Welcome to the Galaxy Training Video Library!
This page shows you the full library of available GTN video tutorials, you can use these for self-study, courses, and more! Below are all of the individual videos, but some videos are part of multi-video “sessions” which can be found in the session library
All Training Videos
Here is the full list of all individual training videos
Assembly
Tutorial Video
| 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. |
| Length: | 25 minutes |
| Captions: | Mehmet Tekman |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: |
Slides:
Tutorial:
Lecture & Tutorial Video
| 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: | |
| Learning Objectives: |
|
Speaker
Lecture Video
| 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: |
|
Speaker
Demo Video
| Description: | This demo walks you through running the VGP Genome Assembly workflows, rather than the whole tutorial (as most GTN Tapas videos do) |
| Length: | 10 minutes |
| Captions: | No captions available for this video. We aim to have captions for all our videos, however sometimes videos get added without captions. Please contact us to indicate your desire to have captions added and we will ask the speakers to provide captions. |
| Created: | 13 March 2022 |
| Materials: |
|
| Support: |
Climate
Tutorial Video
| 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: | |
| Learning Objectives: |
|
Speaker
Lecture Video
| Description: | This lecture provides a brief overview of FATES |
| Length: | 7 minutes |
| Captions: | Anne Fouilloux |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Tutorial Video
| Description: | In this tutorial, you will learn how to manipulate netCDF data files using Xarray Galaxy Tools. NetCDF stands for network Common Data Form and is one of the most popular file format in climate science. It is used for storing multidimensional scientific data variables such as temperature or humidity, and metadata can be added to facilitate sharing of netCDF data. netCDF is widely used outside the Climate Science community and each community has its own set of conventions, especially for metadata. The Climate and Forecast metadata convention, also called CF-convention is used by the Climate community and is designed to promote the processing and sharing of netCDF files. |
| Length: | 1 hour 20 minutes |
| Captions: | Anne Fouilloux |
| Created: | 3 March 2022 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Speaker
Tutorial Video
| Description: | In this tutorial, we will learn about Xarray, one of the most used Python library from the Pangeo ecosystem. We will be using data from Copernicus Atmosphere Monitoring Service and more precisely PM2.5 (Particle Matter < 2.5 μm) 4 days forecast from December, 22 2021. Parallel data analysis with Pangeo is not covered in this tutorial. |
| Length: | 17 minutes |
| Captions: | Anne Fouilloux |
| Created: | 3 March 2022 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Speaker
Community
Speaker
Computational chemistry
Video
| 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). |
| Length: | 1 hour 40 minutes |
| Captions: | Simon Bray |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Data science
Tutorial Video
| 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: | |
| Learning Objectives: |
|
Speaker
Tutorial Video
| 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: | |
| Learning Objectives: |
|
Speaker
Ecology
Lecture Video
| 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. |
| Length: | 2 hours |
| Captions: | Coline Royaux |
| Created: | 3 March 2022 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Speaker
Lecture Video
| Description: | Based on this OBITools official tutorial, you will learn here how to analyze DNA metabarcoding data produced on Illumina sequencers |
| Length: | 1 hour 15 minutes |
| Captions: | Yvan Le Bras |
| Created: | 3 March 2022 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Lecture Video
| Length: | 1 hour |
| Captions: | Olivier Norvez |
| Created: | 3 March 2022 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Epigenetics
Lecture Video
| 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: |
|
Tutorial Video
| 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: | |
| Learning Objectives: |
|
Galaxy interface
Tutorial Video
| Length: | 11 minutes |
| Captions: | Anne Fouilloux, Pia H. |
| Created: | 9 August 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Lecture Video
| 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: |
|
Tutorial Video
| 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: | |
| Learning Objectives: |
|
Tutorial Video
| 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.. |
| Length: | 22 minutes |
| Captions: | Assunta DeSanto |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: |
Speaker
Tutorial Video
| 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. |
| Length: | 30 minutes |
| Captions: | Simon Bray |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: |
Speaker
Sars cov2
Speaker
Speaker
Speaker
Galaxy intro
Tutorial Video
