Galaxy Training Video Session Library

This page shows you only the multi-video “sessions” of available GTN video tutorials, you might also be interested in the full video library which includes every single video known to the GTN Video Library.

All Training Sessions

Sessions are multi-video trainings often taught as a unit, for example a lecture video and a hands-on video from the same GTN tutorial.

Webinar

In this webinar series, we cover resources for different types of Galaxy users and audiences.

Galaxy Resources for.. Researchers (Webinar)

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.
Length: 1 hour 10 minutes
Captions: Saskia Hiltemann
Created: 21 April 2021
Materials:
Support:
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Speaker

Galaxy Resources for.. Educators (Webinar)

Description:

In this webinar series, we cover resources for different types of Galaxy users and audiences.
Length: 1 hour 10 minutes
Captions: Saskia Hiltemann
Created: 28 April 2021
Materials:
Support:
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Speakers

Galaxy Resources for.. Tool Developers (Webinar)

Description:

In this webinar series, we cover resources for different types of Galaxy users and audiences.
Length: 59 minutes
Captions: Helena Rasche
Created: 26 May 2021
Materials:
Support:
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Speakers

Galaxy Resources for.. Admins (Webinar)

Description:

In this webinar series, we cover resources for different types of Galaxy users and audiences.
Length: 1 hour 5 minutes
Captions: The Global Galaxy Community
Created: 12 May 2021
Materials:
Support:
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Speakers

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Tuberculosis

Webinar: Drug resistance prediction (Webinar)

Description:

Principles of drug resistance detection from genomic data
Length: 20 minutes
Captions: This is a non-GTN video, we cannot guarantee captions
Created: 1 January 2023
Support:
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Speaker

Webinar: Phylogenetic mutations (Webinar)

Description:

This video will introduce one special type of mutations to take into account when studying drug resistance patterns
Length: 15 minutes
Captions: This is a non-GTN video, we cannot guarantee captions
Created: 1 January 2023
Support:
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Speaker

Webinar: The Concept of Clustering (Webinar)

Description:

Main aspects of clustering analysis to infer transmission in MTBC
Length: 15 minutes
Captions: This is a non-GTN video, we cannot guarantee captions
Created: 1 January 2023
Support:
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Speaker

Webinar: genetic distance thresholds (Webinar)

Description:

Clustering as an approximation to infer transmission
Length: 15 minutes
Captions: This is a non-GTN video, we cannot guarantee captions
Created: 1 January 2023
Support:
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Speaker

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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.

M. tuberculosis Variant Analysis (Lecture)

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.
Length: 20 minutes
Captions: Saskia Hiltemann
Created: 15 February 2021
Materials:
Support:
Go to the video page to see all versions.

Speaker

M. tuberculosis Variant Analysis (Tutorial)

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.
Length: 40 minutes
Captions: Peter van Heusden, Nadia Goué, Helena Rasche
Created: 15 February 2021
Materials:
Support:
Supported Servers:
Learning Objectives:
  • How should we filter those variants
  • How can we predict drug resistance from those variants
  • How do we annotate those variants
Go to the video page to see all versions.

Speaker

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Sequence analysis

In this sesssion, we will walk you through the basics of quality checking your sequencing data. This session consists of a lecture followed by a hands-on tutorial.

Quality Control (Lecture)

Description:

This lecture goes over the concepts involved in assessing the quality of your sequencing data.
Length: 40 minutes
Captions: Yvonne Hiltemann, Nadia Goué, Helena Rasche
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • Assess short reads FASTQ quality using FASTQE 🧬😎 and FastQC
  • Assess long reads FASTQ quality using Nanoplot and PycoQC
  • Perform quality correction with Cutadapt (short reads)
  • Summarise quality metrics MultiQC
  • Process single-end and paired-end data
Go to the video page to see all versions.

Speaker

Quality Control (Tutorial)

Description:

In this tutorial you will get some hand-on experience performing a quality assessment on sequencing data.
Length: 50 minutes
Captions: Andrew Lonsdale
Created: 19 May 2023
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Assess short reads FASTQ quality using FASTQE 🧬😎 and FastQC
  • Assess long reads FASTQ quality using Nanoplot and PycoQC
  • Perform quality correction with Cutadapt (short reads)
  • Summarise quality metrics MultiQC
  • Process single-end and paired-end data
Go to the video page to see all versions.

Speaker

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In this sesssion, we will walk you through the basics of mapping your sequencing data to a reference genome. This session consists of a lecture followed by a hands-on tutorial.

