Welcome everybody, and thank you for joining the GCC training week!

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.

Schedule

For this training week there is no fixed schedule, instead we provide a set of modules for you to choose from.

  • This week YOU make the schedule, YOU decide which tutorials to follow. YOU decide when to start, stop, and take breaks.
  • New to Galaxy? We suggest you start with the “Introduction to Galaxy” module, followed by the “Inroduction to NGS Analysis” module.
  • Unsure which tutorial to follow? Feel free to ask us for recommendations in Slack!

Training Modules

Scroll down to see all available tutorials, or jump directly to a module:
Note: Problems viewing this page? Try the simple view instead.

Welcome & Practical Information

Lecture

Video Length: 25m
Subtitles By: Saskia Hiltemann
Description: Start here; we will go over all the important things to know to get the most out of this workshop

Speaker

shiltemann
Saskia Hiltemann

Supporting Materials

  • Slides: Welcome & Course Information
  • 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! (Channel: #general )
  • Finished the session? - Let us know that you've finished it, and what you thought of it! On Slack: (Channel: #general ). Thanks!
  • Enjoyed it? - Like the video on YouTube, Tweet, and follow the GTN on Twitter! @gxytraining
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Galaxy logo
Register for a Galaxy Account


Create an account on one of the following Galaxy servers:

You can just pick the one nearest to you. Every tutorial will list which of these servers you can use for it.



tiaas logo
Sign up for TIaaS


Training Infrastructure as a Service (TIaaS) helps Galaxy workshops run smoothly. The procedure for this is different depending on the server you are on:

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



Slack Logo
Join Slack Chat!


Slack is where you can ask all your questions

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.

Certificates of attendance can be requested after the training week.

NOTE: You can follow as few or as many training sessions as you want, we will give you a personalized certificate listing all the sessions you attended.

In order to obtain a certificate please make sure to:

  1. Keep all your Galaxy histories
    • We will ask you to provide links to the histories for all sessions you followed
  2. Answer the icebreakers question on Slack every day
  3. Be active on Slack!
    • Let us know when you are starting with a session in the session’s dedicated Slack channel
    • Talk about the session! Get stuck? Have a question about the science? want to discuss anything? do it in Slack!
    • Whenever you finish a session, let us know on Slack that you have completed the tutorial, and let us know what you thought of it!

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

galaxycommunity
The Global Galaxy Community

Supporting Materials

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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

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

nekrut
Anton Nekrutenko

Supporting Materials

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Webinar Series: Galaxy Resources For..

Each of the 4 webinars in this series highlights avaialble Galaxy resources for a different audience. These videos are a nice way to get an overview of what Galaxy has to offer for different types of users.


..Researchers

Video Length: 1h10m
Subtitles By: We apologize for lack of captions on this video. If you are reliant on captions, please check back here soon.
Description: Wondering how to get started, or how to do a particular type of analysis, or how to scale to thousands of datasets? This webinar will highlight how to find the resources and help you need for each of these questions and more.

Speaker



..Educators and Trainers

Video Length: 1h10m
Subtitles By: Saskia Hiltemann
Description: Galaxy is an exceptional resource for teaching bioinformatics and other data sciences. The Galaxy Platform itself makes sophisticated analysis tools and workflows accessible to learners without requiring them to become system administrators or learn command line interfaces. Galaxy is a graphical user interface that only requires a browser, and allows students and teachers to focus on concepts, rather than compute infrastructure.


..Tool Developers

Video Length:
Subtitles By: We apologize for lack of captions on this video. If you are reliant on captions, please check back here soon.
Description: Galaxy is an excellent platform for increasing the visibility and use of computational tools in any domain that Galaxy has been applied to. If you develop computational analysis or visualization tools then this webinar will demonstrate how porting your tools to Galaxy can significantly increase their visibility and adoption.