| 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. |
| Length: | 1 hour 30 minutes |
| Captions: | Dave Clements |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: |
Galaxy
Tutorial Video
| 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. |
| Length: | 1 hour 15 minutes |
| Captions: | Dave Clements |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Speakers
Tutorial Video
| 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. |
| Length: | 1 hour 30 minutes |
| Captions: | Dave Clements |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: |
Crispr
Lecture Video
| 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: |
|
Tutorial Video
| Description: | This tutorial will walk you through a CRISPR screen analysis. |
| Length: | 45 minutes |
| Captions: | Maria Doyle |
| Created: | 10 March 2022 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Genome annotation
Lecture Video
| 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: |
|
Tutorial Video
| 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: | |
| Learning Objectives: |
|
Speaker
Lecture Video
| Description: | This lecture gives a quick overview of Apollo |
| Length: | 5 minutes |
| Captions: | Anthony Bretaudeau |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Tutorial Video
| 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: | |
| Learning Objectives: |
|
Speaker
Tutorial Video
| Description: | The aim of repeat masking is to identify the location of all repeated elements along a genome sequence. Other tools (like annotation pipelines) can then take this information into account when producing their results. |
| Length: | 16 minutes |
| Captions: | Anthony Bretaudeau |
| Created: | 3 March 2022 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Speaker
Tutorial Video
| Description: | Genome annotation of eukaryotes is a little more complicated than for prokaryotes: eukaryotic genomes are usually larger than prokaryotes, with more genes. The sequences determining the beginning and the end of a gene are generally less conserved than the prokaryotic ones. Many genes also contain introns, and the limits of these introns (acceptor and donor sites) are not highly conserved. In this tutorial we will use a software tool called Funannotate (Palmer and Stajich 2020) to annotate the genome sequence of a small eukaryote: Mucor mucedo (a fungal plant pathogen). |
| Length: | 1 hour 10 minutes |
| Captions: | Anthony Bretaudeau |
| Created: | 3 March 2022 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Speaker
Introduction
Tutorial Video
| Description: | This tutorial will introduce you to Galaxy. You will familiarize yourself with tools, workflows and histories. Those skills will be needed the next days |
| Length: | 13 minutes |
| Captions: | Saskia Hiltemann |
| Created: | 21 July 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Demo Video
| 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). |
| Length: | 15 minutes |
| Captions: | Anton Nekrutenko |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: |
Metagenomics
Speaker
Lecture Video
| 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: |
|
Tutorial Video
| Description: | Metatranscriptomics analysis examines how the microbiome responds to the environment by studying the taxonomic composition and functional analysis of genes expressed by the microbiome, using microbial community RNASeq data and subsequent metatranscriptomics workflows. This workshop will introduce researchers to the basic concepts and tools from the ASaiM-MT workflow. ASaiM-MT provides a curated collection of tools to explore and visualize taxonomic and functional information from metatranscriptomic sequences. |
| Length: | 1 hour 30 minutes |
| Captions: | Engy Nasr, Saskia Hiltemann |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: |
Tutorial Video
| Description: | This lecture briefly introduces 16S sequencing, a popular technique used for taxonomic profiling of microbial communities. |
| Length: | 1 hour 40 minutes |
| Captions: | Saskia Hiltemann |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Tutorial Video
| 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: | |
| Learning Objectives: |
|
Proteomics
Lecture & Demo Video
| 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). |
| Length: | 35 minutes |
| Captions: | Emma Leith |
| Created: | 15 February 2021 |
| Materials: | |
| Support: |
Lecture Video
| Description: | This lecture will introduce EncyclopeDIA. |
| Length: | 20 minutes |
| Captions: | Emma Leith |
| Created: | 25 June 2021 |
| Materials: |
|
| Support: |
Tutorial Video
| 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: | |
| Learning Objectives: |
|
Speaker
Lecture Video
| Description: | This lecture will provide an introduction to mass spectrometry (MS) based proteomics analysis. Slides created by Melanie Föll. |
| Length: | 20 minutes |
| Captions: | Melanie Föll |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Demo Video
| 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. |
| Length: | 1 hour |
| Captions: | Emma Leith |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Speaker