Mapping (Lecture)

Description:

This lecture covers the basic concepts involved in mapping sequencing reads to a reference genome.
Length: 10 minutes
Captions: Daniel Blankenberg
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • You will learn what mapping is
  • A genome browser is shown that helps you to understand your data
Go to the video page to see all versions.

Speaker

Mapping (Tutorial)

Description:

In this tutorial you will map sequencing data to a reference genome, and explore the mapped reads in a genome browser.
Length: 20 minutes
Captions: Saskia Hiltemann
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • You will learn what mapping is
  • A genome browser is shown that helps you to understand your data
Go to the video page to see all versions.

Speaker

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Assembly

This session provides an introduction to Genome Assembly

An Introduction to Genome Assembly (Lecture)

Description:

This lecture walks you through the basic concepts involved in assembling a genome from short-read sequencing data.
Length: 25 minutes
Captions: Saskia Hiltemann, Helena Rasche
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • assemble some paired end reads using Velvet
  • examine the output of the assembly.
Go to the video page to see all versions.

Speaker

Chloroplast genome assembly (Lecture & Tutorial)

Description:

In this tutorial, you will assemble a chloroplast genome using a combination of short and long read data.
Length: 35 minutes
Captions: Anna Syme
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Assemble a chloroplast genome from long reads
  • Polish the assembly with short reads
  • Annotate the assembly and view
  • Map reads to the assembly and view
Go to the video page to see all versions.

Speaker

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Variant analysis

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.

M. tuberculosis Variant Analysis (Lecture)

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.
Length: 20 minutes
Captions: Saskia Hiltemann
Created: 15 February 2021
Materials:
Support:
Go to the video page to see all versions.

Speaker

M. tuberculosis Variant Analysis (Tutorial)

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.
Length: 40 minutes
Captions: Peter van Heusden, Nadia Goué, Helena Rasche
Created: 15 February 2021
Materials:
Support:
Supported Servers:
Learning Objectives:
  • How should we filter those variants
  • How can we predict drug resistance from those variants
  • How do we annotate those variants
Go to the video page to see all versions.

Speaker

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Epigenetics

ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) is a technique used in molecular biology to assess genome-wide chromatin accessibility. This session will introduce ATAC-Seq and walk you through an analysis step by step.

ATAC-Seq data analysis (Lecture)

Description:

This lecture will introduce the basic concepts involved in ATAC-Seq analysis.
Length: 15 minutes
Captions: Lucille Delisle
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • Apply appropriate analysis and quality control steps for ATAC-Seq
  • Generate a heatmap of transcription start site accessibility
  • Visualise peaks for specific regions
Go to the video page to see all versions.

Speaker

ATAC-Seq data analysis (Tutorial)

Description:

This tutorial will walk you through a ATAC-Seq data analysis.
Length: 1 hour 50 minutes
Captions: Hans-Rudolf Hotz
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Apply appropriate analysis and quality control steps for ATAC-Seq
  • Generate a heatmap of transcription start site accessibility
  • Visualise peaks for specific regions
Go to the video page to see all versions.

Speaker

Go to session page.

Transcriptomics

Single-cell RNA-seq analysis is a rapidly evolving field at the forefront of transcriptomic research, used in high-throughput developmental studies

An introduction to scRNA-seq data analysis (Lecture)

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.
Length: 20 minutes
Captions: Mehmet Tekman
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • To understand the pitfalls in scRNA-seq sequencing and amplification, and how they are overcome.
  • Know the types of variation in an analysis and how to control for them.
  • Grasp what dimension reduction is, and how it might be performed.
  • Be familiarised with the main types of clustering techniques and when to use them.
Go to the video page to see all versions.

Speaker

Filter, plot and explore single-cell RNA-seq data (Scanpy) (Demo)

Description:

You’ve done all the work to make a single cell matrix, with gene counts and mitochondrial counts and buckets of cell metadata from all your variables of interest, now it’s time to fully process our data, to remove low quality cells, to reduce the many dimensions of data that make it difficult to work with, and ultimately to try to define our clusters and to find our biological meaning and insights!
Length: 30 minutes
Captions: Wendi Bacon
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Interpret quality control plots to direct parameter decisions
  • Repeat analysis from matrix to clustering
  • Identify decision-making points
  • Appraise data outputs and decisions
  • Explain why single cell analysis is an iterative (i.e. the first plots you generate are not final, but rather you go back and re-analyse your data repeatedly) process
Go to the video page to see all versions.

Speaker

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In plants, miRNAs can silence targets through RNA degradation as well as translational repression pathways, and unlike animals, a large proportion of miRNA and their targets have less than four mismatches. This feature has been exploited for developing miRNAs target prediction tools, providing an efficient approach to elucidate the miRNA-mediated regulatory networks, which can contribute to biotechnological solutions to improve crops productivity.