Speaker

blankenberg
Daniel Blankenberg
abretaud
Anthony Bretaudeau
peternovak
peternovak


..Administrators & Infrastructure Providers

Video Length:
Subtitles By: We apologize for lack of captions on this video. If you are reliant on captions, please check back here soon.
Description: Galaxy can empower your community to create and run their own sophisticated and repeatable data analyses and visualizations, without requiring them to learn command line interfaces or Linux systems administration. If you are interested in helping your researchers help themselves with their data analyses, then this webinar is for you. We will cover resources available in the Galaxy ecosystem to help those who setup and maintain production Galaxy servers.

Supporting Materials

  • 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! @gxytraining
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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


Supported Servers

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Tutorial

Video Length: 1h15m
Subtitles By: Anne Fouilloux
Description: This video tutorial will provide a non-genomics based first look at the Galaxy platform, how to use it, and discusses how you can get support for your data analysis.

Speaker

annefou
Anne Fouilloux

Supporting Materials

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Advanced Galaxy Features

These tutorials cover some more advanced Galaxy features

Tutorial

Video Length: 22m
Subtitles By: We apologize for lack of captions on this video. If you are reliant on captions, please check back here soon.
Description: Through a series of examples, this tutorial aims to familiarize the reader with building Galaxy collections from tabular data containing URLs, sample sheets, list of accessions or identifiers, etc..

Speaker

assuntad23
Assunta DeSanto

Supporting Materials

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Instructors

The following instructors are available online this week for support for this session:

Tutorial

Video Length: 30m
Subtitles By: Simon Bray
Description: This is a more technical tutorial which will teach you how to run workflows from the command line and scale your analyses. If you are on Windows, you will need WSL/WSL2 setup before this session.

Supporting Materials

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Instructors

The following instructors are available online this week for support for this session:

Introduction to NGS Analysis

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

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

nekrut
Anton Nekrutenko

Supported Servers

Supporting Materials

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Lecture and Hands-on Tutorial

This session covers the basics about how to assess and improve the quality of your sequencing data.


Lecture

Video Length: 40m
Subtitles By: Yvonne Hiltemann, Nadia Goué, Helena Rasche
Description: This lecture goes over the concepts involved in assessing the quality of your sequencing data.


Tutorial

Video Length: 1h10m
Subtitles By: Bérénice Batut, Nadia Goué, Saskia Hiltemann
Description: In this tutorial you will get some hand-on experience performing a quality assessment on sequencing data.

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Lecture and Hands-on Tutorial

Mapping sequencing reads to a reference genome is often the next step after QC. This session covers the basic concepts of mapping and the practical will guide you through performing a mapping step on sequending data.


Lecture

Video Length: 10m
Subtitles By: Daniel Blankenberg
Description: This lecture covers the basic concepts involved in mapping sequencing reads to a reference genome.

Speaker

pvanheus
Peter van Heusden


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

pvanheus
Peter van Heusden

Supported Servers

Supporting Materials

  • Slides: Mapping
  • 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! (Channel: #1-4_mapping )
  • Finished the session? - Let us know that you've finished it, and what you thought of it! On Slack: (Channel: #1-4_mapping ). Thanks!
  • Enjoyed it? - Like the video on YouTube, Tweet, and follow the GTN on Twitter! @gxytraining
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Lecture and Hands-on Tutorial

When there is no reference genome available for your organism, you will have to assemble the short reads into larger segments (contigs).


Lecture

Video Length: 25m
Subtitles By: Saskia Hiltemann, Helena Rasche
Description: This lecture walks you through the basic concepts involved in assembling a genome from short-read sequencing data.

Speaker



Tutorial

Video Length: 35m
Subtitles By: Anna Syme
Description: In this tutorial, you will assemble a chloroplast genome using a combination of short and long read data.

Speaker


Supported Servers

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Advanced NGS Analysis

Tutorial

Video Length: 25m
Subtitles By: Mehmet Tekman
Description: This tutorial guides you through the preprocessing of sequencing data of bronchoalveolar lavage fluid (BALF) samples obtained from early COVID-19 patients in China. Since such samples are expected to be contaminated signficantly with human sequenced reads, the goal is to enrich the data for SARS-CoV-2 reads by identifying and discarding reads of human origin before trying to assemble the viral genome sequence.

