GTN Video Library

Introduction to Galaxy Analyses

Automated Videos from Slides

A short introduction to Galaxy

Anna Syme Nicola Soranzo

Options for using Galaxy

Dave Clements Anthony Bretaudeau Anne Pajon Nicola Soranzo Alaa Elghamry

Human Recordings

From peaks to genes

Teresa Müller

A short introduction to Galaxy

Tristan Reynolds

Introduction to Genomics and Galaxy

Natalie Kucher

Galaxy Basics for genomics

Natalie Whitaker-Allen

Galaxy Basics for everyone

Alex Ostrovsky

NGS data logistics

Anton Nekrutenko

Genome Annotation

Automated Videos from Slides

Genome annotation with Prokka

Anna Syme Torsten Seemann Simon Gladman

CRISPR screen analysis

Maria Doyle Kenji Fujihara Twishi Gulati

Refining Genome Annotations with Apollo (prokaryotes)

Anthony Bretaudeau Helena Rasche Nathan Dunn Mateo Boudet

Human Recordings

Genome annotation with Prokka

Automated Text-to-Speech

Genome annotation with Prokka

Anthony Bretaudeau

CRISPR screen analysis

Automated Text-to-Speech

CRISPR screen analysis

Maria Doyle

Bacterial Genome Annotation

Bérénice Batut

Long non-coding RNAs (lncRNAs) annotation with FEELnc

Romane LIBOUBAN

Masking repeats with RepeatMasker

Anthony Bretaudeau

Refining Genome Annotations with Apollo (prokaryotes)

Automated Text-to-Speech

Refining Genome Annotations with Apollo (prokaryotes)

Anthony Bretaudeau

Identification of AMR genes in an assembled bacterial genome

Saim Momin

Genome annotation with Funannotate

Anthony Bretaudeau

Assembly

Human Recordings

An Introduction to Genome Assembly

Simon Gladman

Large genome assembly and polishing

Anna Syme

Using the VGP workflows to assemble a vertebrate genome with HiFi and Hi-C data

Linelle Abueg

Assembly of the mitochondrial genome from PacBio HiFi reads

Delphine Lariviere

Chloroplast genome assembly

Hannah Kim

ERGA post-assembly QC

Delphine Lariviere

Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step

Delphine Lariviere

Decontamination of a genome assembly

Delphine Lariviere

Assembly of metagenomic sequencing data

Giuseppe Defazio

Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data

Meltem Kutnu

Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads

Cristóbal Gallardo

Transcriptomics

Automated Videos from Slides

Whole transcriptome analysis of Arabidopsis thaliana

Cristóbal Gallardo Pavankumar Videm Beatriz Serrano-Solano

Human Recordings

Reference-based RNA-Seq data analysis

Lucille Delisle

Visualization of RNA-Seq results with Volcano Plot

Saim Momin

Whole transcriptome analysis of Arabidopsis thaliana

Automated Text-to-Speech

Whole transcriptome analysis of Arabidopsis thaliana

Cristóbal Gallardo

De novo transcriptome reconstruction with RNA-Seq

Mallory Freeberg

Introduction to Transcriptomics

Fotis E. Psomopoulos

Introduction to Transcriptomics

Fotis E. Psomopoulos

RNA Seq Counts to Viz in R

Fotis E. Psomopoulos

Visualization of RNA-Seq results with Volcano Plot in R

Maria Doyle

Ecology

Human Recordings

Compute and analyze biodiversity metrics with PAMPA toolsuite

Coline Royaux

Metabarcoding/eDNA through Obitools

Yvan Le Bras

Biodiversity data exploration

Olivier Norvez

Variant Analysis

Human Recordings

Exome sequencing data analysis for diagnosing a genetic disease

Khaled Jum'ah

Trio Analysis using Synthetic Datasets from RD-Connect GPAP

Jasper Ouwerkerk

From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis

Anton Nekrutenko

Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data

Wolfgang Maier

M. tuberculosis Variant Analysis

Peter van Heusden

Epigenetics

Automated Videos from Slides

ATAC-Seq data analysis

Lucille Delisle Maria Doyle Florian Heyl

Human Recordings

ATAC-Seq data analysis

Lucille Delisle

ATAC-Seq data analysis

Florian Heyl

Contributing to the Galaxy Training Material

Automated Videos from Slides

Creating Slides

Helena Rasche Bérénice Batut Saskia Hiltemann

Human Recordings

Creating a new tutorial

Bérénice Batut

Creating Slides

Automated Text-to-Speech

Creating Slides

Automated Text-to-Speech

Preview the GTN website as you edit your training material

Saskia Hiltemann

Computational chemistry

Human Recordings

High Throughput Molecular Dynamics and Analysis

Simon Bray Christopher Barnett

Data management in Medicinal Chemistry

Julia Jakiela

Proteomics

Automated Videos from Slides

Introduction to proteomics, protein identification, quantification and statistical modelling