Whole transcriptome analysis of Arabidopsis thaliana (Lecture)

Description:

In plants, miRNAs can silence targets through RNA degradation as well as translational repression pathways, and unlike animals, a large proportion of miRNA and their targets have less than four mismatches. This feature has been exploited for developing miRNAs target prediction tools, providing an efficient approach to elucidate the miRNA-mediated regulatory networks, which can contribute to biotechnological solutions to improve crops productivity.
Length: 10 minutes
Captions: The Global Galaxy Community
Created: 20 April 2021
Materials:
Support:
Learning Objectives:
  • Perform miRNA differential expression analysis
  • Understand the quasi-mapping-based Salmon method for quantifying the expression of transcripts using RNA-Seq data
  • Idenfity potential miRNAs involved in brassinosteroid-mediated regulation networks
Go to the video page to see all versions.

Speaker

Whole transcriptome analysis of Arabidopsis thaliana (Tutorial)

Description:

In plants, miRNAs can silence targets through RNA degradation as well as translational repression pathways, and unlike animals, a large proportion of miRNA and their targets have less than four mismatches. This feature has been exploited for developing miRNAs target prediction tools, providing an efficient approach to elucidate the miRNA-mediated regulatory networks, which can contribute to biotechnological solutions to improve crops productivity.
Length: 1 hour 10 minutes
Captions: Cristóbal Gallardo
Created: 25 July 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Perform miRNA differential expression analysis
  • Understand the quasi-mapping-based Salmon method for quantifying the expression of transcripts using RNA-Seq data
  • Idenfity potential miRNAs involved in brassinosteroid-mediated regulation networks
Go to the video page to see all versions.

Speaker

Go to session page.

Single cell

Single-cell RNA-seq analysis is a rapidly evolving field at the forefront of transcriptomic research, used in high-throughput developmental studies

An introduction to scRNA-seq data analysis (Lecture)

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.
Length: 20 minutes
Captions: Mehmet Tekman
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • To understand the pitfalls in scRNA-seq sequencing and amplification, and how they are overcome.
  • Know the types of variation in an analysis and how to control for them.
  • Grasp what dimension reduction is, and how it might be performed.
  • Be familiarised with the main types of clustering techniques and when to use them.
Go to the video page to see all versions.

Speaker

Filter, plot and explore single-cell RNA-seq data (Scanpy) (Demo)

Description:

You’ve done all the work to make a single cell matrix, with gene counts and mitochondrial counts and buckets of cell metadata from all your variables of interest, now it’s time to fully process our data, to remove low quality cells, to reduce the many dimensions of data that make it difficult to work with, and ultimately to try to define our clusters and to find our biological meaning and insights!
Length: 30 minutes
Captions: Wendi Bacon
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Interpret quality control plots to direct parameter decisions
  • Repeat analysis from matrix to clustering
  • Identify decision-making points
  • Appraise data outputs and decisions
  • Explain why single cell analysis is an iterative (i.e. the first plots you generate are not final, but rather you go back and re-analyse your data repeatedly) process
Go to the video page to see all versions.

Speaker

Go to session page.

Climate

This session will provide a brief overview of FATES, and guide you through a Galaxy analysis step by step.

Functionally Assembled Terrestrial Ecosystem Simulator (FATES) (Lecture)

Description:

This lecture provides a brief overview of FATES
Length: 7 minutes
Captions: Anne Fouilloux
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • Setting up a CLM-FATES case.
  • Customizing your run.
  • Interactive visualization with Panoply.
  • Automating your analyzes and visualisations of your CLM-FATES case.
  • Creating multi-case scenarios.
  • Composing, executing and publishing CML-FATES workflow.
Go to the video page to see all versions.

Speaker

Functionally Assembled Terrestrial Ecosystem Simulator (FATES) (Tutorial)

Description:

This tutorial will walk you through a Galaxy analysis step by step
Length: 1 hour 20 minutes
Captions: Sébastien Fouilloux
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working
Learning Objectives:
  • Setting up a CLM-FATES case.
  • Customizing your run.
  • Interactive visualization with Panoply.
  • Automating your analyzes and visualisations of your CLM-FATES case.
  • Creating multi-case scenarios.
  • Composing, executing and publishing CML-FATES workflow.
Go to the video page to see all versions.

Speaker

Go to session page.

Genome annotation

This tutorial will introduce genome annotation process and give you hands-on experience with annotating a prokaryotic genome using Prokka.