Speaker


Supported Servers

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Lecture & Hands-on Tutorial

Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs, pseudogenes, control regions, direct and inverted repeats, insertion sequences, transposons and other mobile elements.


Lecture

Video Length: 3m
Subtitles By: Anthony Bretaudeau
Description: Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs, pseudogenes, control regions, direct and inverted repeats, insertion sequences, transposons and other mobile elements.

Speaker

awspolly
These slides are narrated by AWS Polly.


Tutorial

Video Length: 20m
Subtitles By: Anthony Bretaudeau
Description: In this tutorial we will use Prokka to annotate a draft genome sequence. Prokka finds and annotates features (both protein coding regions and RNA genes, i.e. tRNA, rRNA) present on on a sequence. Prokka can be used to annotate bacterial, archaeal and viral genomes quickly, generating standard output files in GenBank, EMBL and gff formats.”

Speaker

abretaud
Anthony Bretaudeau

Supporting Materials

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Tutorial

Video Length: 20m
Subtitles By: Anthony Bretaudeau
Description:

Speaker

abretaud
Anthony Bretaudeau

Supporting Materials

  • 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! @gxytraining
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Lecture & Hands-on Tutorial

In many eukaryotic organisms, such as humans, the genome is tightly packed and organized with the help of nucleosomes (chromatin). A nucleosome is a complex formed by eight histone proteins that is wrapped with ~147bp of DNA. When the DNA is being actively transcribed into RNA, the DNA will be opened and loosened from the nucleosome complex. Many factors, such as the chromatin structure, the position of the nucleosomes, and histone modifications, play an important role in the organization and accessibility of the DNA. Consequently, these factors are also important for the activation and inactivation of genes. Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq) is a method to investigate the accessibility of chromatin and thus a method to determine regulatory mechanisms of gene expression. The method can help identify promoter regions and potential enhancers and silencers.


Lecture

Video Length: 15m
Subtitles By: Lucille Delisle
Description: This lecture will introduce the basic concepts involved in ATAC-Seq analysis.


Tutorial

Video Length: 1h50m
Subtitles By: We apologize for lack of captions on this video. If you are reliant on captions, please check back here soon.
Description: This tutorial will walk you through a ATAC-Seq data analysis.

Supported Servers

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Instructors

The following instructors are available online this week for support for this session:

Tutorial

Video Length:
Subtitles By: We apologize for lack of captions on this video. If you are reliant on captions, please check back here soon.
Description: Traditionally, after a list of run accessions has been filtered on the NCBI website, the accessions are used to download and extract fastq using the SRA toolkit to enter into the next steps of the workflow. A newer compressed data type generated from raw submission data for sequences containing hits to SARS-CoV-2 is also accessible to Galaxy users from SRA in the Cloud.

SRA Aligned Read Format (SARFs) provides further output options other than basic fastq format, for example 1) contigs created from the raw reads in the run (FASTA format), 2) reads aligned back to the contigs (SAM format), 3) VCF files generated for each record relative to the SARS-CoV-2 RefSeq record.

We will demonstrate how to access just the reads (FASTA or FASTQ format), just the contigs, the reads aligned to the contigs and VCF files for selected SARFs. These formats can speed up workflows such as assembly and variant calling, and this data format is still referenced by the run accession and accessed using the SRA toolkit.

This workshop describes the SARF data objects and demonstrates a few ways to filter them using the metadata before accessing them and entering them into Galaxy workflows.

Speaker

NCBI
NCBI

Supporting Materials

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Instructors

The following instructors are available online this week for support for this session:

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

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

fpsom
Fotis E. Psomopoulos

Supporting Materials

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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.

Supported Servers

Supporting Materials

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Tutorial

Video Length: 48m
Subtitles By: Mallory Freeberg
Description: In this tutorial, we will use de novo transcript reconstruction to infer transcript structures from aligned reads. We will identify and quantify transcripts present in two different cell state and determine which transcripts are differentially expressed between the two states.

