Anthony Bretaudeau
Yvan Le Bras
Coline Royaux
Fotis E. Psomopoulos
Bérénice Batut
12 October 2021
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 StoryGallantries: Bridging Training Communities in Life Science, Environment and Health
Members
These individuals have noted that they are affiliated in some way with this organisation. This list is non-exhaustive, and randomly ordered.
Former Members
These individuals have noted that they previously were affiliated in some way with this organisation. This list is non-exhaustive.
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.
Tutorials
- Assembly / Genome assembly using PacBio data 💵
- Microbiome / Identification of the micro-organisms in a beer using Nanopore sequencing 💵
- Microbiome / Taxonomic Profiling and Visualization of Metagenomic Data 💵
- Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition 💵
- Microbiome / Assembly of metagenomic sequencing data 💵
- Contributing to the Galaxy Training Material / Design and plan session, course, materials 💵
- 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 💵
- Visualisation / Genomic Data Visualisation with JBrowse 💵
- Visualisation / Ploting a Microbial Genome with Circos 💵
- Visualisation / Visualisation with Circos 💵
- Climate / Getting your hands-on earth data 💵
- Transcriptomics / RNA-seq Alignment with STAR 💵
- Transcriptomics / RNA Seq Counts to Viz in R 💵
- Statistics and machine learning / Introduction to Machine Learning using R 💵
- Introduction to Galaxy Analyses / Data Manipulation Olympics 💵
- Using Galaxy and Managing your Data / RStudio in Galaxy 💵
- Using Galaxy and Managing your Data / Workflow Reports 💵
- Ecology / Metabarcoding/eDNA through Obitools 💵
- Ecology / Obis marine indicators 💵
- Ecology / QGIS Web Feature Services 💵
- Ecology / Biodiversity data exploration 💵
- Ecology / Visualize EBV cube data with Panoply netCDF viewer 💵
- Ecology / Compute and analyze biodiversity metrics with PAMPA toolsuite 💵
- Genome Annotation / Refining Genome Annotations with Apollo (eukaryotes) 💵
- Genome Annotation / Refining Genome Annotations with Apollo (prokaryotes) 💵
- Genome Annotation / Creating an Official Gene Set 💵
- Genome Annotation / Genome annotation with Funannotate 💵
- Genome Annotation / Masking repeats with RepeatMasker 💵
- Genome Annotation / Functional annotation of protein sequences 💵
- Sequence analysis / Quality Control 💵
- Teaching and Hosting Galaxy training / Hybrid training 💵
- 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 / 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 / Train-the-Trainer: putting it all together 💵
- Teaching and Hosting Galaxy training / Course Builder 💵
- Foundations of Data Science / Data visualisation Olympics - Visualization in R 💵
- Foundations of Data Science / Advanced Python 💵
- Foundations of Data Science / Advanced CLI in Galaxy 💵
- Foundations of Data Science / CLI Educational Game - Bashcrawl 💵
- Foundations of Data Science / Variant Calling Workflow 💵
- Foundations of Data Science / Data Manipulation Olympics - SQL 💵
- Foundations of Data Science / Data Manipulation Olympics - JQ 💵
- Foundations of Data Science / Advanced R in Galaxy 💵
- Foundations of Data Science / R basics in Galaxy 💵
- Foundations of Data Science / SQL Educational Game - Murder Mystery 💵
- Foundations of Data Science / Introduction to Python 💵
- Foundations of Data Science / dplyr & tidyverse for data processing 💵
- Foundations of Data Science / Plotting in Python 💵
- Foundations of Data Science / Version Control with Git 💵
- Foundations of Data Science / CLI basics 💵
Slides
- Assembly / An introduction to get started in genome assembly and annotation 💵
- Visualisation / Circos 💵
- Genome Annotation / Refining Genome Annotations with Apollo 💵
- Sequence analysis / Mapping 💵
- Sequence analysis / Quality Control 💵
Learning Pathways
- Genome annotation for eukaryotes 💵
- Genome annotation for prokaryotes 💵
- Introduction to Galaxy and Ecological data analysis 💵
- Introduction to Galaxy and Sequence analysis 💵
- From R to Machine Learning; an introductory course 💵
- Gallantries Grant - Intellectual Output 1 - Introduction to data analysis and -management, statistics, and coding 💵
- Gallantries Grant - Intellectual Output 2 - Large-scale data analysis, and introduction to visualisation and data modelling 💵
- Gallantries Grant - Intellectual Output 3 - Data stewardship, federation, standardisation, and collaboration 💵
- 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 💵
- Introductory Python 💵
- Introductory SQL 💵
- Train the Trainers 💵
Events
News
14 December 2021
| Author(s) |
 
Helena Rasche
|
The Galaxy Training Network will now support annotating Funding Agencies on training materials. This is part of our ongoing effort to better annotate how people are contributing to the GTN and recognise all of the sources of contribution.
Full Story
28 January 2022
| Author(s) |
Helena Rasche
|
Further building on the work in the automatic Jupyter Notebook, we’ve now re-written the Jupyter export to be faster, and more importantly added support for R and RMarkdown! Check out an example material. Here we take the content of the tutorial, written like normal GTN markdown, and we automatically convert it to Jupyter Notebooks and now RMarkdown documents! Check out the documentation on how to setup your tutorials to support this.
Full Story
12 April 2022
| Author(s) |
Helena Rasche
|
It has been a long discussed feature within the GTN Tutorial Author Community: how can we provide trainees with choice in their tutorials, and how can we as trainers not duplicate large tutorials just to show a slightly different path at one point?
Full Story
8 February 2023
| Author(s) |
Helena Rasche
|
Did you ever wonder which was the number one most used tool in the GTN? There is a new page of Top Tools where we list all of the top tools in the GTN, and which tutorials use them. We guessed “upload1”, but it seems like not every author annotates that step explicitly in their tutorial, and of course it doesn’t appear in the workflows which we also scan to create this tool listing.
Full Story
21 March 2023
| Author(s) |
Helena Rasche
Lucille Delisle
|
Numerous other training groups keep “Trainer Directories” as a way to help students meet trainers in their area, especially for hosting workshops for their local community. There have been a handful of attempts at this in the past, both in galaxyproject/galaxy-maps and in a Google Map on the GTN homepage.
Full Story
13 April 2023
| Author(s) |
Saskia Hiltemann
Helena Rasche
|
Introducing Learning Pathways in the GTN! Learning pathways are sets of tutorials curated for you by community experts to form a coherent set of lessons around a topic, building up knowledge step by step.
Full Story
14 June 2024
| Author(s) |
Saskia Hiltemann
Helena Rasche
|
| Infrastructure |
Saskia Hiltemann
Helena Rasche |
Many GTN tutorials already have recordings. These recordings were made by members of the community for a variety of (online) training events. Up until now, this video library were part of the Gallantries Project. We have now integrated this video library directly into the GTN, and made it even easier to add video recordings to GTN tutorials or slide decks! Just use a Google Form to submit your video recordings!
Full Story
External Links
Website: https://www.erasmusplus.nl Grant ID: 2020-1-NL01-KA203-064717Favourite Topics
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