Genome annotation with Prokka (Lecture)

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.
Length: 3 minutes
Captions: Anthony Bretaudeau
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • Load genome into Galaxy
  • Annotate genome with Prokka
  • View annotations in JBrowse
Go to the video page to see all versions.

Speaker

Genome annotation with Prokka (Tutorial)

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.”
Length: 20 minutes
Captions: Anthony Bretaudeau
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Load genome into Galaxy
  • Annotate genome with Prokka
  • View annotations in JBrowse
Go to the video page to see all versions.

Speaker

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This session will introduce the Apollo genome annotation platform, and provide you hands-on experience with using Apollo in Galaxy.

Refining Genome Annotations with Apollo (prokaryotes) (Lecture)

Description:

This lecture gives a quick overview of Apollo
Length: 5 minutes
Captions: Anthony Bretaudeau
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • Load a genome into Galaxy
  • View annotations in JBrowse
  • Learn how to load JBrowse data into Apollo
  • Learn how to manually refine genome annotations within Apollo
  • Export refined genome annotations
Go to the video page to see all versions.

Speaker

Refining Genome Annotations with Apollo (prokaryotes) (Tutorial)

Description:

In this tutorial you will get some hands-on experience using Apollo in Galaxy
Length: 1 hour
Captions: Anthony Bretaudeau
Created: 15 February 2021
Materials:
Support:
Supported Servers: Possibly Working
Learning Objectives:
  • Load a genome into Galaxy
  • View annotations in JBrowse
  • Learn how to load JBrowse data into Apollo
  • Learn how to manually refine genome annotations within Apollo
  • Export refined genome annotations
Go to the video page to see all versions.

Speaker

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Crispr

This lecture will introduce the basic concepts involved in CRISPR screen analysis.

CRISPR screen analysis (Lecture)

Description:

This lecture will introduce the basic concepts involved in CRISPR screen analysis.
Length: 3 minutes
Captions: Maria Doyle
Created: 10 March 2022
Materials:
Support:
Learning Objectives:
  • Apply appropriate analysis and quality control steps for CRISPR screen data
  • Identify differentially enriched genes across conditions
  • Generate volcano plot to visualise results
Go to the video page to see all versions.

Speaker

CRISPR screen analysis (Tutorial)

Description:

This tutorial will walk you through a CRISPR screen analysis.
Length: 45 minutes
Captions: Maria Doyle
Created: 10 March 2022
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Apply appropriate analysis and quality control steps for CRISPR screen data
  • Identify differentially enriched genes across conditions
  • Generate volcano plot to visualise results
Go to the video page to see all versions.

Speaker

Go to session page.

Proteomics

Data independent acquisition (DIA) mass spectrometry is a powerful technique that is improving the reproducibility and throughput of proteomics studies. EncyclopeDIA is library search engine comprised of several algorithms for DIA data analysis and can search for peptides using either DDA-based spectrum libraries or DIA-based chromatogram libraries.

EncyclopeDIA (Lecture)

Description:

This lecture will introduce EncyclopeDIA.
Length: 20 minutes
Captions: Emma Leith
Created: 25 June 2021
Materials:
Support:
Go to the video page to see all versions.

Speakers

EncyclopeDIA (Tutorial)

Description:

This tutorial will walk you through an analysis with EncyclopeDIA step by step.
Length: 30 minutes
Captions: Mehmet Tekman
Created: 25 June 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Understand the difference between DDA and DIA methods
  • Performing quantitative analysis using DIA data
  • Understand the purpose and benefits of using a Chromatogram Library for detection of peptides
  • You can use Bloom's Taxonomy to write effective learning objectives
Go to the video page to see all versions.

Speaker

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Proteogenomics is a field of biological research that utilizes a combination of proteomics, genomics, and transcriptomics to aid in the discovery and identification of peptides

Proteogenomics 1: Database Creation (Tutorial)

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.
Length: 40 minutes
Captions: Emma Leith
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Generating a customized Protein sequence database with variants, indels, splice junctions and known sequences.
Go to the video page to see all versions.

Speaker

Proteogenomics 2: Database Search (Demo)

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
Length: 30 minutes
Captions: Emma Leith
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • A proteogenomic data analysis of mass spectrometry data to identify and visualize variant peptides.
Go to the video page to see all versions.

Speaker

Proteogenomics 3: Novel peptide analysis (Demo)

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
Length: 40 minutes
Captions: Subina Mehta
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • How to assign and visualize the genomic localization of these identified novel proteoforms?
Go to the video page to see all versions.

Speaker

Go to session page.