Speaker

malloryfreeberg
Mallory Freeberg

Supporting Materials

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Tutorial

Video Length:
Subtitles By: We apologize for lack of captions on this video. If you are reliant on captions, please check back here soon.
Description: In this tutorial, we will analyze RNA sequencing data to extract information about potential genes regulated in response to abiotic stress in plants. For this purpose, the chosen approach is the identification of genes with complementary regions to miRNAs upregulated in response to brassinosteroids.

Speaker

Supporting Materials

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RNA-Seq analysis using Rstudio in Galaxy

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

fpsom
Fotis E. Psomopoulos

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! (Channel: #2-2_intro-to-r )
  • Finished the session? - Let us know that you've finished it, and what you thought of it! On Slack: (Channel: #2-2_intro-to-r ). Thanks!
  • Enjoyed it? - Like the video on YouTube, Tweet, and follow the GTN on Twitter! @gxytraining
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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

fpsom
Fotis E. Psomopoulos

Supported Servers

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! (Channel: #2-2_intro-to-r )
  • Finished the session? - Let us know that you've finished it, and what you thought of it! On Slack: (Channel: #2-2_intro-to-r ). Thanks!
  • Enjoyed it? - Like the video on YouTube, Tweet, and follow the GTN on Twitter! @gxytraining
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Tutorial

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

Speaker

fpsom
Fotis E. Psomopoulos

Supported Servers

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! (Channel: #2-3_advanced_r )
  • Finished the session? - Let us know that you've finished it, and what you thought of it! On Slack: (Channel: #2-3_advanced_r ). Thanks!
  • Enjoyed it? - Like the video on YouTube, Tweet, and follow the GTN on Twitter! @gxytraining
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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

fpsom
Fotis E. Psomopoulos

Supported Servers

Supporting Materials

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Single-cell RNA-Seq Analysis

Lecture

Video Length: 20m
Subtitles By: Mehmet Tekman
Description: Single-cell RNA-seq analysis is a rapidly evolving field at the forefront of transcriptomic research, used in high-throughput developmental studies and rare transcript studies to examine cell heterogeneity within a populations of cells. The cellular resolution and genome wide scope make it possible to draw new conclusions that are not otherwise possible with bulk RNA-seq. Slides created by Mehmet Tekman.

Speaker

awspolly
These slides are narrated by AWS Polly.

Supporting Materials

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Instructors

The following instructors are available online this week for support for this session:

Walkthrough for Self-Study Session

Video Length: 30m
Subtitles By: We apologize for lack of captions on this video. If you are reliant on captions, please check back here soon.
Description:

Speaker

nomadscientist
Wendi Bacon

Supporting Materials

  • Tutorial: Generating a single cell matrix using Alevin
  • 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! @gxytraining
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Instructors

The following instructors are available online this week for support for this session:

Self-study with Video Walkthrough

Video Length: 30m
Subtitles By: We apologize for lack of captions on this video. If you are reliant on captions, please check back here soon.
Description:

Speaker

nomadscientist
Wendi Bacon

Supporting Materials

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Instructors

The following instructors are available online this week for support for this session:

Self-study with Video Walkthrough

Video Length: 10m
Subtitles By: We apologize for lack of captions on this video. If you are reliant on captions, please check back here soon.
Description:

Speaker

nomadscientist
Wendi Bacon

Supporting Materials

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Instructors

The following instructors are available online this week for support for this session:

Tutorial

Video Length: 55m
Subtitles By: Mehmet Tekman
Description:

Supporting Materials

  • Tutorial: Analysis of plant scRNA-Seq Data with Scanpy
  • 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! @gxytraining
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Instructors

The following instructors are available online this week for support for this session:

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.

Lecture

Video Length: 20m
Subtitles By: Melanie Föll
Description: This lecture will provide an introduction to mass spectrometry (MS) based proteomics analysis. Slides created by Melanie Föll.

Speaker

awspolly
These slides are narrated by AWS Polly.