Melanie Föll

Human Recordings

EncyclopeDIA

Emma Leith

Proteogenomics 3: Novel peptide analysis

Subina Mehta

Clinical Metaproteomics 1: Database-Generation

Katherine Do

Clinical Metaproteomics 5: Data Interpretation

Katherine Do

Proteogenomics 1: Database Creation

James Johnson

Clinical Metaproteomics 2: Discovery

Katherine Do

Annotating a protein list identified by LC-MS/MS experiments

Yves Vandenbrouck

Clinical Metaproteomics 4: Quantitation

Katherine Do

Proteogenomics 2: Database Search

Andrew Rajczewski

Clinical Metaproteomics 3: Verification

Katherine Do

MaxQuant and MSstats for the analysis of label-free data

Melanie Föll

Metaproteomics tutorial

Pratik Jagtap

Introduction to proteomics, protein identification, quantification and statistical modelling

Automated Text-to-Speech

Introduction to proteomics, protein identification, quantification and statistical modelling

Automated Text-to-Speech

Climate

Automated Videos from Slides

Pangeo Notebook in Galaxy - Introduction to Xarray

Anne Fouilloux

Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools

Anne Fouilloux

Functionally Assembled Terrestrial Ecosystem Simulator (FATES)

Anne Fouilloux Hui Tang

Introduction to climate data

Anne Fouilloux Jean Iaquinta

Human Recordings

Pangeo Notebook in Galaxy - Introduction to Xarray

Anne Fouilloux

Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools

Anne Fouilloux

Functionally Assembled Terrestrial Ecosystem Simulator (FATES)

Automated Text-to-Speech

Functionally Assembled Terrestrial Ecosystem Simulator (FATES)

Anne Fouilloux

Collaboration with JupyterGIS

Anne Fouilloux

Synthetic Biology

Human Recordings

Evaluating and ranking a set of pathways based on multiple metrics

Joan Hérisson

Designing plasmids encoding predicted pathways by using the BASIC assembly method

Joan Hérisson

Generating theoretical possible pathways for the production of Lycopene in E.Coli using Retrosynthesis tools

Joan Hérisson

Materials Science

Human Recordings

Finding the muon stopping site with pymuon-suite in Galaxy

Leandro Liborio

Single Cell

Automated Videos from Slides

Plates, Batches, and Barcodes

Mehmet Tekman Alex Ostrovsky

An introduction to scRNA-seq data analysis

Mehmet Tekman

Human Recordings

Converting NCBI Data to the AnnData Format

Morgan Howells

Bulk RNA Deconvolution with MuSiC

Wendi Bacon

Understanding Barcodes

Wendi Bacon

Filter, plot and explore single-cell RNA-seq data with Scanpy

Wendi Bacon

Analysis of plant scRNA-Seq Data with Scanpy

Mehmet Tekman

Generating a single cell matrix using Alevin

Marisa Loach

Inferring single cell trajectories with Monocle3

Julia Jakiela

Clustering 3K PBMCs with Seurat

Marisa Loach

Clustering 3K PBMCs with Scanpy

Pavankumar Videm

Pseudobulk Analysis with Decoupler and EdgeR

Diana Chiang Jurado

Pre-processing of 10X Single-Cell RNA Datasets

Pavankumar Videm

Importing files from public atlases

Morgan Howells

Combining single cell datasets after pre-processing

Graeme Tyson

Single-cell Formats and Resources

Morgan Howells

Single-cell Formats and Resources

Morgan Howells

An introduction to scRNA-seq data analysis

Automated Text-to-Speech

An introduction to scRNA-seq data analysis

Automated Text-to-Speech

Inferring single cell trajectories with Scanpy (Python)