Tutorial Video
| 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: | |
| Learning Objectives: |
|
Speaker
Demo Video
| 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: | |
| Learning Objectives: |
|
Demo Video
| 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: | |
| Learning Objectives: |
|
Speaker
Tutorial Video
| Description: | This tutorial covers an annotation pipeline for a protein list identified by LC-MS/MS experiments. |
| Length: | 30 minutes |
| Captions: | Florence Combes |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Tutorial Video
| 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. |
| Length: | 1 hour |
| Captions: | Melanie Föll |
| Created: | 15 February 2021 |
| Materials: | |
| Support: | |
| Learning Objectives: |
|
Proteogenomics
Lecture Video
| 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. |
| Length: | 20 minutes |
| Captions: | Emma Leith |
| Created: | 15 February 2021 |
| Materials: | |
| Support: |
Synthetic biology
Demo Video
| Length: | 3 minutes |
| Captions: | Kenza Bazi-Kabbaj |
| Created: | 11 May 2022 |
| Materials: |
|
| Support: |
Speaker
Demo Video
| Length: | 5 minutes |
| Captions: | Kenza Bazi-Kabbaj |
| Created: | 23 June 2022 |
| Materials: |
|
| Support: |
Speaker
Variant analysis
Tutorial Video
| Length: | 1 hour 30 minutes |
| Captions: | Helena Rasche |
| Created: | 9 August 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Lecture Video
| 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: |
Speaker
Tutorial Video
| 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: | |
| Learning Objectives: |
|
Speaker
Sequence analysis
Self-study Tutorial
This is a self-study session. Please work through the materials on your own, and ask the instructors for help if you get stuck or have any questions!
| Tutorial: | |
| Material: | GTN Tutorial |
| Support: |
|
Lecture Video
| 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: |
|
Speaker
Tutorial Video
| 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: | |
| Learning Objectives: |
|
Speaker
Lecture Video
| 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: |
|
Tutorial Video
| Description: | In this tutorial you will get some hand-on experience performing a quality assessment on sequencing data. |
| Length: | 1 hour 10 minutes |
| Captions: | Bérénice Batut, Nadia Goué, Saskia Hiltemann |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Statistics
Lecture Video
| 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. |
| Length: | 15 minutes |
| Captions: | Anup Kumar |
| Created: | 15 February 2021 |
| Materials: | |
| Support: |
Tutorial Video
| Description: | This hands-on tutorial covers Convolutional Neural Networks (CNN) |
| Length: | 1 hour |
| Captions: | Filippos Zacharopoulos |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: |
Speaker
Tutorial Video
| Description: | This hands-on tutorial covers Feedforward Neural Networks (FNN) |
| Length: | 1 hour 10 minutes |
| Captions: | Kaivan Kamali |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: |
Speaker
Tutorial Video
| Description: | This hands-on tutorial covers Recurrenct Neural Networks (RNN) |
| Length: | 50 minutes |
| Captions: | Kaivan Kamali |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: |
Speaker
Tutorial Video
| Description: | The classification of fruits and vegetables offers many useful applications such as automated harvesting by robots, building up stocks for supermarkets, effective detection of specific defects, and determining fruit ripeness (Duong et al. 2020, Naranjo-Torres et al. 2020, Iswari et al. 2017). Machine Learning (ML) techniques such as Deep Learning (DL) are commonly used for image classification problems in various domains, including in agriculture (Kamilaris and Prenafeta-Boldú 2018). DL is a technique inspired by how a human brain operates. Due to the increased availability of compute capacity and training data, DL techniques have become very popular in recent years. In this tutorial, we will use Galaxy’s ML toolkit to build a DL model to classify fruit and vegetable images. Our DL model is trained and evaluated on Fruit 360 dataset (Mureşan and Oltean 2018) |
| Length: | 1 hour |
| Captions: | Kaivan Kamali |
| Created: | 19 January 2022 |
| Materials: |
|
| Support: |
Speaker
Tutorial Video
| 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. |
| Length: | 1 hour 50 minutes |
| Captions: | Anup Kumar |
| Created: | 15 February 2021 |
| Materials: | |
| Support: | |
| Learning Objectives: |
|
Video
| Description: | This is an Introduction to Machine Learning in R, in which you’ll learn the basics of unsupervised learning for pattern recognition and supervised learning for prediction. At the end of this workshop, we hope that you will - appreciate the importance of performing exploratory data analysis (or EDA) before starting to model your data. - understand the basics of unsupervised learning and know the examples of principal component analysis (PCA) and k-means clustering. - understand the basics of supervised learning for prediction and the differences between classification and regression. - understand modern machine learning techniques and principles, such as test train split, k-fold cross validation and regularization. - be able to write code to implement the above techniques and methodologies using R, caret and glmnet. We will not be focusing on the mathematical foundation for each of the methods and approaches we’ll be discussing. There are many resources that can provide this context, but for the purposes of this workshop we believe that they are beyond the scope. |