Supporting Materials

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Instructors

The following instructors are available online this week for support for this session:

Tutorial

Video Length: 1h
Subtitles By: Saskia Hiltemann
Description: Modern mass spectrometry-based proteomics enables the identification and quantification of thousands of proteins. Therefore, quantitative mass spectrometry represents an indispensable technology for biological and clinical research. Statistical analyses are required for the unbiased answering of scientific questions and to uncover all important information in the proteomic data. In this training we will cover the full analysis workflow from label-free, data dependent acquisition (DDA) raw data to statistical results. We’ll use two popular quantitative proteomics software: MaxQuant and MSstats.

Supporting Materials

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Instructors

The following instructors are available online this week for support for this session:

Tutorial

Video Length:
Subtitles By: We apologize for lack of captions on this video. If you are reliant on captions, please check back here soon.
Description: Data Independent Acquisition Mass Spectrometry (DIA-MS) provides reproducible quantitative information as an improvement over the Data Dependent Acquisition (DDA). The EncyclopeDIA workflow tutorial will guide the user through the steps of a) conversion of the input DIA-MS RAW data files to mzML; b) the generation of a Chromatogram Library using the gas-phase fractionation (GPF) method and spectral library and c) generation of peptide and protein quantitation outputs.

Supporting Materials

  • 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! @gxytraining
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Instructors

The following instructors are available online this week for support for this session:

Tutorial

Video Length: 30m
Subtitles By: Florence Combes
Description: This tutorial covers an annotation pipeline for a protein list identified by LC-MS/MS experiments.

Speaker


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Instructors

The following instructors are available online this week for support for this session:

Self-Study Tutorial

A biomarker is a measurable biological component that can be routinely detected in clinical practice and reflects a disease state, response to therapeutic treatment, or other relevant biological state. In this tutorial we introduce successively the tools of this pipeline, and guide you to execute them in order to complete the entire pipeline on a concrete example.


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Instructors

The following instructors are available online this week for support for this session:

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


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Instructors

The following instructors are available online this week for support for this session:

Lecture and Demo

Video Length: 35m
Subtitles By: We apologize for lack of captions on this video. If you are reliant on captions, please check back here soon.
Description: The Coronavirus Disease 2019 (COVID-19) global pandemic has had a profound, lasting impact on the world’s population. Accurate and timely diagnosis of COVID-19 infection is an important step for providing care and containing its further spread. In this tutorial, attendees will be introduced to two workflows – a) database search workflow and b) peptide validation workflow. Attendees of the workshop will get an in-depth knowledge of the Galaxy workflows that detect SARS-CoV-2 peptides (10.1186/s12014-021-09321-1)) and co-infecting pathogen peptides (10.1021/acs.jproteome.0c00822).

Speaker

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Instructors

The following instructors are available online this week for support for this session:

Proteogenomics

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

Lecture

Video Length: 20m
Subtitles By: Emma Leith
Description: In this opening presentation, the basic components of proteogenomics are described, including the main steps in the bioinformatics analysis workflow that make up this approach and will be detailed in the following tutorials. Some examples of research questions that benefit from a proteogenomics approach are also highlighted.

Speaker

timothygriffin
Timothy J. Griffin

Supporting Materials

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Instructors

The following instructors are available online this week for support for this session:

Tutorial

Video Length: 40m
Subtitles By: Emma Leith
Description: In this tutorial, we will provide a walkthrough on how to generate a customized protein sequence database using RNA-Seq data. The resultant FASTA database contains sequences with single amino acid variants (SAVs), insertions and deletions (indels)and transcript assemblies (splicing variants). This database can then be used to identify protein sequence variants from the mass spectrometry data.

