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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)

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Galaxy Resources for.. Educators (Webinar)

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Galaxy Resources for.. Tool Developers (Webinar)

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Galaxy Resources for.. Admins (Webinar)

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Tuberculosis

Webinar: Drug resistance prediction (Webinar)

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Webinar: Phylogenetic mutations (Webinar)

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Webinar: The Concept of Clustering (Webinar)

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Webinar: genetic distance thresholds (Webinar)

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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)

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M. tuberculosis Variant Analysis (Tutorial)

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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)

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Quality Control (Tutorial)

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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)

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Mapping (Tutorial)

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Assembly

This session provides an introduction to Genome Assembly

An Introduction to Genome Assembly (Lecture)

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Chloroplast genome assembly (Lecture & Tutorial)

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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)

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M. tuberculosis Variant Analysis (Tutorial)

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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)

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ATAC-Seq data analysis (Tutorial)

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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)

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

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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)

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Whole transcriptome analysis of Arabidopsis thaliana (Tutorial)

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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)

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

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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)

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Functionally Assembled Terrestrial Ecosystem Simulator (FATES) (Tutorial)

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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)

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Genome annotation with Prokka (Tutorial)

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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)

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Refining Genome Annotations with Apollo (prokaryotes) (Tutorial)

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Crispr

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

CRISPR screen analysis (Lecture)

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CRISPR screen analysis (Tutorial)

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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)

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EncyclopeDIA (Tutorial)

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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)

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Proteogenomics 2: Database Search (Demo)

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Proteogenomics 3: Novel peptide analysis (Demo)

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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)

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

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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)

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

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Antibiotic resistance detection (Tutorial)

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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)

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

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Antibiotic resistance detection (Tutorial)

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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)

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Recurrent Neural Networks (RNN) (Tutorial)

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Convolutional Neural Networks (CNN) (Tutorial)

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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)

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

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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)

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R basics in Galaxy (Tutorial)

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Advanced R in Galaxy (Tutorial)

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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)

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Galaxy Code Architecture: Models and Managers (Lecture)

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Galaxy Code Architecture: app and Dependency Injection (Lecture)

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Galaxy Code Architecture: Project Management (Lecture)

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Galaxy Code Architecture: Web Client (Lecture)

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Galaxy Code Architecture: Pluggable Components (Lecture)

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Galaxy Code Architecture: Principles (Lecture)

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Galaxy Code Architecture: Web Requests (Lecture)

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Galaxy Code Architecture: Files and Directories (Lecture Series)

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This series of videos will guide (future) Galaxy contributors through the process of debugging Galaxy.

Introduction (Tutorial)

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Unit Testing (Tutorial)

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API tests (Tutorial)

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Client Unit Tests (Tutorial)

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Client Linting (Tutorial)

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Selenium (Tutorial)

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Runtime Errors (Tutorial)

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Debugging Wisdom (Lecture)

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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)

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R basics in Galaxy (Tutorial)

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Advanced R in Galaxy (Tutorial)

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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)

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Visualisation with Circos (Tutorial)

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Admin

Here you'll learn the basics of Ansible

Ansible (Lecture)

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Ansible (Tutorial)

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Reference data management is easier than ever with CVMFS

Reference Data with CVMFS (Tutorial)

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Reference Data with CVMFS (Tutorial)

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Remote compute made possible with Pulsar

Running Jobs on Remote Resources with Pulsar (Lecture)

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Running Jobs on Remote Resources with Pulsar (Tutorial)

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

Galaxy Monitoring with Telegraf and Grafana (Lecture)

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Speaker

Galaxy Monitoring with Telegraf and Grafana (Tutorial)

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Speaker

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Learn how to install and manage tools in Galaxy

Galaxy Tool Management with Ephemeris (Lecture)

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Galaxy Tool Management with Ephemeris (Tutorial)

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