Training

Friends Don't Let Friends Make Bad Graphs

Visualisation with Circos

Ploting a Microbial Genome with Circos

Visualisations in Galaxy

Calculating CHEK2 variant effect scores from MAVE data with CountESS

Identification of somatic and germline variants from tumor and normal sample pairs

Calling variants in non-diploid systems

Calling variants in diploid systems

Deciphering Virus Populations - Single Nucleotide Variants (SNVs) and Specificities in Baculovirus Isolates

Exome sequencing data analysis for diagnosing a genetic disease

Somatic Variant Discovery from WES Data Using Control-FREEC

Trio Analysis using Synthetic Datasets from RD-Connect GPAP

Mapping and molecular identification of phenotype-causing mutations

Calling very rare variants

Working with Beacon V2: A Comprehensive Guide to Creating, Uploading, and Searching for Variants with Beacons

Querying the University of Bradford GDC Beacon Database for Copy Number Variants (CNVs)

Introduction to Variant analysis

RNA Seq Counts to Viz in R

Reference-based RNAseq data analysis (long)

RNA-seq Alignment with STAR

Visualization of RNA-Seq results with Volcano Plot in R

RNA-Seq analysis with AskOmics Interactive Tool

Visualization of RNA-Seq results with CummeRbund

Visualization of RNA-Seq results with heatmap2

Small Non-coding RNA Clustering using BlockClust

2: RNA-seq counts to genes

RNA-Seq data analysis, clustering and visualisation tutorial

3: RNA-seq genes to pathways

RNA-RNA interactome data analysis

De novo transcriptome assembly, annotation, and differential expression analysis

GO Enrichment Analysis

Differential abundance testing of small RNAs

CLIP-Seq data analysis from pre-processing to motif detection

1: RNA-Seq reads to counts

Network analysis with Heinz

Visualization of RNA-Seq results with Volcano Plot

Genome-wide alternative splicing analysis

De novo transcriptome reconstruction with RNA-Seq

Pathway analysis with the MINERVA Platform

Reference-based RNA-Seq data analysis

Introduction to Transcriptomics

Running a workshop as an instructor

Live Coding is a Skill

Hybrid training

Asynchronous training

Training Infrastructure as a Service

Course Builder

Galaxy Admin Training

Set up a Galaxy for Training

Teaching online

Organizing a workshop

Teaching experiences

Overview of the Galaxy Training Material for Instructors

Workshop Kickoff

Designing plasmids encoding predicted pathways by using the BASIC assembly method

Evaluating and ranking a set of pathways based on multiple metrics

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

Introduction to Machine Learning using R

Supervised Learning with Hyperdimensional Computing

Fine tune large protein model (ProtTrans) using HuggingFace

Regression in Machine Learning

Prepare Data from CbioPortal for Flexynesis Integration

Identifing Survival Markers of Brain tumor with Flexynesis

Interval-Wise Testing for omics data

Introduction to deep learning

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

PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis

Unsupervised Analysis of Bone Marrow Cells with Flexynesis

GLEAM Image Learner - Validating Skin Lesion Classification on HAM10000

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

Galaxy Tabular Learner - Building a Model using Chowell clinical data

Modeling Breast Cancer Subtypes with Flexynesis

Train and Test a Deep learning image classifier with Galaxy-Ludwig

Age prediction using machine learning

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

Basics of machine learning

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

GTEx Tissue Modeling with Galaxy Image Learner

Text-mining with the SimText toolset

A Docker-based interactive Jupyterlab powered by GPU for artificial intelligence in Galaxy

Image classification in Galaxy with fruit 360 dataset

Classification in Machine Learning

Clustering in Machine Learning

Machine learning: classification and regression

GO Enrichment Analysis on Single-Cell RNA-Seq Data

Pseudobulk Analysis with Decoupler and EdgeR

Automated Cell Annotation

Trajectory analysis

Inferring single cell trajectories with Monocle3

Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution

Inferring single cell trajectories with Monocle3 (R)