Speaker


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Instructors

The following instructors are available online this week for support for this session:

Demo

Video Length: 30m
Subtitles By: Emma Leith
Description: In this demonstration, we’re continuing the process of proteogenomic analysis. Here, we search mass spectrometry data against a custom proteogenomics FASTA database to create peptide spectral matches (PSMs) for each dataset; we also isolate non-canonical peptides from the resulting data for further analysis. If you would like to view the results yourself, we provide example histories in the FAQ document

Speaker

andrewr
Andrew Rajczewski

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The following instructors are available online this week for support for this session:

Demo

Video Length: 40m
Subtitles By: Subina Mehta
Description: In this demonstration, we will investigate the peptides that were identified during proteogenomics tutorial 2. We will identify the presence of novel proteoforms that are absent in the reference database, annotate the novel peptides and visualize them using the Multi-omics Visualization Platform (MVP). If you would like to view the results yourself, we provide example histories in the FAQ document

Speaker


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Instructors

The following instructors are available online this week for support for this session:

Microbial Analysis using Galaxy

Lecture & Hands-on Tutorial

Tuberculosis (TB) is an infectious disease caused by the bacterium Mycobacterium tuberculosis. According to the WHO, in 2018 there were 10.0 million new cases of TB worldwide and 1.4 million deaths due to the disease, making TB the world’s most deadly infectious disease.


Lecture

Video Length: 20m
Subtitles By: Saskia Hiltemann
Description: Tuberculosis (TB) is an infectious disease caused by the bacterium Mycobacterium tuberculosis. According to the WHO, in 2018 there were 10.0 million new cases of TB worldwide and 1.4 million deaths due to the disease, making TB the world’s most deadly infectious disease.

Speaker

pvanheus
Peter van Heusden


Tutorial

Video Length: 40m
Subtitles By: Peter van Heusden, Nadia Goué, Helena Rasche
Description: Variation in the genome of M. tuberculosis (Mtb) is associated with changes in phenotype, for example drug resistance and virulence. It is also useful for outbreak investigation as the single nucleotide polymorphisms (SNPs) in a sample can be used to build a phylogeny.

Speaker

pvanheus
Peter van Heusden

Supported Servers

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Lecture & Hands-on Tutorial

This lecture briefly introduces 16S sequencing, a popular technique used for taxonomic profiling of microbial communities.


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

shiltemann
Saskia Hiltemann


Tutorial

Video Length: 1h40m
Subtitles By: Saskia Hiltemann
Description: This lecture briefly introduces 16S sequencing, a popular technique used for taxonomic profiling of microbial communities.

Speaker

shiltemann
Saskia Hiltemann

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Demo

Video Length: 20m
Subtitles By: Saskia Hiltemann
Description: This video will show you the full process of sequencing a bacterial genome using the Oxford Nanopore MinION sequencer.

Speaker

miaomiaozhou88
Miaomiao Zhou

Supporting Materials

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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


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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

willemdek11
Willem de Koning

Supporting Materials

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Tutorial

Video Length:
Subtitles By: We apologize for lack of captions on this video. If you are reliant on captions, please check back here soon.
Description:

Speaker

Supporting Materials

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Instructors

The following instructors are available online this week for support for this session:

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


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Instructors

The following instructors are available online this week for support for this session:

Machine Learning

Lecture

Video Length: 15m
Subtitles By: We apologize for lack of captions on this video. If you are reliant on captions, please check back here soon.
Description: The lecture explains introductory concepts in machine learning such as supervised and unsupervised learning, classification and regression, hyperparameter optimisation, cross-validation, train, test and validation sets.

Supporting Materials

  • Slides: Introduction to Machine Learning
  • 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!
  • 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! @gxytraining
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Tutorial

Video Length: 1h50m
Subtitles By: We apologize for lack of captions on this video. If you are reliant on captions, please check back here soon.
Description: The talk includes a lecture followed by a hands-on session to apply multiple classification algorithms on the Quantitative structure-activity relationship (QSAR) dataset to predict the biodegradable activity of chemical compounds. QSAR models attempt to predict the activity or property of chemicals based on their chemical structure. To achieve this, a database of compounds is collected for which the property of interest is known. For each compound, molecular descriptors are collected which describe the structure (for example - molecular weight, number of nitrogen atoms, number of carbon-carbon double bonds). Using these descriptors, a model is constructed which is capable of predicting the property of interest for a new, unknown molecule. In this tutorial, we will use a database assembled from experimental data of the Japanese Ministry of International Trade and Industry to create a classification model by applying simple and complex classifiers to learn the nature of biodegradation. We will use this model to classify new molecules into one of two classes - biodegradable or non-biodegradable. Different visualisations are used to analyze the results after applying each classification algorithm. Hyperparameters of one of the classifiers are also optimised.