Wendi Bacon

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

Morgan Howells

Visualisation

Automated Videos from Slides

Friends Don't Let Friends Make Bad Graphs

Chenxin Li

Human Recordings

Visualisation with Circos

Helena Rasche

Visualisation with Circos

Helena Rasche

Sequence analysis

Human Recordings

Mapping

Peter van Heusden

Mapping

Tristan Reynolds

Quality Control

Florian Heyl

Quality Control

Diana Chiang Jurado

Identification and Evolutionary Analysis of Transcription-Associated Proteins in Streptophyte algae and Land plants

Deepti Varshney

Quality and contamination control in bacterial isolate using Illumina MiSeq Data

Clea Siguret

Microbiome

Automated Videos from Slides

Introduction to Microbiome Analysis

Paul Zierep Bérénice Batut Saskia Hiltemann

Human Recordings

Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition

Engy Nasr

Taxonomic Profiling and Visualization of Metagenomic Data

Tarnima Omara

Metatranscriptomics analysis using microbiome RNA-seq data

Paul Zierep

Antibiotic resistance detection

Willem de Koning

Clinical Metaproteomics 1: Database-Generation

Katherine Do

Calculating α and β diversity from microbiome taxonomic data

Paul Zierep

Clinical Metaproteomics 5: Data Interpretation

Katherine Do

Identification of the micro-organisms in a beer using Nanopore sequencing

Bérénice Batut

Clinical Metaproteomics 2: Discovery

Katherine Do

Metatranscriptomics analysis using microbiome RNA-seq data (short)

Paul Zierep

Remove contamination and host reads

Mina Hojat Ansari

Binning of metagenomic sequencing data

Paul Zierep

Assembly of metagenomic sequencing data

Giuseppe Defazio

Clinical Metaproteomics 4: Quantitation

Katherine Do

Clinical Metaproteomics 3: Verification

Katherine Do

16S Microbial Analysis with mothur (short)

Saskia Hiltemann

Building an amplicon sequence variant (ASV) table from 16S data using DADA2

Matthias Bernt

Introduction to Microbiome Analysis

Saskia Hiltemann

Introduction to Microbiome Analysis

Saskia Hiltemann

Building and Annotating Metagenome-Assembled Genomes (MAGs) from Short Metagenomics Paired Reads

Bérénice Batut

Statistics and machine learning

Human Recordings

GLEAM Image Learner - Validating Skin Lesion Classification on HAM10000

Paulo Cilas Morais Lyra Junior

Image classification in Galaxy with fruit 360 dataset

Kaivan Kamali

Modeling Breast Cancer Subtypes with Flexynesis

Amirhossein Naghsh Nilchi

Basics of machine learning

Anup Kumar

Gleam Multimodal Learner - Head and Neck cancer Recurrence Prediction with HANCOCK

Paulo Cilas Morais Lyra Junior

Regression in Machine Learning

Anup Kumar

Galaxy Tabular Learner - Building a Model using Chowell clinical data

Paulo Cilas Morais Lyra Junior

Deep Learning (Part 3) - Convolutional neural networks (CNN)

Michelle Terese Savage

Deep Learning (Part 2) - Recurrent neural networks (RNN)

Kaivan Kamali

Classification in Machine Learning

Anup Kumar

Deep Learning (Part 1) - Feedforward neural networks (FNN)

Kaivan Kamali

Fine tune large protein model (ProtTrans) using HuggingFace

Anup Kumar

Introduction to Machine Learning using R

Fotis E. Psomopoulos

FAIR Data, Workflows, and Research

Automated Videos from Slides

An earth-system RO-Crate

Marie Josse

DataPLANT ARCs

Saskia Hiltemann Dominik Brilhaus Sabrina Zander Cristina Martins Rodrigues Kevin Frey Martin Kuhl Stella Eggels

Human Recordings

Data management in Medicinal Chemistry

Julia Jakiela

Making clinical datasets FAIR

Sandra Ng

RO-Crate - Introduction

Stian Soiland-Reyes

REMBI - Recommended Metadata for Biological Images – metadata guidelines for bioimaging data

