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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:

  1. Follow one of the video tutorials available (see below)
  2. Follow one of the recommended tutorials; these do not have videos, but there are expert instructors online for support today
  3. 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.

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