Story
Bérénice Batut
Do you use Galaxy for Training? Have your say! Please take a few minutes to let us know about your training experiences.
Full Story
Bérénice Batut
As you have probably already seen, a feedback form is embedded on the bottom of each tutorial.
Full Story
Bérénice BatutWolfgang Maier
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.
Full Story
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.
Full Story
Jennifer Hillman-Jackson
Delphine Lariviere
Anna Syme
Maria DoyleEvery 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!
Full Story