| Length: | 1 hour 30 minutes |
| Captions: | Maria Tsagiopoulou |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Speaker
Video
| 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. |
| Length: | 1 hour 29 minutes |
| Captions: | Anup Kumar |
| Created: | 15 February 2021 |
| Materials: | |
| Support: | |
| Learning Objectives: |
|
Transcriptomics
Tutorial Video
| 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. |
| Length: | 48 minutes |
| Captions: | Mallory Freeberg |
| Created: | 15 February 2021 |
| Materials: | |
| Support: | |
| Learning Objectives: |
|
Speaker
Demo Video
| Description: | This tutorial will take you from raw FASTQ files to a cell x gene data matrix in AnnData format. What’s a data matrix, and what’s AnnData format? Well you’ll find out! Importantly, this is the first step in processing single cell data in order to start analysing it. |
| Length: | 30 minutes |
| Captions: | Wendi Bacon |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Speaker
Lecture Video
| Description: | RNA sequencing is used to assess the expression levels of genes. This video introduces the important concepts related to RNA-seq analysis. |
| Length: | 30 minutes |
| Captions: | Nadia Goué, Saskia Hiltemann |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Speaker
Lecture Video
| Length: | 10 minutes |
| Captions: | The Global Galaxy Community |
| Created: | 20 April 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Tutorial Video
| Length: | 1 hour 10 minutes |
| Captions: | Cristóbal Gallardo |
| Created: | 25 July 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Tutorial Video
| 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. |
| Length: | 2 hours 30 minutes |
| Captions: | Helena Rasche, Saskia Hiltemann |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Tutorial Video
| Description: | In this tutorial, we will visualize our RNA-seq analysis results using R. |
| Length: | 30 minutes |
| Captions: | Helena Rasche, Saskia Hiltemann, Fotis E. Psomopoulos |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Speaker
Tutorial Video
| Description: | The previous tutorial introduced volcano plots and showed how they can be generated with the Galaxy Volcano plot tool. In this tutorial we show how you can customise a plot using the R script output from the tool. |
| Length: | 15 minutes |
| Captions: | Maria Doyle |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Tutorial Video
| Description: | This tutorial will show you how you can create volcano plots from your RNA-Seq analysis results using Galaxy tools. |
| Length: | 10 minutes |
| Captions: | Maria Doyle |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Tutorial Video
| Description: | Bulk RNA-seq data contains a mixture of transcript signatures from several types of cells. We wish to deconvolve this mixture to obtain estimates of the proportions of cell types within the bulk sample. To do this, we can use single cell RNA-seq data as a reference for estimating the cell type proportions within the bulk data. In this tutorial, we will use bulk and single-cell RNA-seq data, including matrices of similar tissues from different sources, to illustrate how to infer cell type abundances from bulk RNA-seq. |
| Length: | 20 minutes |
| Captions: | Mehmet Tekman, Wendi Bacon |
| Created: | 8 March 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Speaker
Demo Video
| Description: | You’ve done all the hard work of preparing a single cell matrix, processing it, plotting it, interpreting it, finding lots of lovely genes, all within the glorious Galaxy interface. Now you want to infer trajectories, or relationships between cells… and you’ve been threatened with learning Python to do so! Well, fear not. If you can have a run-through of a basic python coding introduction, then that will help you make more sense of this tutorial, however you’ll be able to make and interpret glorious plots even without understanding the Python coding language. This is the beauty of Galaxy - all the ‘set-up’ is identical across computers, because it’s browser based. So fear not! |
| Length: | 10 minutes |
| Captions: | Wendi Bacon |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Speaker
Lecture Video
| 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: |
|
Demo Video
| Description: | This tutorial demonstrates the what barcodes in your sequencing data are, and how to handle them during analysis. Please work through the full tutorial yourself to get all the details. |
| Length: | 10 minutes |
| Captions: | Alireza Khanteymoori |
