GCC2021 Training Week

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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: For questions regarding registration, please contact the VIB Conference Team, for any other questions, 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.

Many people have had questions about tickets, so, here is a short guide of which tickets you need for which training tracks:

If you want to do admin training you need an admin ticket
If you want to do either science or developer training, you need a non-admin ticket.

Or as a table to list all of the combinations

Admin	Science	Dev	Which Tickets you need
No	No	No	None!
No	No	Yes	Non-admin
No	Yes	No	Non-admin
No	Yes	Yes	Non-admin
Yes	No	No	Admin
Yes	No	Yes	Admin + Non-admin
Yes	Yes	No	Admin + Non-admin
Yes	Yes	Yes	Admin + Non-admin

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.

Science Track
Admin Track
Developer Track

Note: The schedule is subject to change

Science Track: Overview table

Welcome & Practical Information

Start here. This will cover all the logistics and practical information for this training week.

Topic	Presentor
Welcome & Course Information	Helena Rasche, Saskia Hiltemann
Get set up for the course
About Certificates
Meet & Join the Galaxy Community!	The Global GTN Community
Daily Icebreaker Questions

Introduction to Galaxy

Start here if you are new to Galaxy. These videos will introduce you to the Galaxy platform, and walk you through your first analyses

Topic	Presentor
A Very Short Introduction to Galaxy	Anton Nekrutenko
Your First Galaxy Analysis (genomics-based)	Dave Clements
Galaxy Intro for Everyone (non-genomics)	Anne Fouilloux
Webinar Series: Galaxy Resources For..

Advanced Galaxy Features

These tutorials cover some more advanced Galaxy features

Topic	Presentor
Uploading data with the Rule Based Uploader	Assunta DeSanto
Running Workflows from the Command Line using Planemo	Simon Bray

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	Florian Heyl
Mapping	Peter van Heusden
Genome Assembly

Advanced NGS Analysis

Topic	Presentor
Assembly: Unicycler assembly of SARS-CoV-2 genome	Cristóbal Gallardo
Genome Annotation: Annotation of a prokaryotic genome
Genome Annotation: Refining Genome Annotations with Apollo	Anthony Bretaudeau
Epigenetics - ATAC-Seq data analysis
SRA Aligned Read Formats to Speed Up SARS-CoV-2 Analysis	Jonathan Trow

Transcriptomics

The following module cover transcriptomic 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
Whole transcriptome analysis of Arabidopsis thaliana	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
Visualization of RNA-Seq results with Volcano Plot in Galaxy and R	Maria Doyle

Single-cell RNA-Seq Analysis

Why smash tissues up to analyse them, when you can find what’s inside each individual cell? In these scRNA-seq tutorials, you’ll move from FASTQ to trajectory using the same dataset throughout – a case study of previously published, real mouse data. And for the plant enthusiasts, you’ll do the same thing in Arabidopsis! Enjoy life at a single cell scale!

Topic	Presentor
An introduction to scRNA-seq data analysis	These slides are narrated by AWS Polly.
Generating a single cell matrix using Alevin	Wendi Bacon
Filter, Plot and Explore Single-cell RNA-seq Data	Wendi Bacon
Trajectory Analysis using Python (Jupyter Notebook) in Galaxy	Wendi Bacon
Analysis of plant scRNA-Seq Data with Scanpy	Mehmet Tekman

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	Emma Leith, James Johnson, Pratik Jagtap
ProteoRE tool for Functional Analysis of a Protein List	Yves Vandenbrouck
ProteoRE tool for biomarker discovery
Metaproteomics Introduction	Pratik Jagtap
Pandemics Research using Mass Spectrometry	Timothy J. Griffin, Subina Mehta, Andrew Rajczewski, Pratik Jagtap

Proteogenomics

Proteogenomics utilizes a combination of proteomics, genomics, and transcriptomics to aid in the discovery and identification of peptides

Topic	Presentor
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

Microbial Analysis using Galaxy

Topic	Presentor
Variant Analysis: M. Tuberculosis Variant Analysis	Peter van Heusden
16S Microbial Analysis with mothur	Saskia Hiltemann
Antimicrobial Resistance Detection using Nanopore long-read sequencing
Metatranscriptomics analysis using microbiome RNA-seq data	Pratik Jagtap, Timothy J. Griffin, Subina Mehta, Saskia Hiltemann
Metaproteomics Introduction	Pratik Jagtap

Machine Learning

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

SARS-CoV-2 analysis

Here we have collected all the training sessions that cover SARS-CoV-2 analysis. These sessions also appear in other modules and cover a range of topics, but one thing they have in common is that they use SARS-CoV-2 or COVID-19 data.

