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 StoryBérénice Batut
Affiliations
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.
GitHub Activity
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.
- Contributing to the Galaxy Training Material
- Foundations of Data Science
- Development in Galaxy
- Microbiome
- Sequence analysis
- Teaching and Hosting Galaxy training
- Transcriptomics
- Variant Analysis
- Detection of AMR genes in bacterial genomes
- Gallantries Grant - Intellectual Output 2 - Large-scale data analysis, and introduction to visualisation and data modelling
- Gallantries Grant - Intellectual Output 4 - Data analysis and modelling for evidence and hypothesis generation and knowledge discovery
- Gallantries Grant - Intellectual Output 5 - Train-the-Trainer and mentoring programme
- Metagenomics data processing and analysis for microbiome
- Train the Trainers
Tutorials
- Assembly / Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data) ✍️
- Assembly / Assembly of metagenomic sequencing data ✍️
- Assembly / Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data ✍️
- Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data (short)
- Microbiome / Identification of the micro-organisms in a beer using Nanopore sequencing ✍️
- Microbiome / Taxonomic Profiling and Visualization of Metagenomic Data ✍️
- Microbiome / Analyses of metagenomics data - The global picture
- Microbiome / Building an amplicon sequence variant (ASV) table from 16S data using DADA2 ✍️
- Microbiome / Metatranscriptomics analysis using microbiome RNA-seq data
- Microbiome / 16S Microbial Analysis with mothur (extended)
- Microbiome / 16S Microbial Analysis with mothur (short)
- Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition ✍️
- Microbiome / Assembly of metagenomic sequencing data ✍️
- Microbiome / Calculating α and β diversity from microbiome taxonomic data ✍️
- Development in Galaxy / Adding and updating best practice metadata for Galaxy tools using the bio.tools registry ✍️
- Development in Galaxy / Creation of an interactive Galaxy tools table for your community ✍️
- Development in Galaxy / Data source integration
- Contributing to the Galaxy Training Material / Creating Interactive Galaxy Tours
- Contributing to the Galaxy Training Material / Contributing with GitHub via its interface
- Contributing to the Galaxy Training Material / Generating PDF artefacts of the website
- Contributing to the Galaxy Training Material / Contributing with GitHub via command-line
- Contributing to the Galaxy Training Material / Tools, Data, and Workflows for tutorials
- Contributing to the Galaxy Training Material / Creating a new tutorial
- Contributing to the Galaxy Training Material / Design and plan session, course, materials ✍️
- Contributing to the Galaxy Training Material / Running the GTN website locally
- Contributing to the Galaxy Training Material / Including a new topic ✍️
- Contributing to the Galaxy Training Material / Creating content in Markdown ✍️
- Contributing to the Galaxy Training Material / Principles of learning and how they apply to training and teaching ✍️
- Epigenetics / Identification of the binding sites of the Estrogen receptor
- Epigenetics / Formation of the Super-Structures on the Inactive X
- Single Cell / Clustering 3K PBMCs with Scanpy
- Single Cell / Pre-processing of Single-Cell RNA Data
- Transcriptomics / Reference-based RNA-Seq data analysis ✍️
- Transcriptomics / CLIP-Seq data analysis from pre-processing to motif detection
- Transcriptomics / RNA Seq Counts to Viz in R ✍️
- Statistics and machine learning / Machine learning: classification and regression
- Introduction to Galaxy Analyses / From peaks to genes ✍️
- Introduction to Galaxy Analyses / A short introduction to Galaxy 📝
- Introduction to Galaxy Analyses / Upload data to Galaxy
- Variant Analysis / Exome sequencing data analysis for diagnosing a genetic disease
- Variant Analysis / Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data ✍️
- Using Galaxy and Managing your Data / Understanding Galaxy history system 📝
- Using Galaxy and Managing your Data / RStudio in Galaxy ✍️
- Ecology / Species distribution modeling
- Ecology / Checking expected species and contamination in bacterial isolate ✍️
- Ecology / Regional GAM
- Genome Annotation / Bacterial Genome Annotation ✍️
- Genome Annotation / Essential genes detection with Transposon insertion sequencing
