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In June/July 2021, we will organize a global 5-day Galaxy Training event as part of the Galaxy Community Conference (GCC2021)

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 24/7 online support to answer all your questions on Slack (a chat platform).

We will have 3 Training Tracks, aimed at scientists, developers and system administrators.

The Galaxy for Scientists Track will cover a wide range of topics including NGS Analysis (DNA & RNA), Proteomics, Microbial Analysis, Machine Learning, using R in Galaxy, Visualisation, Clinical workflows (including COVID-19), Nanopore Analysis, Single-cell RNASeq, Epigenetics, Climate Science, Cheminformatics, Advanced Galaxy features (scaling your analysis) and more! YOU can choose which of these training modules you want to follow during the week of training.

The Galaxy for Developers Track will teach you how Galaxy works internally (frontend and backend), how to add new features for Galaxy, how to build the best tools and visualisations, how to interact with the Galaxy API using BioBlend, and more!

The Galaxy for Administrators Track teaches you how to be a stellar admin, easily deploying a production-ready Galaxy with Ansible!

The Science and Developer tracks do not have a predetermined path, there will be a number of training “modules” covering a variety of topics from which you can choose to build your own training program for the week. For the Admin track, there is a set 5-day curriculum that will guide you through the end-to-end process of building your own Galaxy. For all 3 tracks you can work through the materials at your own pace and according to your own time schedule. A global community of instructors will be online to provide 24/7 support to help you with these trainin sessions.

Please see the full program below for more details on the training

Practical Information

When: June 28- July 2, 2021 (all time zones)
Who: Participants of the Galaxy Community Conference
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 and Remo
Contact: Saskia Hiltemann, Helena Rasche

Registration

Please sign up the Galaxy Community Conference to join this event. Registration can be done via the VIB Conference Website.

Program

Welcome! We will have 3 tracks during this GCC Training Week. A short overview of the program for each of these sessions can also be found below.

Note: The schedule is subject to change

Science Track

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

Introduction to Galaxy

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
A Very Short Introduction to Galaxy Anton Nekrutenko
A Longer Introduction to Galaxy Jennifer Hillman-Jackson
Galaxy 101 for Everyone Anne Fouilloux
Your First Galaxy Analysis Dave Clements

Introduction to NGS Analysis

This module will introduce the basics of NGS analysis, from cleaning your data to mapping and assembly

Topic Presentor
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

Advanced NGS Analysis

Topic Presentor
Assembly: Unicycler assembly of SARS-CoV-2 genome Cristóbal Gallardo
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
Genome Annotation with Apollo Anthony Bretaudeau
Epigenetics: ATAC-Seq data analysis Hans-Rudolf Hotz, Lucille Delisle, Florian Heyl
SRA Aligned Read Formats to Speed Up Analysis Jonathan Trow

RNA-Seq

The following module cover RNA-Seq analysis in Galaxy, from bulk RNA-seq to Single-cell RNA-Seq, from Quality control to Visualisation

Introduction to RNA-Seq

Topic Presentor
Introduction to RNA-Seq Fotis E. Psomopoulos
Reference-based RNA-seq Analysis Bérénice Batut
De novo transcriptome reconstruction with RNA-Seq Mallory Freeberg
Differential gene expression in plants Cristóbal Gallardo

RNA-Seq analysis using Rstudio in Galaxy

Topic Presentor
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

Single-cell RNA-Seq Analysis

Topic Presentor
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

Proteomics

In this module 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
Introduction to mass spectrometry based proteomics data analysis These slides are narrated by AWS Polly.
Maxquant + MSstats on a clinical cohort Melanie Föll
DIA Mass-spectrometry with EncyclopeDIA
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
ProteoRE tool for Functional Analysis of a Protein List Yves Vandenbrouck
ProteoRE tool for biomarker discovery Yves Vandenbrouck
Annotation and GO enrichment analysis of differentially expressed proteins Yves Vandenbrouck
Metaproteomics Introduction Pratik Jagtap
Metaproteomics Analysis of COVID-19 Data Pratik Jagtap

Microbial Analysis using Galaxy

Topic Presentor
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
Metagenomics Wetlab Demo: Genomic DNA sequencing by Oxford Nanopore MinIon Miaomiao Zhou
Metagenomics in the Clinic: Nanopore Whole Bacterial Genome Sequencing Astrid Heikema
Metagenomics: Antibiotic Resistance Detection with Nanopore Data Willem de Koning
Metatranscriptomics analysis using microbiome RNA-seq data Subina Mehta
Metaproteomics Introduction Pratik Jagtap
Metaproteomics Analysis of COVID-19 Data Pratik Jagtap

Machine Learning

Topic Presentor
Introduction to Machine Learning Alireza Khanteymoori
Introduction to Deep Learning Alireza Khanteymoori
Deep Neural Networks Demystified Kaivan Kamali
Clustering in Machine Learning Anup Kumar
Classification in Machine Learning Anup Kumar
Regression in Machine Learning Alireza Khanteymoori
Machine Learning using R in Galaxy Fotis E. Psomopoulos

Visualisation in Galaxy

This module will cover various ways of visualizing your data in Galaxy

Topic Presentor
Introduction to Visualisations in Galaxy Saskia Hiltemann
Circos Visualisation in Galaxy: Intro Helena Rasche
Circos Visualisation in Galaxy: Hands-on! Helena Rasche
Genomic Data Visualization with JBrowse Helena Rasche

Galaxy for Non-Genomics

Galaxy is widely used for analysis of genomics data, but is not limited to any scientific domain. This module covers some non-genomics topics such as Climate research and cheminformatics.

