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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.

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
About Certificates
Meet & Join the Galaxy Community! The Global Galaxy Community

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
Webinar Series: Galaxy Resources For..
Your First Galaxy Analysis Dave Clements
Galaxy Intro for Everyone (non-genomics) Anne Fouilloux

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 with Apollo Anthony Bretaudeau
Epigenetics - ATAC-Seq data analysis
SRA Aligned Read Formats to Speed Up SARS-CoV-2 Analysis

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
Plant transcriptome analysis 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.
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 (Lecture) Peter van Heusden
Metagenomics: 16S Microbial Analysis with mothur 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 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

Topic Presentor
1: Feedforward Neural Networks Kaivan Kamali
2: Recurrent Neural Networks Kaivan Kamali
3: Convolutional Neural Networks Kaivan Kamali

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 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
Cheminformatics: High Throughput Molecular Dynamics and Analysis Simon Bray, Chris Barnett
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

Introduction

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
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
Storage management Gianmauro Cuccuru

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
Contributing to BioBlend Development Nicola Soranzo,
Galaxy Tools: From Conda Through Deployment - Planemo Tool Init & Structure Alex Ostrovsky
Galaxy Tools: From Conda Through Deployment - Writing the Wrapper Alex Ostrovsky
Galaxy Tools: From Conda Through Deployment - Planemo Testing
Galaxy Tools: From Conda Through Deployment - Contributing Alex Ostrovsky
ToolFactory: Generating Tools From Simple Scripts: Slides These slides are narrated by AWS Polly.
ToolFactory: Generating Tools From Simple Scripts: Quick Hands On These slides are narrated by AWS Polly.
ToolFactory: Generating Tools From Simple Scripts: Longer Hands-on Ross Lazarus
BioBlend Nicola Soranzo
The GTN & Training Material Development Saskia Hiltemann, Bérénice Batut, Helena Rasche, Simon Gladman
TBC: Galaxy Visualization Integration Dannon Baker

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, Nate Coraor, Dannon Baker
Debugging and testing Galaxy core Sergey Golitsynskiy, Assunta DeSanto, John Chilton, Marius van den Beek
Contributing extensions to Galaxy core (backend and frontend) John Chilton, Dannon Baker, Sergey Golitsynskiy, Assunta DeSanto, Marius van den Beek
CYOA

Acknowledgements

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

Presenters & Instructors & Facilitators & Community Caption Contributors

delphine-l
Delphine Lariviere
malloryfreeberg
Mallory Freeberg
pvanheus
Peter van Heusden
nekrut
Anton Nekrutenko
abretaud
Anthony Bretaudeau
MariaTsayo
Maria Tsagiopoulou
ddan
Dinh Duy An Nguyen
assuntad23
Assunta DeSanto
timothygriffin
Timothy J. Griffin
kmurat1
Katarzyna Kamieniecka
blankenberg
Daniel Blankenberg
ennovytje
Yvonne Hiltemann
nsoranzo
Nicola Soranzo
miaomiaozhou88
Miaomiao Zhou
s3by01
Sébastien Fouilloux
willemdek11
Willem de Koning
eancelet
Estelle Ancelet
fubar2
Ross Lazarus
jvanbraekel
Julien Van Braekel
hexylena
Helena Rasche
shiltemann
Saskia Hiltemann
rwinand
Raf Winand
andrewr
Andrew Rajczewski
jennaj
Jennifer Hillman-Jackson
annefou
Anne Fouilloux
fpsom
Fotis E. Psomopoulos
nomadscientist
Wendi Bacon
kpoterlowicz
Krzysztof Poterlowicz
ic4f
Sergey Golitsynskiy
cat-bro
Catherine Bromhead
mvdbeek
Marius van den Beek
davelopez
David Lopez
galaxycommunity
The Global Galaxy Community

Institutions

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