Welcome! The course has ended, but you can still work through the materials on your own.

This course will familiarise you with the Galaxy Platform as a part of the Belgrade Bioinformatics Conference.

Thank you for joining this course! Everything you need for this course can be found on this webpage. More information including links to all training materials can be found by clicking on each session.

Join Slack Chat!

Welcome & Practical Information

Register for a Galaxy Account

Create an account on one of the following Galaxy servers:

🌍 UseGalaxy.eu (Europe)
🌏 UseGalaxy.org.au (Australia)
🌎 UseGalaxy.org (USA)

Join Slack Chat!

Slack is where you can ask all your questions

Invite link

You will find different channels here, one for each training session where you can ask your questions, as well as some more general channels for socializing, general discussions, feedback and more.

Video Tutorial

Video Length: 5m
Subtitles By: Saskia Hiltemann
Description: This short video gives an overview of the worldwide Galaxy community, and different ways you can get involved! *Video created by Beatriz Serrano-Solano*.

Speaker

The Global Galaxy Community

Supporting Materials

GalaxyProject Home: galaxyproject.org
Galaxy servers: Find a Galaxy server near you!
Galaxy Training Network: Start learning Galaxy
Support: Galaxy Help Forum
Galaxy Publications: Zotero
Galaxy Communities: Find and Join a community
Events: Galaxy Event Horizon
Mailing Lists: Stay informed of Galaxy activity!
Galaxy Working Groups: Find and join a WG
GitHub: galaxyproject
Gitter Chat: Start talking with the Galaxy Community!
GTN Gitter: Join the training discussion here!
PaperCuts: Monthly Collaboration Fest
GTN CoFest: Everybody Welcome!
Twitter: follow @galaxyproject
Twitter: follow the GTN @gxytraining
Ask an instructor - Have question about the training? Did you run into a problem? Just wanna chat? Ask away on Slack!
Finished the session? - Let us know that you've finished it, and what you thought of it! On slack!: . Thanks!
Enjoyed it? - Like the video on YouTube, Tweet, and follow the GTN on Twitter! @gxy-training. Hashtag: #usegalaxy

Introduction to Galaxy

Today we start by introducing the Galaxy Platform

Come say Hi in Slack! Let us know you are joining today and are getting started!

Icebreaker

Introduce yourself, tell us where you're joining from, and one thing about your surroundings (e.g. it's snowing outside, there's a squirrel on my porch, my cat is on my keyboard)

Post your answers on Slack in #social!

And of course please feel free to respond to anybody here, this channel is for socializing and getting to know each other :)

Video Tutorial

Video Length: 1h30m
Subtitles By: Dave Clements
Description: In this tutorial, we will walk you through your first (toy) analysis in Galaxy. This tutorial is aimed at familiarizing you with the Galaxy platform, and some basic NGS concepts.

Speaker

Dave Clements

Johns Hopkins University

Supporting Materials

Slides: Overview Prsentations
Tutorial: Introduction to Genomics and Galaxy
Tutorial: Extracting Workflows from Histories
FAQ Document - Have a question about this training? Check here to see if it has already been answered
Ask an instructor - Have question about the training? Did you run into a problem? Just wanna chat? Ask away on Slack! (Slack Channel: #galaxy-introduction )
Finished the session? - Let us know that you've finished it, and what you thought of it! On slack!: (Slack Channel: #galaxy-introduction ). Thanks!
Enjoyed it? - Like the video on YouTube, Tweet, and follow the GTN on Twitter! @gxy-training. Hashtag: #usegalaxy

Introduction to NGS

Here we show you how to analyze your NGS data using Galaxy.

Video Demo

Video Length: 15m
Subtitles By: Anton Nekrutenko
Description: In this demo video, we will show how to perform an NGS data analysis, using a SARS-CoV-2 example dataset. If you would like to run the full tutorial yourself, please find the link below (duration 1h-1.5h).

Speaker

Anton Nekrutenko

Penn State University

Supporting Materials

Tutorial: Demo: NGS Data Logistics using SARS-CoV-2 data
FAQ Document - Have a question about this training? Check here to see if it has already been answered
Ask an instructor - Have question about the training? Did you run into a problem? Just wanna chat? Ask away on Slack! (Slack Channel: #ngs_data-logistics )
Finished the session? - Let us know that you've finished it, and what you thought of it! On slack!: (Slack Channel: #ngs_data-logistics ). Thanks!
Enjoyed it? - Like the video on YouTube, Tweet, and follow the GTN on Twitter! @gxy-training. Hashtag: #usegalaxy

Video Lecture

Video Length: 40m
Subtitles By: Yvonne Hiltemann, Nadia Goué, Helena Rasche
Description: This tutorial covers the basics about how to assess and improve the quality of your sequencing data.

