GTN Smörgåsbord: A Global Galaxy Course
In February 2021, we will organize a global 5-day Galaxy Training event showcasing a wide variety of GTN (Galaxy Training Network) tutorials. This will be an online event, spanning all time zones. All training sessions are pre-recorded, so you can work through them at your own pace, and manage your own time. A large community of GTN trainers will be available via online support to answer all your questions.
The program covers a general introduction to the Galaxy platform, NGS Analysis (DNA-seq and RNA-seq), Proteomics, and also features a Choose your own adventure day on Friday, where we encourage you to explore all the tutorials that the GTN training repository has to offer, and follow those that are of interest to you. The GTN tutorials cover a wide range of scientific topics, from NGS to ecology, climate science, machine learning, visualization, and many more. All the tutorials can be found on the GTN website
Practical Information
When: February 15-19, 2021 (all time zones)
Who: Open for everybody
Cost: Free
Format: Virtual event, all training session are pre-recorded, you can work through these at your own pace, with instructors available online for support
Support: Slack Channel (link will be provided here before the course)
Contact: Saskia Hiltemann
Organized by: The Galaxy Training Network (GTN), CINECA, The Galaxy Project, Australian BioCommons, Erasmus Medical Center,
Albert-Ludwigs-Universität Freiburg, Avans Hogeschool, The Gallantries Project, University of Melbourne, The GalaxyP Team, The ProteoRE Team, INAB-CERTH, EMBL-EBI, Institute of Surgical Pathology - University Medical Center Freiburg, Centre National pour la Recherche Scientifique (CNRS), Clermont Auvergne University.
Registration
Please fill out the registration form to sign up for this course.
Program
Day 1: Introduction to Galaxy and NGS analyses
| Topic | Presentor | Type | Duration | Video | GTN material |
|---|---|---|---|---|---|
| Welcome & Course information | Saskia Hiltemann | lecture | 15m | ||
| What is Galaxy? | Anton Nekrutenko | lecture | 30m | ||
| Using Galaxy: An introduction to NGS analysis | Anton Nekrutenko | practical | 1h30m | ||
| Quality Control | Florian Heyl | practical | 1h30m | Tutorial | |
| Mapping | Saskia Hiltemann | lecture | 30m | Slides | |
| Mapping | Saskia Hiltemann | practical | 45m | Tutorial | |
| Assembly | Simon Gladman | practical |
Day 2: Reference-based RNA-seq analysis with Galaxy and R
| Topic | Presentor | Type | Duration | Video | GTN material |
|---|---|---|---|---|---|
| Introduction to RNA-seq | Fotis Psomopoulos / Bérénice Batut | lecture | 30m | Slides | |
| Reference-based RNA-seq with Galaxy | Fotis Psomopoulos / Bérénice Batut | practical | 3h | Tutorial | |
| Introduction to R in Galaxy | Fotis Psomopoulos / Bérénice Batut | practical | 1h | Tutorial | |
| Advanced R in Galaxy | Fotis Psomopoulos / Bérénice Batut | practical | 30m | Tutorial | |
| RNA-seq post-processing with R | Fotis Psomopoulos / Bérénice Batut | practical | 1h | Tutorial |
Day 3: Single-cell RNA-seq
| Topic | Presentor | Type | Duration | Video | GTN material |
|---|---|---|---|---|---|
| Introduction to scRNA-seq | Wendi Bacon / Mehmet Tekman | lecture | 30m | ||
| Understanding Barcodes | Wendi Bacon / Mehmet Tekman | practical | 2h | Tutorial | |
| Pre-processing of 10X Single-Cell RNA Datasets | Wendi Bacon / Mehmet Tekman | practical | 2h | Tutorial | |
| Clustering 3K PBMCs with Scanpy | Wendi Bacon / Mehmet Tekman | practical | 3h | Tutorial |
Day 4: Proteomics
| Topic | Presentor | Type | Duration | Video | GTN material |
|---|---|---|---|---|---|
| Introduction to Proteomics and Protein identification | Melanie Föll | lecture | 20min | ||
| Introduction to Protein quantification and stats | Melanie Föll | lecture | 15min | ||
| Maxquant + MSstats on a clinical cohort | Melanie Föll | practical | 1h30m | ||
| Introduction to Proteogenomics | Tim Griffin | lecture | 15min | ||
| Proteogenomics 1: Database Creation | James Johnson | practical | 1h | Tutorial | |
| Proteogenomics 2: Database search | Andrew Rajczewski | practical | 45min | Tutorial | |
| Proteogenomics 3: Novel peptide analysis | Subina Mehta | practical | 1h | Tutorial | |
| Metaproteomics | Pratik Jagtap | practical | 1h | Tutorial | |
| ProteoRE workflow: Functional analysis of a large protein list | Florence Combes & Yves Vandenbrouck | practical | 1h |
Day 5: Choose your own Adventure!
This day is a little bit different; today, YOU create the program. There are a few different options here:
- Follow one of the video tutorials available (see below)
- Follow one of the recommended tutorials; these do not have videos, but there are expert instructors online for support today
- Follow any other tutorial from the GTN website that looks interesting to you, and we will do our best to guide you!
NOTE: more training sessions may be added here over time!
Video Tutorials
| Topic | Presentor | Type | Duration | Video | GTN material |
|---|---|---|---|---|---|
| Antibiotic Resistance Detection with Nanopore Data | Astrid Heikema / Willem de Koning | lecture & practical | 2h | Tutorial | |
| 16S Microbial analysis with mothur | Saskia Hiltemann | practical | 2h | Tutorial | |
| Circos visualization in Galaxy | Helena Rasche / Saskia Hiltemann | practical | 1h | Slides, Tutorial | |
| Annotation of a prokaryotic genome | Anthony Bretaudeau | Lecture & Practical | 2h | ||
| Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads | Cristóbal Gallardo | practical | 4h | Tutorial |
Supported Tutorials
These tutorials do not have videos, but there are experienced instructors online in Slack to help you!
| Tutorial | Instructor | Duration | GTN material |
|---|---|---|---|
| Genomic Data Visualization with JBrowse | Helena Rasche | 1h | Tutorial |
| Ecology: PAMPA toolsuite | Coline Royaux | 2h | Tutorial |
| ProteoRE tool for biomarkers discovery | Florence Combes / Yves Vandenbrouck | 1h | Tutorial |
Instructors welcome!
Are you a trainer and would you like to teach (record) a GTN training session for the Choose your own Adventure day? Please see the instructors page for more information.
Acknowledgements
This Global Galaxy course is only possible thanks to a Global network of instructors and institutes.