| Created: | 18 March 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Speaker
Demo Video
| Description: | 10x genomics has provided not only a cost-effective high-throughput solution to understanding sample heterogeneity at the individual cell level, but has defined the standards of the field that many downstream analysis packages are now scrambling to accommodate. Please work through the full tutorial yourself to get all the details. |
| Length: | 5 minutes |
| Captions: | Alireza Khanteymoori |
| Created: | 18 March 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Speaker
Demo Video
| Description: | In this tutorial, we will investigate clustering of single-cell data from 10x Genomics, including preprocessing, clustering and the identification of cell types via known marker genes, using Scanpy. It will be illustrated using a dataset of Peripheral Blood Mononuclear Cells (PBMC), containing 2,700 single cells. Please work through the full tutorial yourself to get all the details. |
| Length: | 45 minutes |
| Captions: | Hans-Rudolf Hotz |
| Created: | 18 March 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Speaker
Tutorial Video
| Description: | This tutorial replicates the paper “Spatiotemporal Developmental Trajectories in the Arabidopsis Root Revealed Using High-Throughput Single-Cell RNA Sequencing” (Denyer et al. 2019), where the major plant cell types are recovered in the data as well as distinguishing between QC and meristematic cells. The original paper used the Seurat analysis suite (Satija et al. 2015), but here we will use the ScanPy analysis suite (Wolf et al. 2018) integrated within the single-cell resources in Galaxy (Tekman et al. 2020). |
| Length: | 55 minutes |
| Captions: | Mehmet Tekman |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Demo Video
| 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: | |
| Learning Objectives: |
|
Speaker
Visualisation
Tutorial Video
| Description: | The previous tutorial introduced volcano plots and showed how they can be generated with the Galaxy Volcano plot tool. In this tutorial we show how you can customise a plot using the R script output from the tool. |
| Length: | 15 minutes |
| Captions: | Maria Doyle |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Tutorial Video
| Description: | This tutorial will show you how you can create volcano plots from your RNA-Seq analysis results using Galaxy tools. |
| Length: | 10 minutes |
| Captions: | Maria Doyle |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Lecture Video
| 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: |
|
Tutorial Video
| 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: | |
| Learning Objectives: |
|
Single cell
Tutorial Video
| Description: | Bulk RNA-seq data contains a mixture of transcript signatures from several types of cells. We wish to deconvolve this mixture to obtain estimates of the proportions of cell types within the bulk sample. To do this, we can use single cell RNA-seq data as a reference for estimating the cell type proportions within the bulk data. In this tutorial, we will use bulk and single-cell RNA-seq data, including matrices of similar tissues from different sources, to illustrate how to infer cell type abundances from bulk RNA-seq. |
| Length: | 20 minutes |
| Captions: | Mehmet Tekman, Wendi Bacon |
| Created: | 8 March 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Speaker
Demo Video
| Description: | You’ve done all the hard work of preparing a single cell matrix, processing it, plotting it, interpreting it, finding lots of lovely genes, all within the glorious Galaxy interface. Now you want to infer trajectories, or relationships between cells… and you’ve been threatened with learning Python to do so! Well, fear not. If you can have a run-through of a basic python coding introduction, then that will help you make more sense of this tutorial, however you’ll be able to make and interpret glorious plots even without understanding the Python coding language. This is the beauty of Galaxy - all the ‘set-up’ is identical across computers, because it’s browser based. So fear not! |
| Length: | 10 minutes |
| Captions: | Wendi Bacon |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Speaker
Lecture Video
| 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: |
|
Demo Video
| Description: | 10x genomics has provided not only a cost-effective high-throughput solution to understanding sample heterogeneity at the individual cell level, but has defined the standards of the field that many downstream analysis packages are now scrambling to accommodate. Please work through the full tutorial yourself to get all the details. |
| Length: | 5 minutes |
| Captions: | Alireza Khanteymoori |
| Created: | 18 March 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Speaker
Demo Video
| Description: | In this tutorial, we will investigate clustering of single-cell data from 10x Genomics, including preprocessing, clustering and the identification of cell types via known marker genes, using Scanpy. It will be illustrated using a dataset of Peripheral Blood Mononuclear Cells (PBMC), containing 2,700 single cells. Please work through the full tutorial yourself to get all the details. |