Speaker

Florian Heyl

Albert-Ludwigs-Universität Freiburg

Supporting Materials

Slides: Introduction to Quality Control
FAQ Document - Have a question about this training? Check here to see if it has already been answered
Ask an instructor - Have question about the training? Did you run into a problem? Just wanna chat? Ask away on Slack! (Slack Channel: #ngs_quality-control )
Finished the session? - Let us know that you've finished it, and what you thought of it! On slack!: (Slack Channel: #ngs_quality-control ). Thanks!
Enjoyed it? - Like the video on YouTube, Tweet, and follow the GTN on Twitter! @gxy-training. Hashtag: #usegalaxy

Video Tutorial

Video Length: 1h10m
Subtitles By: Bérénice Batut, Nadia Goué, Saskia Hiltemann
Description: Get hands-on experience assessing and improving the quality of your sequencing data in Galaxy.

Speaker

Florian Heyl

Albert-Ludwigs-Universität Freiburg

Supporting Materials

Tutorial: Quality Control: Hands-on!
FAQ Document - Have a question about this training? Check here to see if it has already been answered
Ask an instructor - Have question about the training? Did you run into a problem? Just wanna chat? Ask away on Slack! (Slack Channel: #ngs_quality-control )
Finished the session? - Let us know that you've finished it, and what you thought of it! On slack!: (Slack Channel: #ngs_quality-control ). Thanks!
Enjoyed it? - Like the video on YouTube, Tweet, and follow the GTN on Twitter! @gxy-training. Hashtag: #usegalaxy

Video Lecture

Video Length: 10m
Subtitles By: Daniel Blankenberg
Description: Mapping sequencing reads to a reference genome is often the next step after QC. This session covers the basic concepts of mapping.

Speaker

Peter van Heusden

SANBI/UWC

Supporting Materials

Slides: Mapping
FAQ Document - Have a question about this training? Check here to see if it has already been answered
Ask an instructor - Have question about the training? Did you run into a problem? Just wanna chat? Ask away on Slack! (Slack Channel: #ngs_mapping )
Finished the session? - Let us know that you've finished it, and what you thought of it! On slack!: (Slack Channel: #ngs_mapping ). Thanks!
Enjoyed it? - Like the video on YouTube, Tweet, and follow the GTN on Twitter! @gxy-training. Hashtag: #usegalaxy

Video Tutorial

Video Length: 20m
Subtitles By: Saskia Hiltemann
Description: In this tutorial you will map sequencing data to a reference genome, and explore the mapped reads in a genome browser.

Speaker

Peter van Heusden

SANBI/UWC

Supporting Materials

Tutorial: Mapping
FAQ Document - Have a question about this training? Check here to see if it has already been answered
Ask an instructor - Have question about the training? Did you run into a problem? Just wanna chat? Ask away on Slack! (Slack Channel: #ngs_mapping )
Finished the session? - Let us know that you've finished it, and what you thought of it! On slack!: (Slack Channel: #ngs_mapping ). Thanks!
Enjoyed it? - Like the video on YouTube, Tweet, and follow the GTN on Twitter! @gxy-training. Hashtag: #usegalaxy

Introduction to RNA-Seq analysis with Galaxy and R

Here 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.

Video Lecture

Video Length: 30m
Subtitles By: Nadia Goué, Saskia Hiltemann
Description: RNA sequencing is used to assess the expression levels of genes. This video introduces the important concepts related to RNA-seq analysis.

Speaker

Fotis E. Psomopoulos

INAB|CERTH

Supporting Materials

Slides: Introduction to Transcriptomics
FAQ Document - Have a question about this training? Check here to see if it has already been answered
Ask an instructor - Have question about the training? Did you run into a problem? Just wanna chat? Ask away on Slack! (Slack Channel: #transcriptomics_ref-based-rna-seq )
Finished the session? - Let us know that you've finished it, and what you thought of it! On slack!: (Slack Channel: #transcriptomics_ref-based-rna-seq ). Thanks!
Enjoyed it? - Like the video on YouTube, Tweet, and follow the GTN on Twitter! @gxy-training. Hashtag: #usegalaxy

Video Tutorial

Video Length: 2h30m
Subtitles By: Helena Rasche, Saskia Hiltemann
Description: In this tutorial we will walk you through the process of an RNA-seq analysis, comparing gene expression levels between different conditions and assessing impacted gene pathways.