Microbiome

To determine the composition of a microbiome sample, sequencing of the 16S rRNA gene is often used. This allows us to identify the bacterial species present in our sample. This lecture and practical session introduces you to 16S analysis in Galaxy using the mothur tool suite.

Introduction to Microbiome Analysis (Lecture)

Description:

This lecture briefly introduces 16S sequencing, a popular technique used for taxonomic profiling of microbial communities.
Length: 15 minutes
Captions: Saskia Hiltemann
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
Go to the video page to see all versions.

Speaker

16S Microbial Analysis with mothur (short) (Tutorial)

Description:

This lecture briefly introduces 16S sequencing, a popular technique used for taxonomic profiling of microbial communities.
Length: 1 hour 37 minutes
Captions: Saskia Hiltemann
Created: 19 May 2023
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Analyze of 16S rRNA sequencing data using the mothur toolsuite in Galaxy
  • Using a mock community to assess the error rate of your sequencing experiment
  • Visualize sample diversity using Krona and Phinch
Go to the video page to see all versions.

Speaker

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In this 3-part module, you will learn about Nanopore long-read sequencing for the detection of antimicrobial resistance (AMR). There is a short video showing you the wetlab steps involved in using the MinION sequencer. A talk about the clinical applications, and finally a practical tutorial walking you through an AMR analysis in Galaxy.

MinION Wetlab demo (Demo)

Description:

This video will show you the full process of sequencing a bacterial genome using the Oxford Nanopore MinION sequencer.
Length: 20 minutes
Captions: Saskia Hiltemann
Created: 15 February 2021
Support:
Go to the video page to see all versions.

Speaker

Nanopore Whole Bacterial Genome Sequencing in a Clinical Setting (Lecture)

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.
Length: 30 minutes
Captions: Helena Rasche
Created: 15 February 2021
Support:
Go to the video page to see all versions.

Speaker

Antibiotic resistance detection (Tutorial)

Description:

This tutorial will guide you through the process of assembling your Nanopore-sequenced bacterial samples and determining the presence of antibiotic resistance genes.
Length: 45 minutes
Captions: Bérénice Batut
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Perform Quality control on your reads
  • Assemble a genome with Minimap2/Miniasm/Racon
  • Determine the structure of the genome(s)
  • Scan for antimicrobial resistance genes with Staramr
Go to the video page to see all versions.

Speaker

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Wetlab

In this 3-part module, you will learn about Nanopore long-read sequencing for the detection of antimicrobial resistance (AMR). There is a short video showing you the wetlab steps involved in using the MinION sequencer. A talk about the clinical applications, and finally a practical tutorial walking you through an AMR analysis in Galaxy.

MinION Wetlab demo (Demo)

Description:

This video will show you the full process of sequencing a bacterial genome using the Oxford Nanopore MinION sequencer.
Length: 20 minutes
Captions: Saskia Hiltemann
Created: 15 February 2021
Support:
Go to the video page to see all versions.

Speaker

Nanopore Whole Bacterial Genome Sequencing in a Clinical Setting (Lecture)

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.
Length: 30 minutes
Captions: Helena Rasche
Created: 15 February 2021
Support:
Go to the video page to see all versions.

Speaker

Antibiotic resistance detection (Tutorial)

Description:

This tutorial will guide you through the process of assembling your Nanopore-sequenced bacterial samples and determining the presence of antibiotic resistance genes.
Length: 45 minutes
Captions: Bérénice Batut
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Perform Quality control on your reads
  • Assemble a genome with Minimap2/Miniasm/Racon
  • Determine the structure of the genome(s)
  • Scan for antimicrobial resistance genes with Staramr
Go to the video page to see all versions.

Speaker

Go to session page.

Statistics

This 3-part session will introduce you to the world of deep learning and cover Feedforward Neural Networks (FNN), Recurrent Neural Networks (FNN), and Convolutional Neural Networks (CNN).

Feedforward Neural Networks (FNN) (Tutorial)

Description:

This hands-on tutorial covers Feedforward Neural Networks (FNN)
Length: 1 hour 10 minutes
Captions: Kaivan Kamali
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Go to the video page to see all versions.

Speaker

Recurrent Neural Networks (RNN) (Tutorial)

Description:

This hands-on tutorial covers Recurrenct Neural Networks (RNN)
Length: 50 minutes
Captions: Kaivan Kamali
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Go to the video page to see all versions.

