GTN Smörgåsbord: A Global Galaxy Course

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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

Start the Workshop!

Welcome! Click the button below to start the workshop!

Practical Information

When: February 15-19, 2021 (all time zones)
Who: Open for everybody
Cost: Free
Format: Virtual and asynchronous. All training session are pre-recorded, you can work through these at your own pace, with instructors available online for support
Support: Slack Channel (invite link)
Contact: Saskia Hiltemann
Organized by: The Galaxy Training Network (GTN), CINECA, The Gallantries Project, The Galaxy Project, Australian BioCommons, Erasmus Medical Center, Albert-Ludwigs-Universität Freiburg, Avans Hogeschool, 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, SANBI/UWC, EOSC-Nordic, Institut Français de Bioinformatique, Birla Institute of Scientific Research.

Registration

Please fill out the registration form to sign up for this course.

Over 1100 Participants and counting!

Note: Click here for exact numbers.

Program

Welcome & Practical Information

Topic	Presentor
Welcome & Course Information	Saskia Hiltemann
Get set up for the course
Meet & Join the Galaxy Community!	The Global Galaxy Community

Day 1: Introduction to Galaxy and NGS analysis

Today we start by introducing the Galaxy Platform, and show you how to analyze your NGS data using Galaxy. Today we have a mixture of lecutres, demos, and hands-on tutorials.

Topic	Presentor
Icebreaker: Introduce yourself in Slack!
A Very Short Introduction to Galaxy	Anton Nekrutenko
Your First Galaxy Analysis	Dave Clements
Demo: NGS Data Logistics using SARS-CoV-2 data	Anton Nekrutenko
Quality Control: Intro	Florian Heyl
Quality Control: Hands-on!	Florian Heyl
Mapping: Introduction	Peter van Heusden
Mapping: Hands-on!	Peter van Heusden
Genome Assembly: Introduction	Simon Gladman
Genome Assembly: Hands-on!	Anna Syme
Wrap up & Socialize

Day 2: Introduction to RNA-Seq analysis with Galaxy and R

Today we dive into (bulk) RNA-seq analysis. We will walk you through an end-to-end analysis and Galaxy, and show you how to perform downstream analysis on the results using Rstudio in Galaxy.

Topic	Presentor
Icebreaker: Say Hi in Slack!
Introduction to RNA-Seq	Fotis E. Psomopoulos
Reference-based RNA-seq Analysis	Bérénice Batut
Starting Rstudio in Galaxy	Fotis E. Psomopoulos
Introduction to R	Fotis E. Psomopoulos
Advanced R in Galaxy	Fotis E. Psomopoulos
Visualisation: RNASeq postprocessing with R	Fotis E. Psomopoulos
Wrap up & Socialize

Day 3: Single-cell RNA-Seq Analysis

Today's videos provide a short demo of the analysis, please work through the tutorials on your own first to get all the details and background information, and refer to the videos if you get stuck.

Topic	Presentor
Icebreaker: Let us know you've joined in Slack!
An introduction to scRNA-seq data analysis	These slides are narrated by AWS Polly.
Understanding Barcodes	Wendi Bacon
Pre-processing of 10X Single-Cell RNA Datasets	Wendi Bacon
Clustering 3K PBMCs with Scanpy	Wendi Bacon
Wrap up & Socialize

Day 4: Proteomics

Today we explore the world of proteomics! Today we have a mixture of lectures, hands-on tutorials, and workflow demonstrations. The FAQ document provides links to example histories if you would like to explore the outputs of the demos yourself.

Topic	Presentor
Icebreaker: Say Hi in Slack!
Introduction to mass spectrometry based proteomics data analysis	These slides are narrated by AWS Polly.
Maxquant + MSstats on a clinical cohort	Melanie Föll
Introduction to Proteogenomics	Timothy J. Griffin
Proteogenomics 1: Database Creation	James Johnson
Proteogenomics 2: Database search	Andrew Rajczewski
Proteogenomics 3: Novel peptide analysis	Subina Mehta
Metaproteomics	Pratik Jagtap
Wrap up & Socialize

Choose Your Own Adventure!

Today YOU create the program. Below are set of suggested tutorials. Some have videos, some are self-study tutorials. All have experienced instructors online for support. Want to try something else from the GTN website? Also fine! We will do our best to help you with it.

Video Tutorials

Topic	Presentor
Icebreaker: Say Hi in Slack!
Variant Analysis: M. Tuberculosis Variant Analysis (Lecture)	Peter van Heusden
Variant Analysis: M. Tuberculosis Variant Analysis (Hands-on!)	Peter van Heusden
Metagenomics: 16S Microbial Analysis with mothur (Lecture)	Saskia Hiltemann
Metagenomics: 16S Microbial Analysis with mothur (Hands-on!)	Saskia Hiltemann
Wetlab Demo: Genomic DNA sequencing by Oxford Nanopore MinIon	Miaomiao Zhou
Clinical Microbiomics: Nanopore Whole Bacterial Genome Sequencing	Astrid Heikema
Metagenomics: Antibiotic Resistance Detection with Nanopore Data	Willem de Koning
Assembly: Unicycler assembly of SARS-CoV-2 genome	Cristóbal Gallardo
Climate: Functionally Assembled Terrestrial Ecosystem Simulator (FATES): Lecture	These slides are narrated by AWS Polly.
Climate: Functionally Assembled Terrestrial Ecosystem Simulator (FATES): Hands-on!	Anne Fouilloux
Circos Visualisation in Galaxy: Intro	Helena Rasche
Circos Visualisation in Galaxy: Hands-on!	Helena Rasche
Genome Annotation: Annotation of a prokaryotic genome: Slides	These slides are narrated by AWS Polly.
Genome Annotation: Annotation of a prokaryotic genome: Hands-on!	Anthony Bretaudeau
Proteomics: ProteoRE tool for Functional Analysis of a Protein List	Yves Vandenbrouck

Supported Tutorials (Self-Study)

These tutorials do not have videos, but experienced instructors will be online today to help you with them

Topic	Presentor
Genomic Data Visualization with JBrowse	Helena Rasche
Ecology: Compute and analyze biodiversity metrics with PAMPA toolsuite	Coline Royaux Yvan Le Bras
Epigenetics: ATAC-Seq data analysis	Hans-Rudolf Hotz Lucille Delisle Florian Heyl
Proteomics: ProteoRE tool for biomarker discovery	Yves Vandenbrouck Florence Combes
Cheminformatics: Protein-ligand docking	Simon Bray
Cheminformatics: Running molecular dynamics simulations using GROMACS	Simon Bray

All other Tutorials

Please also feel free to explore all the other tutorials on the GTN website, and do any that sound interesting to you. Our instructors will do their best to support you in any of these tutorials.

All done?

Please feel free to hang around in Slack and talk to us and the rest of the Galaxy community! Thanks for joining!!

Topic	Presentor
Wrap up & Socialize
Useful links: Stay involved in the Galaxy Community!	The Global Galaxy Community
Feedback Survey, Certificates & GCC2021

After the Course

All these materials will remain online, so you can continue working on them for as long as you want. The only difference will be that you should ask your questions on the GTN Gitter channel, instead of Slack.

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.