Topic	Presentor
Demo: NGS Data Logistics using SARS-CoV-2 data	Anton Nekrutenko
SRA Aligned Read Formats to Speed Up SARS-CoV-2 Analysis	Jonathan Trow
Assembly: Unicycler assembly of SARS-CoV-2 genome	Cristóbal Gallardo
Pandemics Research using Mass Spectrometry	Timothy J. Griffin, Subina Mehta, Andrew Rajczewski, Pratik Jagtap

Plant data analysis

Here we have collected all the training sessions that cover plant data analysis. These sessions also appear in other modules and cover a range of topics, but one thing they have in common is that they use plant datasets.

Topic	Presentor
Whole transcriptome analysis of Arabidopsis thaliana	Cristóbal Gallardo
Analysis of plant scRNA-Seq Data with Scanpy	Mehmet Tekman

Visualisation in Galaxy

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

Topic	Presentor
Circos Visualisation	Helena Rasche
Genomic Data Visualization with JBrowse
Visualization of RNA-Seq results with Volcano Plot in Galaxy and R	Maria Doyle

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)
Cheminformatics: High Throughput Molecular Dynamics and Analysis	Simon Bray, Chris Barnett
Cheminformatics: Protein-ligand docking
Cheminformatics: Running molecular dynamics simulations using GROMACS
Ecology: Compute and analyze biodiversity metrics with PAMPA toolsuite

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 GTN Community
Feedback Survey & Certificates

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: Overview table

Introduction

Start here. This will cover all the logistics and practical information for this training week.

Topic	Presentor
Welcome to GCC2021 & Course Information	Helena Rasche, Saskia Hiltemann
Admin Training Logistics	Helena Rasche
About Certificates
Meet & Join the Galaxy Community!	The Global GTN Community
Webinar Series: Galaxy Resources For..

Introduction to Galaxy

Start here if you are new to Galaxy. These videos will introduce you to the Galaxy platform, and walk you through your first analyses

Topic	Presentor
A Very Short Introduction to Galaxy	Anton Nekrutenko
Galaxy Intro for Everyone (non-genomics)	Anne Fouilloux

Day 1

Topic	Presentor
Daily Icebreaker Question
Ansible
Installing Galaxy with Ansible	Helena Rasche

Day 2

Topic	Presentor
Daily Icebreaker Question
Running jobs in Singularity	Simon Gladman
Ephemeris	Catherine Bromhead
Users, Groups, and Quotas	These slides are narrated by AWS Polly.
Reference Data	These slides are narrated by AWS Polly.
Data Libraries	Saskia Hiltemann

Day 3

Topic	Presentor
Daily Icebreaker Question
Galaxy Cluster Computing	Helena Rasche
Mapping Jobs to Destinations	Helena Rasche

Day 4

Topic	Presentor
Daily Icebreaker Question
Pulsar	Simon Gladman
DB queries, command line & scripts	These slides are narrated by AWS Polly.
Monitoring: Telegraf, InfluxDB, Grafana
Maintenance, Backup and Restore	These slides are narrated by AWS Polly.
Upgrading Galaxy	Simon Gladman

Day 5 - Choose Your OWN Adventure

Topic	Presentor
Daily Icebreaker Question
Meet & Join the Galaxy Community!	The Global GTN Community
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
Storage management	Gianmauro Cuccuru

Developer Track: Overview table

Welcome & Practical Information

Start here. This will cover all the logistics and practical information for this training week.

Topic	Presentor
Welcome & Course Information	Helena Rasche, Saskia Hiltemann
Get set up for the course
About Certificates
Meet & Join the Galaxy Community!	The Global GTN Community
Webinar Series: Galaxy Resources For..
Daily Icebreaker Questions

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
Galaxy Tools: From Conda Through Deployment	Alex Ostrovsky
ToolFactory: Generating Tools From Simple Scripts

Galaxy Training Material Development

Here you can learn about contributing to the GTN’s development, adding new tutorials or slides, and correcting any typos you might spot in the training materials this week.

Topic	Presentor
The GTN & Training Material Development

Galaxy Core Development

Ever wanted to contribute features to Galaxy? Here you’ll learn a bit about how Galaxy works and how to debug issues in features in Galaxy.

Topic	Presentor
Debugging Galaxy

Galaxy Architecture Lectures

Here you’ll learn about the internals of Galaxy in a lecture from John Chilton

Topic	Presentor
Galaxy Architecture	John Chilton

Self-Study Galaxy Development

These tutorials don’t have video walkthroughs, but will all be supported by their authors during the week. So please work through these tutorials by yourself, and ask LOTS of questions in Slack!