Speaker

Convolutional Neural Networks (CNN) (Tutorial)

Description:

This hands-on tutorial covers Convolutional Neural Networks (CNN)
Length: 1 hour
Captions: Filippos Zacharopoulos
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working
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Galaxy interface

This session will introduce the SRA Aligned Read format, and show you how to use this in Galaxy to analyze a SARS-CoV-2 dataset.

SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis (Lecture)

Description:

This lecture will introduce the SRA Aligned Read format available in the cloud from SRA, as well as some accompanying metadata that can help you search and filter the data. This sessions is aimed specifically at SARS-CoV-2 runs in SRA.
Length: 15 minutes
Captions: Jonathan Trow
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • Learn about SRA aligned read format and vcf files for Runs containing SARS-CoV-2 content
  • Understand how to search the metadata for these Runs to find your dataset of interest and then import that data in your preferred format
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SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis (Tutorial)

Description:

This tutorial will walk you through accessing and using SRA Aligned read format in Galaxy.
Length: 40 minutes
Captions: Jonathan Trow
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Learn about SRA aligned read format and vcf files for Runs containing SARS-CoV-2 content
  • Understand how to search the metadata for these Runs to find your dataset of interest and then import that data in your preferred format
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Want a bit more control over your Analyses? You can run R in Rstudio directly within Galaxy

Running RStudio on Galaxy (Demo)

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/)
Length: 20 minutes
Captions: Saskia Hiltemann
Created: 15 February 2021
Materials:
Support:
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Speaker

R basics in Galaxy (Tutorial)

Description:

This tutorial will provide an introduction to using R with Rstudio in Galaxy.
Length: 50 minutes
Captions: Sébastien Fouilloux, Anne Fouilloux, Kaivan Kamali
Created: 15 February 2021
Materials:
Support:
Supported Servers:
Learning Objectives:
  • Know advantages of analyzing data using R within Galaxy.
  • Compose an R script file containing comments, commands, objects, and functions.
  • Be able to work with objects (i.e. applying mathematical and logical operators, subsetting, retrieving values, etc).
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Speaker

Advanced R in Galaxy (Tutorial)

Description:

An advanced tutorial covering downstream analysis of RNA-seq data using R.
Length: 1 hour
Captions: Keith Suderman, Nadia Goué
Created: 15 February 2021
Materials:
Support:
Supported Servers:
Learning Objectives:
  • Be able to load and explore the shape and contents of a tabular dataset using base R functions.
  • Understand factors and how they can be used to store and work with categorical data.
  • Apply common `dplyr` functions to manipulate data in R.
  • Employ the ‘pipe’ operator to link together a sequence of functions.
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Dev

In this 9-part Lecture series, John Chilton will walk you through the Galaxy Code Architecture.

Galaxy Code Architecture: Galaxy Ecosystem (Lecture)

Description:

TODO
Length: 25 minutes
Captions: No captions available for this video. We aim to have captions for all our videos, and are working to add captions to this video as soon as possible.
Created: 15 February 2021
Materials:
Support:
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Speaker

Galaxy Code Architecture: Models and Managers (Lecture)

Description:

TODO
Length: 15 minutes
Captions: No captions available for this video. We aim to have captions for all our videos, and are working to add captions to this video as soon as possible.
Created: 15 February 2021
Materials:
Support:
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Galaxy Code Architecture: app and Dependency Injection (Lecture)

Description:

TODO
Length: 15 minutes
Captions: No captions available for this video. We aim to have captions for all our videos, and are working to add captions to this video as soon as possible.
Created: 15 February 2021
Materials:
Support:
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Speaker

Galaxy Code Architecture: Project Management (Lecture)

Description:

TODO
Length: 25 minutes
Captions: Mallory Freeberg
Created: 15 February 2021
Materials:
Support:
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Speaker

Galaxy Code Architecture: Web Client (Lecture)

Description:

TODO
Length: 15 minutes
Captions: No captions available for this video. We aim to have captions for all our videos, and are working to add captions to this video as soon as possible.
Created: 15 February 2021
Materials:
Support:
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Galaxy Code Architecture: Pluggable Components (Lecture)

Description:

TODO
Length: 45 minutes
Captions: No captions available for this video. We aim to have captions for all our videos, and are working to add captions to this video as soon as possible.
Created: 15 February 2021
Materials:
Support:
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Speaker

Galaxy Code Architecture: Principles (Lecture)

Description:

TODO
Length: 5 minutes
Captions: Saskia Hiltemann
Created: 15 February 2021
Materials:
Support:
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Speaker

Galaxy Code Architecture: Web Requests (Lecture)

Description:

TODO
Length: 35 minutes
Captions: No captions available for this video. We aim to have captions for all our videos, and are working to add captions to this video as soon as possible.
Created: 15 February 2021
Materials:
Support:
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Speaker

Galaxy Code Architecture: Files and Directories (Lecture Series)

Description:

TODO
Length: 17 minutes
Captions: No captions available for this video. We aim to have captions for all our videos, and are working to add captions to this video as soon as possible.
Created: 15 February 2021
Materials:
Support:
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This series of videos will guide (future) Galaxy contributors through the process of debugging Galaxy.