Speaker

Bérénice Batut

Albert-Ludwigs-Universität Freiburg

Supporting Materials

Tutorial: Reference-based RNA-Seq data analysis
FAQ Document - Have a question about this training? Check here to see if it has already been answered
Ask an instructor - Have question about the training? Did you run into a problem? Just wanna chat? Ask away on Slack! (Slack Channel: #transcriptomics_ref-based-rna-seq )
Finished the session? - Let us know that you've finished it, and what you thought of it! On slack!: (Slack Channel: #transcriptomics_ref-based-rna-seq ). Thanks!
Enjoyed it? - Like the video on YouTube, Tweet, and follow the GTN on Twitter! @gxy-training. Hashtag: #usegalaxy

Video Demo

Video Length: 20m
Subtitles By: Saskia Hiltemann
Description: This tutorial will show you how you can start Rstudio from within Galaxy. This option is only available on Galaxy EU for the time being. If you are working on a different Galaxy server, you can use [RStudio Cloud](https://rstudio.cloud/)

Speaker

Fotis E. Psomopoulos

INAB|CERTH

Supporting Materials

FAQ Document - Have a question about this training? Check here to see if it has already been answered
Ask an instructor - Have question about the training? Did you run into a problem? Just wanna chat? Ask away on Slack! (Slack Channel: #transcriptomics_intro-to-r )
Finished the session? - Let us know that you've finished it, and what you thought of it! On slack!: (Slack Channel: #transcriptomics_intro-to-r ). Thanks!
Enjoyed it? - Like the video on YouTube, Tweet, and follow the GTN on Twitter! @gxy-training. Hashtag: #usegalaxy

Video Tutorial

Video Length: 50m
Subtitles By: Sébastien Fouilloux, Anne Fouilloux, Kaivan Kamali
Description: This tutorial will provide an introduction to using R with Rstudio in Galaxy.

Speaker

Fotis E. Psomopoulos

INAB|CERTH

Supporting Materials

Tutorial: R basics in Galaxy
FAQ Document - Have a question about this training? Check here to see if it has already been answered
Ask an instructor - Have question about the training? Did you run into a problem? Just wanna chat? Ask away on Slack! (Slack Channel: #transcriptomics_intro-to-r )
Finished the session? - Let us know that you've finished it, and what you thought of it! On slack!: (Slack Channel: #transcriptomics_intro-to-r ). Thanks!
Enjoyed it? - Like the video on YouTube, Tweet, and follow the GTN on Twitter! @gxy-training. Hashtag: #usegalaxy

Video Tutorial

Video Length: 1h
Subtitles By: Keith Suderman, Nadia Goué
Description: An advanced tutorial covering downstream analysis of RNA-seq data using R.

Speaker

Fotis E. Psomopoulos

INAB|CERTH

Supporting Materials

Tutorial: Advanced R in Galaxy
FAQ Document - Have a question about this training? Check here to see if it has already been answered
Ask an instructor - Have question about the training? Did you run into a problem? Just wanna chat? Ask away on Slack! (Slack Channel: #transcriptomics_advanced_r )
Finished the session? - Let us know that you've finished it, and what you thought of it! On slack!: (Slack Channel: #transcriptomics_advanced_r ). Thanks!
Enjoyed it? - Like the video on YouTube, Tweet, and follow the GTN on Twitter! @gxy-training. Hashtag: #usegalaxy

Video Tutorial

Video Length: 30m
Subtitles By: Helena Rasche, Saskia Hiltemann, Fotis E. Psomopoulos
Description: In this tutorial, we will visualize our RNA-seq analysis results using R.