Topic Presentor
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
Cheminformatics: Protein-ligand docking Simon Bray
Cheminformatics: Running molecular dynamics simulations using GROMACS Simon Bray
Ecology: Compute and analyze biodiversity metrics with PAMPA toolsuite Coline Royaux, Yvan Le Bras

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.

Admin Track

intro

Topic Presentor
Welcome and introduction Helena Rasche

Day 1

Topic Presentor
Intro to Ansible Sergey Golitsynskiy
Ansible Martin Čech
Galaxy Ansible Introduction Helena Rasche
Part 0: Playbook Overview Helena Rasche
Part 1: Basic Installation Helena Rasche
Database Helena Rasche
SystemD Helena Rasche
Part 2: Towards Production Helena Rasche
Production Helena Rasche
Part 3: Advanced Install Helena Rasche

Day 2

Topic Presentor
Running jobs in Singularity Helena Rasche
Ephemeris (Intro) Catherine Bromhead
Ephemeris Catherine Bromhead
Users, Groups, and Quotas These slides are narrated by AWS Polly.
Reference Data (Intro) These slides are narrated by AWS Polly.
Reference Data Simon Gladman
Data Libraries Saskia Hiltemann

Day 3

Topic Presentor
Galaxy Cluster Computing (Intro) Helena Rasche
Connecting Galaxy to a compute cluster Helena Rasche
Mapping Jobs to Destinations Helena Rasche
Recording Job Metrics Helena Rasche

Day 4

Topic Presentor
Pulsar (Intro) Simon Gladman
Pulsar Simon Gladman
Storage management Gianmauro Cuccuru
DB Query (Intro) These slides are narrated by AWS Polly.
DB queries, command line & scripts
Monitoring (Intro) These slides are narrated by AWS Polly.
Monitoring: Telegraf, InfluxDB, Grafana Simon Gladman
Maintenance, Backup and Restore These slides are narrated by AWS Polly.

Day 5 - Choose Your OWN Adventure

Topic Presentor
Monitoring With Reports
Training Infrastructure as a Service (TIaaS) Helena Rasche
Interactive Tools Anthony Bretaudeau
Jenkins & Automation
Advanced Customisation
When things go wrong: Galaxy Server Troubleshooting
Python 2 to Python 3!
Tool Development
Dataset Collections
Developing your own Training

Developer Track

Welcome & Practical Information

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

Galaxy Tool Development

This module covers everything you need to start developing your own Galaxy Tools. This module will likely take you several days to complete.

Topic Presentor
Introduction to Galaxy Tool Development Björn Grüning, John Chilton, Nicola Soranzo
Conda Packages Björn Grüning, John Chilton, Nicola Soranzo
Galaxy Interactive Tool Development Daniel Blankenberg, Björn Grüning, Anthony Bretaudeau
BioBlend Nicola Soranzo
Galaxy Visualization Integration Dannon Baker
Data Sources Daniel Blankenberg, Helena Rasche
The GTN & Training Material Development Saskia Hiltemann, Bérénice Batut, Helena Rasche
Bring Your Own Tool Björn Grüning
Tool Factory
Introduction to running workflows with planemo Simon Bray

Galaxy Core Development

This covers everything you need to start developing for Galaxy, understanding the codebase, adding APIs, implementing features. This module will likely take you several days to complete.

Topic Presentor
Galaxy architecture John Chilton
Galaxy Backend & APIs John Chilton, Marius van den Beek, David Lopez, Sergey Golitsynskiy
Galaxy Frontend: Client, Vue, Webhooks Dannon Baker, , Björn Grüning, John Chilton, Assunta DeSanto,
CYOA

Acknowledgements

This Global Galaxy course is only possible thanks to a Global network of instructors and institutes.

Presenters & Instructors & Facilitators & Community Caption Contributors

hexylena
Helena Rasche
ic4f
Sergey Golitsynskiy
willemdek11
Willem de Koning
nomadscientist
Wendi Bacon
ennovytje
Yvonne Hiltemann
andrewr
Andrew Rajczewski
davelopez
David Lopez
cat-bro
Catherine Bromhead
assuntad23
Assunta DeSanto
nekrut
Anton Nekrutenko
kpoterlowicz
Krzysztof Poterlowicz
miaomiaozhou88
Miaomiao Zhou
eancelet
Estelle Ancelet
annefou
Anne Fouilloux
timothygriffin
Timothy J. Griffin
malloryfreeberg
Mallory Freeberg
delphine-l
Delphine Lariviere
galaxycommunity
The Global Galaxy Community
jennaj
Jennifer Hillman-Jackson
pvanheus
Peter van Heusden
nsoranzo
Nicola Soranzo
blankenberg
Daniel Blankenberg
kmurat1
Katarzyna Kamieniecka
fpsom
Fotis E. Psomopoulos
shiltemann
Saskia Hiltemann
abretaud
Anthony Bretaudeau
s3by01
Sébastien Fouilloux
mvdbeek
Marius van den Beek

Institutions

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