Introduction (Tutorial)

Description:

This is the first video in the Debugging Galaxy series.
Length: 11 minutes
Captions: Dave Clements
Created: 15 February 2021
Materials:
Support:
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Speakers

Unit Testing (Tutorial)

Description:

What to do when a unit test fails.
Length: 14 minutes
Captions: John Davis
Created: 15 February 2021
Materials:
Support:
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API tests (Tutorial)

Description:

What to do when an API test fails.
Length: 23 minutes
Captions: John Davis
Created: 15 February 2021
Materials:
Support:
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Client Unit Tests (Tutorial)

Description:

What to do when your client throws a unit test failure.
Length: 6 minutes
Captions: Beatriz Serrano-Solano
Created: 15 February 2021
Materials:
Support:
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Speaker

Client Linting (Tutorial)

Description:

This video covers working through the client linting error hit in the previous tutorial.
Length: 6 minutes
Captions: Beatriz Serrano-Solano
Created: 15 February 2021
Materials:
Support:
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Speaker

Selenium (Tutorial)

Description:

Selenium is used to test Galaxy development. Learn more about test failure and how to address them.
Length: 18 minutes
Captions: Assunta DeSanto, John Davis, Dave Clements, Beatriz Serrano-Solano
Created: 15 February 2021
Materials:
Support:
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Speaker

Runtime Errors (Tutorial)

Description:

How to fix a runtime error
Length: 40 minutes
Captions: John Davis
Created: 15 February 2021
Materials:
Support:
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Speaker

Debugging Wisdom (Lecture)

Description:

A summary of wisdom to debug Galaxy with.
Length: 3 minutes
Captions: Dave Clements
Created: 15 February 2021
Materials:
Support:
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Speakers

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Data science

Want a bit more control over your Analyses? You can run R in Rstudio directly within Galaxy

Running RStudio on Galaxy (Demo)

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/)
Length: 20 minutes
Captions: Saskia Hiltemann
Created: 15 February 2021
Materials:
Support:
Go to the video page to see all versions.

Speaker

R basics in Galaxy (Tutorial)

Description:

This tutorial will provide an introduction to using R with Rstudio in Galaxy.
Length: 50 minutes
Captions: Sébastien Fouilloux, Anne Fouilloux, Kaivan Kamali
Created: 15 February 2021
Materials:
Support:
Supported Servers:
Learning Objectives:
  • Know advantages of analyzing data using R within Galaxy.
  • Compose an R script file containing comments, commands, objects, and functions.
  • Be able to work with objects (i.e. applying mathematical and logical operators, subsetting, retrieving values, etc).
Go to the video page to see all versions.

Speaker

Advanced R in Galaxy (Tutorial)

Description:

An advanced tutorial covering downstream analysis of RNA-seq data using R.
Length: 1 hour
Captions: Keith Suderman, Nadia Goué
Created: 15 February 2021
Materials:
Support:
Supported Servers:
Learning Objectives:
  • Be able to load and explore the shape and contents of a tabular dataset using base R functions.
  • Understand factors and how they can be used to store and work with categorical data.
  • Apply common `dplyr` functions to manipulate data in R.
  • Employ the ‘pipe’ operator to link together a sequence of functions.
Go to the video page to see all versions.

Speaker

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Visualisation

Circos (Krzywinski et al. 2009) is a software package for visualizing data in a circular layout. This makes Circos ideal for exploring relationships between objects or positions. Circos plots have appeared in thousands of scientific publications. Although originally designed for visualizing genomic data, it can create figures from data in any field.