Speaker

Fotis E. Psomopoulos

INAB|CERTH

Supporting Materials

Tutorial: RNA Seq Counts to Viz in R
FAQ Document - Have a question about this training? Check here to see if it has already been answered
Ask an instructor - Have question about the training? Did you run into a problem? Just wanna chat? Ask away on Slack! (Slack Channel: #transcriptomics_visualisation-with-r )
Finished the session? - Let us know that you've finished it, and what you thought of it! On slack!: (Slack Channel: #transcriptomics_visualisation-with-r ). Thanks!
Enjoyed it? - Like the video on YouTube, Tweet, and follow the GTN on Twitter! @gxy-training. Hashtag: #usegalaxy

Give us Feedback

Let us know what you thought about today! What did you like? Suggestions for improvements? Spot a typo? Tell us about it!

About the Materials? (slides, training manuals) use the feedback forms at the end of the tutorial
About other things? - Let us know in Slack (channel #feedback )

Socialize with each other!

Join one of the social sessions These include games, quizzes, discussions and more Check out all channels in Slack starting with #social- Want to organize something yourself? Tell us your idea and we will make a channel for it!

Meet the Galaxy Community!

Enjoying the course so far? Learn more about the Global Galaxy Community and how YOU can become part of it, by watching this video!

Visualisation

These tutorials go briefly into the visualisation aspect of Galaxy and how to use that in your workflows

Video Lecture

Video Length: 6m
Subtitles By: Assunta DeSanto, Saskia Hiltemann
Description: Circos is a popular tool for creating circular graphs to display genomic data. This video will introduce this tool and how to use it within Galaxy

Speaker

Helena Rasche

Avans Hogeschool

Supporting Materials

Tutorial: Visualisation with Circos
FAQ Document - Have a question about this training? Check here to see if it has already been answered
Ask an instructor - Have question about the training? Did you run into a problem? Just wanna chat? Ask away on Slack! (Slack Channel: #visualisation_circos )
Finished the session? - Let us know that you've finished it, and what you thought of it! On slack!: (Slack Channel: #visualisation_circos ). Thanks!
Enjoyed it? - Like the video on YouTube, Tweet, and follow the GTN on Twitter! @gxy-training. Hashtag: #usegalaxy

Video Tutorial

Video Length: 50m
Subtitles By: Beatriz Serrano-Solano, Helena Rasche, Saskia Hiltemann, Alireza Khanteymoori
Description: Circos is a popular tool for creating circular graphs to display genomic data. In this tutorial you will create a Circos plot for a cancer dataset

Speaker

Helena Rasche

Avans Hogeschool

Supporting Materials

Tutorial: Visualisation with Circos
FAQ Document - Have a question about this training? Check here to see if it has already been answered
Ask an instructor - Have question about the training? Did you run into a problem? Just wanna chat? Ask away on Slack! (Slack Channel: #visualisation_circos )
Finished the session? - Let us know that you've finished it, and what you thought of it! On slack!: (Slack Channel: #visualisation_circos ). Thanks!
Enjoyed it? - Like the video on YouTube, Tweet, and follow the GTN on Twitter! @gxy-training. Hashtag: #usegalaxy

Self-Study Tutorial

JBrowse is a popular Genome Browser. It can be used directly within Galaxy. You may have seen it in our Mapping tutorial on Day 1. This tutorial will go into more depth about JBrowse and how to use it to explore your genome.

Supporting Materials

Slides: JBrowse
Tutorial: Genomic Data Visualization with JBrowse
FAQ Document - Have a question about this training? Check here to see if it has already been answered
Ask an instructor - Have question about the training? Did you run into a problem? Just wanna chat? Ask away on Slack! (Slack Channel: #visualisation_jbrowse )
Finished the session? - Let us know that you've finished it, and what you thought of it! On slack!: (Slack Channel: #visualisation_jbrowse ). Thanks!
Enjoyed it? - Like the video on YouTube, Tweet, and follow the GTN on Twitter! @gxy-training. Hashtag: #usegalaxy

All done?

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

Give us Feedback

Let us know what you thought about today! What did you like? Suggestions for improvements? Spot a typo? Tell us about it!

About the Materials? (slides, training manuals) use the feedback forms at the end of the tutorial
About other things? - Let us know in Slack (channel #feedback )

Socialize with each other!

Meet the Galaxy Community!

Enjoying the course so far? Learn more about the Global Galaxy Community and how YOU can become part of it, by watching this video!

Feedback Survey

Please take a moment to fill out this feedback survey . This helps use improve this event in the future.

Survey (~5 minutes): Click here!

Want more training? Join the Galaxy Community Conference (GCC)!

GCC 2021 will be virtual this year, and feature a week of training. More information can be found here: VIB GCC2021 Event Page

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.