Supporting Materials

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Tutorial

Video Length: 1h29m
Subtitles By: We apologize for lack of captions on this video. If you are reliant on captions, please check back here soon.
Description: The talk includes a lecture followed by a hands-on session to apply multiple regression algorithms on the DNA-methylation dataset to predict biological age. In this tutorial, we will build a regression model for chronological age prediction, based on DNA methylation. This is based on the work of Jana Naue et al. 2017, in which biomarkers are examined to predict the chronological age of humans by analyzing the DNA methylation patterns. Different machine learning algorithms are used in this study to make an age prediction. It has been recognized that within each individual, the level of DNA methylation changes with age. This knowledge is used to select useful biomarkers from DNA methylation datasets. The CpG sites with the highest correlation to age are selected as the biomarkers (and therefore features for building a regression model). In this tutorial, specific biomarkers are analyzed by machine learning algorithms to create an age prediction model. Multiple visualisations are also used to analyse the predictions made by simple and complex regressors and hyperparameters of one of the regressors also optimised.

Supporting Materials

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Tutorial

Video Length:
Subtitles By: Maria Tsagiopoulou
Description:

Speaker

fpsom
Fotis E. Psomopoulos

Supporting Materials

  • 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! @gxytraining
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Deep Neural Networks Demystified

Tutorial

Video Length: 1h10m
Subtitles By: We apologize for lack of captions on this video. If you are reliant on captions, please check back here soon.
Description:

Speaker

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Tutorial

Video Length: 50m
Subtitles By: We apologize for lack of captions on this video. If you are reliant on captions, please check back here soon.
Description:

Speaker

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Tutorial

Video Length: 1h
Subtitles By: We apologize for lack of captions on this video. If you are reliant on captions, please check back here soon.
Description:

Speaker

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Visualisation in Galaxy

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

Tutorial

Video Length:
Subtitles By: We apologize for lack of captions on this video. If you are reliant on captions, please check back here soon.
Description: This tutorial will cover various ways to visualize your data in Galaxy

Speaker

shiltemann
Saskia Hiltemann

Supporting Materials

  • 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! @gxytraining
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Lecture & Hands-on Tutorial

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


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

hexylena
Helena Rasche


Tutorial

Video Length: 50m
Subtitles By: Beatriz Serrano-Solano, Helena Rasche, Saskia Hiltemann, Alireza Khanteymoori
Description: This tutorial will walk you through creating your own Circos Visualisaions in Galaxy. We will build the plot up step by step.

Speaker

hexylena
Helena Rasche

Supported Servers

Supporting Materials

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Instructors

The following instructors are available online this week for support for this session:
hexylena
Helena Rasche
shiltemann
Saskia Hiltemann

Tutorial

Video Length:
Subtitles By: We apologize for lack of captions on this video. If you are reliant on captions, please check back here soon.
Description: 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.

Speaker

hexylena
Helena Rasche

Supporting Materials

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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.

Lecture & Hands-on Tutorial

Terrestrial ecosystem models have been widely used to study the impact of climate changes on vegetation and terrestrial biogeochemical cycles in climate modelling community. They are also more and more applied in ecological studies to help ecologists to better understand the processes. But the technical challenges are still too high for most of the ecologists to use them. This practical aims at familiarizing you (especially ecologists) with running a terrestrial ecosystem model (i.e., CLM-FATES) at site-level in Galaxy and analyzing the model results.