- Genome Annotation / Identification of AMR genes in an assembled bacterial genome ✍️
- Sequence analysis / Quality and contamination control in bacterial isolate using Illumina MiSeq Data ✍️
- Sequence analysis / Mapping
- Sequence analysis / Quality Control ✍️
- Teaching and Hosting Galaxy training / Teaching experiences
- Teaching and Hosting Galaxy training / Hybrid training ✍️
- Teaching and Hosting Galaxy training / Running a workshop as instructor
- Teaching and Hosting Galaxy training / Motivation and Demotivation ✍️
- Teaching and Hosting Galaxy training / Training techniques to enhance learner participation and engagement ✍️
- Teaching and Hosting Galaxy training / Live Coding is a Skill
- Teaching and Hosting Galaxy training / Asynchronous training ✍️
- Teaching and Hosting Galaxy training / Assessment and feedback in training and teachings ✍️
- Teaching and Hosting Galaxy training / Teaching online ✍️
- Teaching and Hosting Galaxy training / Set up a Galaxy for Training
- Teaching and Hosting Galaxy training / Organizing a workshop
- Teaching and Hosting Galaxy training / Train-the-Trainer: putting it all together ✍️
- Foundations of Data Science / One protein along the UniProt page ✍️
- Foundations of Data Science / Advanced R in Galaxy ✍️
- Foundations of Data Science / R basics in Galaxy 📝
- Foundations of Data Science / Learning about one gene across biological resources and formats ✍️
Slides
- Development in Galaxy / Galaxy from a developer point of view
- Galaxy Server administration / Docker and Galaxy
- Microbiome / Introduction to Microbiome Analysis
- Development in Galaxy / Galaxy Interactive Tours
- Development in Galaxy / Tool Shed: sharing Galaxy tools
- Development in Galaxy / Tool development and integration into Galaxy
- Contributing to the Galaxy Training Material / Contributing with GitHub via command-line
- Contributing to the Galaxy Training Material / Overview of the Galaxy Training Material
- Contributing to the Galaxy Training Material / Creating Slides
- Epigenetics / Introduction to ChIP-Seq data analysis
- Epigenetics / ChIP-seq data analysis
- Transcriptomics / Introduction to Transcriptomics
- Introduction to Galaxy Analyses / Introduction to Galaxy
- Variant Analysis / Introduction to Variant analysis
- Sequence analysis / Quality Control ✍️
Video Recordings
- Assembly / Assembly of metagenomic sequencing data 💬 🗣
- Microbiome / Identification of the micro-organisms in a beer using Nanopore sequencing 🗣
- Microbiome / Antibiotic resistance detection 💬
- Microbiome / Taxonomic Profiling and Visualization of Metagenomic Data 🗣
- Microbiome / Assembly of metagenomic sequencing data 💬 🗣
- Contributing to the Galaxy Training Material / Creating a new tutorial 🗣
- Transcriptomics / Reference-based RNA-Seq data analysis 🗣
- Genome Annotation / Bacterial Genome Annotation 💬 🗣
- Sequence analysis / Quality Control 💬
Events
News
Author(s) | Saskia Hiltemann Helena Rasche Bérénice Batut |
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 StoryAuthor(s) | 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 StoryAuthor(s) | Bérénice Batut |
As you have probably already seen, a feedback form is embedded on the bottom of each tutorial.
Full StoryAuthor(s) | 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 StoryAs 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 StoryAuthor(s) | Bérénice Batut Saskia Hiltemann Helena Rasche |
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 StoryAuthor(s) | 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 StoryAuthor(s) | Helena Rasche Bérénice Batut |
Infrastructure | Helena Rasche |
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.
Full StoryAuthor(s) | Helena Rasche |
Infrastructure | Saskia Hiltemann Helena Rasche Bérénice Batut |
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.
Full StoryAuthor(s) | Bérénice Batut Helena Rasche Saskia Hiltemann |
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.
Full StoryAuthor(s) | Bérénice Batut |
The GTN hosts its 400th tutorial: Building an amplicon sequence variant (ASV) table from 16S data using DADA2
Full StoryAuthor(s) | Saskia Hiltemann Helena Rasche |
Infrastructure | Saskia Hiltemann Helena Rasche Bérénice Batut |
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.
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