Single-cell Formats and Resources

Inferring single cell trajectories with Scanpy

Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution

Batch Correction and Integration with Seurat or Scanpy

Inferring single cell trajectories with Scanpy (Python)

Plates, Batches, and Barcodes

Scanpy Parameter Iterator

Clustering 3K PBMCs with Seurat

Multi-sample batch correction with Harmony and SnapATAC2

Converting NCBI Data to the AnnData Format

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

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

Evaluating Reference Data for Bulk RNA Deconvolution

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

Importing files from public atlases

Combining single cell datasets after pre-processing

Single-cell ATAC-seq standard processing with SnapATAC2

Comparing inferred cell compositions using MuSiC deconvolution

Clustering 3K PBMCs with Scanpy

Downstream Single-cell RNA analysis with RaceID

Removing the effects of the cell cycle

Filter, plot, and explore single cell RNA-seq data with Seurat (R)

Understanding Barcodes

Generating a single cell matrix using Alevin and combining datasets (bash + R)

An introduction to scRNA-seq data analysis

Pre-processing of 10X Single-Cell ATAC-seq Datasets

Generating a single cell matrix using Alevin

Single-cell quality control with scater

Pre-processing of Single-Cell RNA Data

Bulk RNA Deconvolution with MuSiC

Pre-processing of 10X Single-Cell RNA Datasets

Converting between common single cell data formats

Mapping

Clean and manage Sanger sequences from raw files to aligned consensus

Primer and primer scheme design for pan-specific detection and sequencing of viral pathogens across genotypes

Screening assembled genomes for contamination using NCBI FCS

Quality Control

Quality and contamination control in bacterial isolate using Illumina MiSeq Data

Label-free versus Labelled - How to Choose Your Quantitation Method

Proteogenomics 1: Database Creation

Peptide and Protein ID using SearchGUI and PeptideShaker

MaxQuant and MSstats for the analysis of TMT data

Label-free data analysis using MaxQuant

Peptide Library Data Analysis

metaQuantome 2: Function

Multiomics data analysis using MultiGSEA

Biomarker candidate identification

Peptide and Protein ID using OpenMS tools

Metaproteomics tutorial

Secretome Prediction

Single Cell Proteomics data analysis with bioconductor-scp

Clinical Metaproteomics 3: Verification

Protein FASTA Database Handling

Proteogenomics 3: Novel peptide analysis

Neoantigen 4: Variant Annotation

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

Neoantigen 5b: IEDB binding Validated Neopeptides

Clinical Metaproteomics 1: Database-Generation

metaQuantome 3: Taxonomy

Clinical Metaproteomics 2: Discovery

Peptide and Protein Quantification via Stable Isotope Labelling (SIL)

EncyclopeDIA

Neoantigen 5a: Predicting HLA Binding

Neoantigen 1a: Fusion-Database-Generation

DIA Analysis using OpenSwathWorkflow

Library Generation for DIA Analysis

Mass spectrometry imaging: Loading and exploring MSI data

Proteogenomics 2: Database Search

Clinical Metaproteomics 4: Quantitation

MaxQuant and MSstats for the analysis of label-free data

Clinical Metaproteomics 5: Data Interpretation

Neoantigen 1b: Non-Reference-Database-Generation

Machine Learning Modeling of Anticancer Peptides

Neoantigen 3: PepQuery2 Verification

Detection and quantitation of N-termini (degradomics) via N-TAILS

Neoantigen 2: Database merge and FragPipe discovery

metaQuantome 1: Data creation

Statistical analysis of DIA data

Introduction to proteomics, protein identification, quantification and statistical modelling