| Length: | 45 minutes |
| Captions: | Hans-Rudolf Hotz |
| Created: | 18 March 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Speaker
Tutorial Video
| Description: | This tutorial replicates the paper “Spatiotemporal Developmental Trajectories in the Arabidopsis Root Revealed Using High-Throughput Single-Cell RNA Sequencing” (Denyer et al. 2019), where the major plant cell types are recovered in the data as well as distinguishing between QC and meristematic cells. The original paper used the Seurat analysis suite (Satija et al. 2015), but here we will use the ScanPy analysis suite (Wolf et al. 2018) integrated within the single-cell resources in Galaxy (Tekman et al. 2020). |
| Length: | 55 minutes |
| Captions: | Mehmet Tekman |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Demo Video
| 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: | |
| Learning Objectives: |
|
Speaker
Webinar
Wetlab
Speaker
Event
Lecture Video
| Description: | Start here; we will go over all the important things to know to get the most out of this workshop |
| Length: | 15 minutes |
| Captions: | Saskia Hiltemann, Helena Rasche |
| Created: | 15 February 2021 |
| Materials: | |
| Support: |
Admin
Speakers
Tutorial Video
| Length: | 2 hours 50 minutes |
| Captions: | Nate Coraor, Helena Rasche |
| Created: | 28 June 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Tutorial Video
| Length: | 61 minutes |
| Captions: | Martin Čech |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Lecture Video
| Length: | 5 minutes |
| Captions: | Martin Čech |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Tutorial Video
| Length: | 31 minutes |
| Captions: | Catherine Bromhead, Saskia Hiltemann |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: |
Tutorial Video
| Length: | 3 minutes |
| Captions: | The Global Galaxy Community |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Tutorial Video
| Length: | 23 minutes |
| Captions: | Simon Gladman |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Speaker
Tutorial Video
| Length: | 22 minutes |
| Captions: | Helena Rasche, Saskia Hiltemann |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Tutorial Video
| Length: | 2 minutes |
| Captions: | The Global Galaxy Community |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Lecture Video
| Length: | 14 minutes |
| Captions: | Saskia Hiltemann |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Speaker
Tutorial Video
| Length: | 1 hour 28 minutes |
| Captions: | Helena Rasche |
| Created: | 28 June 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Speaker
Tutorial Video
| Length: | 44 minutes |
| Captions: | Anthony Bretaudeau, Helena Rasche |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: |
Speaker
Tutorial Video
| Length: | 31 minutes |
| Captions: | Saskia Hiltemann |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Tutorial Video
| Description: | Here you’ll learn to setup TUS an open source resumable file upload server to process uploads for Galaxy. We use an external process here to offload the main Galaxy processes for more important work and not impact the entire system during periods of heavy uploading. |
| Length: | 7 minutes |
| Captions: | Helena Rasche |
| Created: | 11 March 2022 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Tutorial Video
| Length: | 6 minutes |
| Captions: | Beatriz Serrano-Solano |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: |
Lecture Video
| Length: | 2 minutes |
| Captions: | The Global Galaxy Community |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Lecture Video
| Length: | 2 minutes |
| Captions: | The Global Galaxy Community |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Speaker
Tutorial Video
| Length: | 73 minutes |
| Captions: | Saskia Hiltemann, Helena Rasche |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Speaker
Tutorial Video
| Description: | Running jobs in Singularity |
| Length: | 43 minutes |
| Captions: | Cristóbal Gallardo, Simon Gladman |
| Created: | 28 June 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Speaker
Tutorial Video
| Length: | 24 minutes |
| Captions: | Helena Rasche, Saskia Hiltemann |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Lecture Video
| Length: | 17 minutes |
| Captions: | Catherine Bromhead |
| Created: | 28 June 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Tutorial Video
| Length: | 27 minutes |
| Captions: | Catherine Bromhead |
| Created: | 28 June 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Speaker
Lecture Video
| Length: | 4 minutes |
| Captions: | The Global Galaxy Community |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: | |
| Learning Objectives: |
|
Contributing
Tutorial Video
| Description: | This tutorial will show you how you can preview your contributions to the GTN online using GitPod. |
| Length: | 20 minutes |
| Captions: | Saskia Hiltemann |
| Created: | 15 February 2021 |
| Materials: |
|
| Support: |
|
| Learning Objectives: |
|