Laura Cooper

Introduction to Data Management Plan (DMP) for Peatland Research and PeatDataHub

Gabriela Lopez-Gonzalez

Using Galaxy and Managing your Data

Human Recordings

Workflow Reports

Saskia Hiltemann

Using Workflow Parameters

Marius van den Beek

Automating Galaxy workflows using the command line

Simon Bray

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

Jonathan Trow

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

Jonathan Trow

Using dataset collections

Delphine Lariviere

Use Jupyter notebooks in Galaxy

Teresa Müller

Rule Based Uploader: Advanced

Assunta DeSanto

Rule Based Uploader

Assunta DeSanto

Understanding Galaxy history system

Ahmed Hamid Awan

Teaching and Hosting Galaxy training

Automated Videos from Slides

Overview of the Galaxy Training Material for Instructors

Helena Rasche

Foundations of Data Science

Automated Videos from Slides

Learning about one gene across biological resources and formats

Lisanna Paladin Bérénice Batut Teresa Müller

Human Recordings

R basics in Galaxy

Fotis E. Psomopoulos

Advanced R in Galaxy

Fotis E. Psomopoulos

Image analysis using Deep Learning

Automated Videos from Slides

Contribute to the BioImage.IO models

Caterina Fuster-Barceló

Welcome to the BioImage Model Zoo

Caterina Fuster-Barceló

BioImage Model Zoo: Advanced models in one-click

Caterina Fuster-Barceló

Development in Galaxy

Automated Videos from Slides

Scripting Galaxy using the API and BioBlend

Nicola Soranzo

ToolFactory: Generating Tools From Simple Scripts

Ross Lazarus Helena Rasche

Human Recordings

ToolFactory: Generating Tools From Simple Scripts

Ross Lazarus

ToolFactory: Generating Tools From More Complex Scripts

Ross Lazarus

Creating Galaxy tools from Conda Through Deployment

Cristóbal Gallardo Alex Ostrovsky

Galaxy Server administration

Automated Videos from Slides

Controlling Galaxy with systemd or Supervisor

Nate Coraor Helena Rasche

Ansible

Helena Rasche Saskia Hiltemann

Galaxy Installation with Ansible

Helena Rasche Nate Coraor Simon Gladman

Server Maintenance: Cleanup, Backup, and Restoration

Helena Rasche Lucille Delisle Nate Coraor

Gearing towards production

Nate Coraor Daniel Blankenberg Abdulrahman Azab Martin Čech

User, Role, Group, Quota, and Authentication managment

Nate Coraor Björn Grüning Helena Rasche

Galaxy Monitoring with Telegraf and Grafana

Helena Rasche Tomas Vondrak

Connecting Galaxy to a compute cluster

Nate Coraor Björn Grüning Helena Rasche

Galaxy Interactive Tools

Nate Coraor Simon Gladman Helena Rasche Anthony Bretaudeau José Manuel Domínguez

Galactic Database

Martin Čech Nicola Soranzo Nate Coraor Helena Rasche

Data Libraries

Helena Rasche Saskia Hiltemann

Reference Data with CVMFS

Simon Gladman Helena Rasche

Galaxy Monitoring with gxadmin

Helena Rasche

Human Recordings

Ansible

John Davis

Ansible

Martin Čech

Galaxy Installation with Ansible

Nate Coraor Helena Rasche

Running Jobs on Remote Resources with Pulsar

Simon Gladman

Running Jobs on Remote Resources with Pulsar

Simon Gladman

User, Role, Group, Quota, and Authentication managment

Automated Text-to-Speech

User, Role, Group, Quota, and Authentication managment

Automated Text-to-Speech

Galaxy Monitoring with Telegraf and Grafana

Automated Text-to-Speech

Galaxy Monitoring with Telegraf and Grafana

Galaxy Tool Management with Ephemeris

Catherine Bromhead

Galaxy Tool Management with Ephemeris

Catherine Bromhead

Connecting Galaxy to a compute cluster

Helena Rasche

Galaxy Interactive Tools

Anthony Bretaudeau

Distributed Object Storage

Gianmauro Cuccuru

Data Libraries

Saskia Hiltemann

Reference Data with CVMFS

Automated Text-to-Speech

Reference Data with CVMFS

Simon Gladman

Galaxy Monitoring with gxadmin

Automated Text-to-Speech

Performant Uploads with TUS

Helena Rasche

Mapping Jobs to Destinations using TPV

Helena Rasche

Training Infrastructure as a Service (TIaaS)

Helena Rasche

Use Apptainer containers for running Galaxy jobs

Simon Gladman

Upgrading Galaxy

Simon Gladman