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:

🌍 GalaxyEU India

Sign up for TIaaS

Training Infrastructure as a Service (TIaaS) helps Galaxy workshops run smoothly. Click the link to join the event

🌍 GalaxyEU India

This lets us monitor how tools are doing, and can speed up your jobs!

Join Slack Chat!

Slack is where you can ask all your questions

Invite link
Chat channel: #event_functional_microbiome

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

Day 1 Tutorials: 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 Lecture/Demo

Video Length: 10m
Subtitles By: Anton Nekrutenko
Description: This video will introduce the Galaxy data analysis platform, and give a short demo on how to use it.

Speaker

Anton Nekrutenko

Penn State University

Supporting Materials

Slides: A Slightly Longer Introduction to 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: #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

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

Optional: Want to learn more?

Have some extra time? Try these tutorials as well

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

Day 2 Tutorials: Metagenomics of the Microbiome

Today we will perform taxonomic analysis of microbiome data using 16S amplicon sequencing, and analyze the microbiome for antibiotic resistance using Nanopore data

Video Lecture

Video Length: 15m
Subtitles By: Saskia Hiltemann
Description: This lecture briefly introduces 16S sequencing, a popular technique used for taxonomic profiling of microbial communities.

Speaker

Saskia Hiltemann

Erasmus Medical Center

Supporting Materials

Tutorial: Metagenomics: 16S Microbial Analysis with mothur (Lecture)
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: #5-b_16s-microbial-analysis )
Finished the session? - Let us know that you've finished it, and what you thought of it! On slack!: (Slack Channel: #5-b_16s-microbial-analysis ). Thanks!
Enjoyed it? - Like the video on YouTube, Tweet, and follow the GTN on Twitter! @gxy-training. Hashtag: #usegalaxy

Video Tutorial

Video Length: 1h40m
Subtitles By: Saskia Hiltemann
Description: In this tutorial you will perform the mothur MiSeq SOP (Standard Operating Procedure) in Galaxy.

Speaker

Saskia Hiltemann

Erasmus Medical Center

Supporting Materials

Tutorial: Metagenomics: 16S Microbial Analysis with mothur (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: #5-b_16s-microbial-analysis )
Finished the session? - Let us know that you've finished it, and what you thought of it! On slack!: (Slack Channel: #5-b_16s-microbial-analysis ). Thanks!
Enjoyed it? - Like the video on YouTube, Tweet, and follow the GTN on Twitter! @gxy-training. Hashtag: #usegalaxy

Optional: Want to learn more?

Can't get enough? Have some extra time? We recommend the following optional tutorials.

Video Lecture

Video Length: 30m
Subtitles By: Helena Rasche
Description: Nanopore Sequencing has many applications in a clinical setting. In this lecture, Astrid Heikema discusses how her group at the Erasmus Medical Center uses Nanopore for sequencing of bacterial Genomes.

Speaker

Astrid Heikema

Erasmus Medical Center

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: #5-a_antibiotic-resistance-detection-nanopore )
Finished the session? - Let us know that you've finished it, and what you thought of it! On slack!: (Slack Channel: #5-a_antibiotic-resistance-detection-nanopore ). Thanks!
Enjoyed it? - Like the video on YouTube, Tweet, and follow the GTN on Twitter! @gxy-training. Hashtag: #usegalaxy

Video Tutorial

Video Length: 45m
Subtitles By: Bérénice Batut
Description: This tutorial will guide you through the process of assembling your Nanopore-sequenced bacterial samples and determining the presence of antibiotic resistance genes.

Speaker

Willem de Koning

Erasmus Medical Center

Supporting Materials

Tutorial: Metagenomics: Antibiotic Resistance Detection with Nanopore 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: #5-a_antibiotic-resistance-detection-nanopore )
Finished the session? - Let us know that you've finished it, and what you thought of it! On slack!: (Slack Channel: #5-a_antibiotic-resistance-detection-nanopore ). Thanks!
Enjoyed it? - Like the video on YouTube, Tweet, and follow the GTN on Twitter! @gxy-training. Hashtag: #usegalaxy

Day 3 Tutorials: Metatranscriptomics

Today we dive into the analysis on the transcriptiomics level

Video Tutorial

Video Length: 1h30m
Subtitles By: , Saskia Hiltemann
Instructors , Pratik Jagtap, Timothy J. Griffin, Subina Mehta, Saskia Hiltemann, James Johnson, Andrew Rajczewski, , Emma Leith
Description: Metatranscriptomics analysis examines how the microbiome responds to the environment by studying the taxonomic composition and functional analysis of genes expressed by the microbiome, using microbial community RNASeq data and subsequent metatranscriptomics workflows. This workshop will introduce researchers to the basic concepts and tools from the ASaiM-MT workflow. ASaiM-MT provides a curated collection of tools to explore and visualize taxonomic and functional information from metatranscriptomic sequences.

Speaker

Supporting Materials

Slides from video: Metatranscriptomics analysis using microbiome RNA-seq data
Related Slides: Introduction to Metatranscriptomics
Tutorial: Metatranscriptomics analysis using microbiome RNA-seq data
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

Day 4 Tutorials: Metaproteomics

Video Tutorial

Video Length: 1h
Subtitles By: Emma Leith
Description: In this tutorial, the basic workflow for metaproteomics is described, which includes database search, seeking taxonomy information and functional analysis. Related metaproteomics and functional microbiome tools and GTN tutorials are also mentioned in this tutorial.

Speaker

Pratik Jagtap

University of Minnesota

Supporting Materials

Tutorial: Metaproteomics
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: #4-3_metaproteomics )
Finished the session? - Let us know that you've finished it, and what you thought of it! On slack!: (Slack Channel: #4-3_metaproteomics ). Thanks!
Enjoyed it? - Like the video on YouTube, Tweet, and follow the GTN on Twitter! @gxy-training. Hashtag: #usegalaxy

Optional: Want to learn more?

Can't get enough? Have some extra time? We recommend the following optional tutorials.

Self-Study Tutorial

Supporting Materials

Tutorial: Metaquantome 1: Data Creation
Tutorial: Metaquantome 2: Function
Tutorial: Metaquantome3: Taxonomy
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

All done?

Please feel free to hang around in Slack and talk to us and the rest of the Galaxy community! Thanks for joining!! For further learning, please see our full set of video tutorials below.

All GTN Video Tutorials

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.