Visualisation with Circos (Lecture)

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
Length: 6 minutes
Captions: Assunta DeSanto, Saskia Hiltemann
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • Create a number of Circos plots using the Galaxy tool
  • Familiarise yourself with the various different track types
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Speaker

Visualisation with Circos (Tutorial)

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
Length: 50 minutes
Captions: Beatriz Serrano-Solano, Helena Rasche, Saskia Hiltemann, Alireza Khanteymoori
Created: 15 February 2021
Materials:
Support:
Supported Servers: Known Working Possibly Working
Learning Objectives:
  • Create a number of Circos plots using the Galaxy tool
  • Familiarise yourself with the various different track types
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Speaker

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Admin

Here you'll learn the basics of Ansible

Ansible (Lecture)

Description:

Here you’ll learn the basics of Ansible
Length: 5 minutes
Captions: Martin Čech
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • Learn Ansible basics
  • Write a simple role
  • Install a role from Ansible Galaxy
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Speaker

Ansible (Tutorial)

Description:

Here you’ll learn the basics of Ansible
Length: 61 minutes
Captions: Martin Čech
Created: 15 February 2021
Materials:
Support:
Supported Servers:
Learning Objectives:
  • Learn Ansible basics
  • Write a simple role
  • Install a role from Ansible Galaxy
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Speaker

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Reference data management is easier than ever with CVMFS

Reference Data with CVMFS (Tutorial)

Description:

Reference data management is easier than ever with CVMFS
Length: 3 minutes
Captions: The Global Galaxy Community
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • Have an understanding of what CVMFS is and how it works
  • Install and configure the CVMFS client on a linux machine and mount the Galaxy reference data repository
  • Configure your Galaxy to use these reference genomes and indices
  • Use an Ansible playbook for all of the above.
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Speaker

Reference Data with CVMFS (Tutorial)

Description:

Reference data management is easier than ever with CVMFS
Length: 23 minutes
Captions: Simon Gladman
Created: 15 February 2021
Materials:
Support:
Supported Servers:
Learning Objectives:
  • Have an understanding of what CVMFS is and how it works
  • Install and configure the CVMFS client on a linux machine and mount the Galaxy reference data repository
  • Configure your Galaxy to use these reference genomes and indices
  • Use an Ansible playbook for all of the above.
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Remote compute made possible with Pulsar

Running Jobs on Remote Resources with Pulsar (Lecture)

Description:

Remote compute made possible with Pulsar
Length: 14 minutes
Captions: Saskia Hiltemann
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • Have an understanding of what Pulsar is and how it works
  • Install and configure a RabbitMQ message queueing server
  • Install and configure a Pulsar server on a remote linux machine
  • Be able to get Galaxy to send jobs to a remote Pulsar server
Go to the video page to see all versions.

Speaker

Running Jobs on Remote Resources with Pulsar (Tutorial)

Description:

Remote compute made possible with Pulsar
Length: 1 hour 28 minutes
Captions: Helena Rasche
Created: 28 June 2021
Materials:
Support:
Supported Servers:
Learning Objectives:
  • Have an understanding of what Pulsar is and how it works
  • Install and configure a RabbitMQ message queueing server
  • Install and configure a Pulsar server on a remote linux machine
  • Be able to get Galaxy to send jobs to a remote Pulsar server
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Speaker

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Learn advanced Galaxy monitoring with Telegraf, Influx, and Grafana.

Galaxy Monitoring with Telegraf and Grafana (Lecture)

Description:

Learn advanced Galaxy monitoring with Telegraf, Influx, and Grafana.
Length: 2 minutes
Captions: The Global Galaxy Community
Created: 15 February 2021
Materials:
Support:
Learning Objectives:
  • Setup InfluxDB
  • Setup Telegraf
  • Setup Grafana
  • Create several charts
Go to the video page to see all versions.

Speaker

Galaxy Monitoring with Telegraf and Grafana (Tutorial)

Description:

Learn advanced Galaxy monitoring with Telegraf, Influx, and Grafana.
Length: 73 minutes
Captions: Saskia Hiltemann, Helena Rasche
Created: 15 February 2021
Materials:
Support:
Supported Servers:
Learning Objectives:
  • Setup InfluxDB
  • Setup Telegraf
  • Setup Grafana
  • Create several charts
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Speaker

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Learn how to install and manage tools in Galaxy

Galaxy Tool Management with Ephemeris (Lecture)

Description:

Learn how to install and manage tools in Galaxy
Length: 17 minutes
Captions: Catherine Bromhead
Created: 28 June 2021
Materials:
Support:
Learning Objectives:
  • Learn about Ephemeris
  • Extract a list of tools from a workflow
  • Install these tools on a given Galaxy
Go to the video page to see all versions.

Speaker

Galaxy Tool Management with Ephemeris (Tutorial)

Description:

Learn how to install and manage tools in Galaxy
Length: 27 minutes
Captions: Catherine Bromhead
Created: 28 June 2021
Materials:
Support:
Supported Servers:
Learning Objectives:
  • Learn about Ephemeris
  • Extract a list of tools from a workflow
  • Install these tools on a given Galaxy
Go to the video page to see all versions.

Speaker

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