Lecture

Video Length: 7m
Subtitles By: Anne Fouilloux
Description: Terrestrial ecosystem models have been widely used to study the impact of climate changes on vegetation and terrestrial biogeochemical cycles in climate modelling community. They are also more and more applied in ecological studies to help ecologists to better understand the processes. But the technical challenges are still too high for most of the ecologists to use them. This practical aims at familiarizing you (especially ecologists) with running a terrestrial ecosystem model (i.e., CLM-FATES) at site-level in Galaxy and analyzing the model results.

Speaker

awspolly
These slides are narrated by AWS Polly.


Tutorial

Video Length: 0h20m
Subtitles By:
Description: Terrestrial ecosystem models have been widely used to study the impact of climate changes on vegetation and terrestrial biogeochemical cycles in climate modelling community. They are also more and more applied in ecological studies to help ecologists to better understand the processes. But the technical challenges are still too high for most of the ecologists to use them. This practical aims at familiarizing you (especially ecologists) with running a terrestrial ecosystem model (i.e., CLM-FATES) at site-level in Galaxy and analyzing the model results.

Speaker

annefou
Anne Fouilloux

Supported Servers

Supporting Materials

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Tutorial

Video Length: 1h40m
Subtitles By: Simon Bray
Description: Molecular dynamics (MD) is a method to simulate molecular motion by iterative application of Newton’s laws of motion. This tutorial provides an introduction to using high-throughput molecular dynamics to study protein-ligand interaction, as applied to the N-terminal domain of Hsp90 (heat shock protein 90).

Supporting Materials

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Instructors

The following instructors are available online this week for support for this session:

Tutorial

Video Length:
Subtitles By: We apologize for lack of captions on this video. If you are reliant on captions, please check back here soon.
Description: Cheminformatics is the use of computational techniques and information about molecules to solve problems in chemistry. This involves a number of steps: retrieving data on chemical compounds, sorting data for properties which are of interest, and extracting new information. This tutorial will provide a brief overview of all of these, centered around protein-ligand docking, a molecular modelling technique.

Supported Servers

Supporting Materials

  • Tutorial: Protein-ligand docking
  • 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! (Channel: #5-m_cheminformatics )
  • Finished the session? - Let us know that you've finished it, and what you thought of it! On Slack: (Channel: #5-m_cheminformatics ). Thanks!
  • Enjoyed it? - Like the video on YouTube, Tweet, and follow the GTN on Twitter! @gxytraining
GTN logo

Tutorial

Video Length:
Subtitles By: We apologize for lack of captions on this video. If you are reliant on captions, please check back here soon.
Description: Molecular dynamics (MD) is a method to simulate molecular motion by iterative application of Newton’s laws of motion. It is often applied to large biomolecules such as proteins or nucleic acids. This is a introductory guide to using GROMACS (Abraham et al. 2015) in Galaxy to prepare and perform molecular dynamics on a small protein. For the tutorial, we will perform our simulations on hen egg white lysozyme.

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Supporting Materials

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Tutorial

Video Length:
Subtitles By: We apologize for lack of captions on this video. If you are reliant on captions, please check back here soon.
Description: This tutorial aims to present the PAMPA Galaxy workflow, how to use it to compute common biodiversity metrics from species abundance data and analyse it through generalized linear (mixed) models (GLM and GLMM). This workflow made up of 5 tools will allow you to process temporal series data that include at least year, location and species sampled along with abundance value and, finally, generate article-ready data products.

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Supporting Materials

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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!!

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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 )



Socializing Pictograph
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!



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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!

Self-Study Tutorial

This short video gives an overview of the worldwide Galaxy community, and different ways you can get involved!

Speaker

The Global Galaxy Community

The Global Galaxy Community

Supporting Materials

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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!



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Course Certificates


Do you require a certificate for this course? We will add a form to request your certificate here in about 1 week time.

You do not need to complete everything to receive a certificate. In the request form you will be able to indicate which parts you followed. We will also ask you to provide links to your Galaxy histories.



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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.




Acknowledgements

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

Presenters & Instructors & Facilitators & Community Caption Contributors

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

Institutions

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