NCBI BLAST+ against the MAdLand

Whole transcriptome analysis of Arabidopsis thaliana

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

Analysis of plant scRNA-Seq Data with Scanpy

Avian influenza viral strain analysis from gene segment sequencing data

Pox virus genome analysis from tiled-amplicon sequencing data

M. tuberculosis Variant Analysis

16S Microbial Analysis with mothur (extended)

16S Microbial Analysis with mothur (short)

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

QIIME 2 Moving Pictures

Indexing and profiling microbes with MetaSBT

QIIME 2 Cancer Microbiome Intervention

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

Metatranscriptomics analysis using microbiome RNA-seq data

Binning of metagenomic sequencing data

Metatranscriptomics analysis using microbiome RNA-seq data (short)

16S Microbial analysis with Nanopore data

Clinical Metaproteomics 3: Verification

Identifying Mycorrhizal Fungi from ITS2 sequencing using LotuS2

Clinical Metaproteomics 1: Database-Generation

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

Clinical Metaproteomics 2: Discovery

Antibiotic resistance detection

Remove contamination and host reads

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

Calculating α and β diversity from microbiome taxonomic data

Clinical Metaproteomics 4: Quantitation

Clinical Metaproteomics 5: Data Interpretation

Assembly of metagenomic sequencing data

Query an annotated mobile genetic element database to identify and annotate genetic elements (e.g. plasmids) in metagenomics data

MGnify v5.0 Amplicon Pipeline

Taxonomic Profiling and Visualization of Metagenomic Data

Analyses of metagenomics data - The global picture

Introduction to Microbiome Analysis

Mass spectrometry: LC-MS data processing

Mass spectrometry: GC-MS analysis with the metaMS package

Mass spectrometry: LC-MS preprocessing with XCMS

Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms)

Mass spectrometry imaging: Examining the spatial distribution of analytes

Mass spectrometry: LC-MS analysis

Mass spectrometry imaging: Finding differential analytes

Molecular formula assignment and mass recalibration with MFAssignR package

Predicting EI+ mass spectra with QCxMS

Introduction to Metabolomics

Finding the muon stopping site with pymuon-suite in Galaxy

Best Practices for Citing Galaxy

Introduction to the Dataverse Integration in Galaxy

Upload data to Galaxy

IGV Introduction

Options for using Galaxy

Data Manipulation Olympics

Introduction to Genomics and Galaxy

How to reproduce published Galaxy analyses

NGS data logistics

From peaks to genes

Very Short Introductions: QC

Introduction to Galaxy as an RDM platform

Galaxy Basics for genomics

Galaxy Basics for everyone

A short introduction to Galaxy

Introduction to Galaxy

AI pipeline for annotating marine species (Project Moorev - Marine)

Quantification of electrophoresis gel bands using QuPath and Galaxy imaging tools

Quantitative Analysis of Histological Staining Using Color Deconvolution

Segmentation of Anatomical Structures in Medical 3-D Images

Where to start with bioimage analysis in Galaxy

Introduction to Image Analysis using Galaxy

Object tracking using CellProfiler

Analyse HeLa fluorescence siRNA screen

Tracking of mitochondria and capturing mitoflashes

Training Custom YOLO Models for Segmentation of Bioimages

Execute a BiaPy workflow in Galaxy

Overview of the Galaxy OMERO-suite - Upload images and metadata in OMERO using Galaxy

Voronoi segmentation

Quantification of single-molecule RNA fluorescence in situ hybridization (smFISH) in yeast cell lines

Nucleoli segmentation and feature extraction using CellProfiler

Parameter tuning and optimization - Evaluating nuclei segmentation with Galaxy

End-to-End Tissue Microarray Image Analysis with Galaxy-ME

Content Tracking and Verification in Galaxy Workflows with ISCC-SUM

Using BioImage.IO models for image analysis in Galaxy

Genomic Data Visualisation with JBrowse2

Genomic Data Visualisation with JBrowse

Microbial Variant Calling

Dataset construction for bacterial comparative genomics

Genome Annotation

Pangenome analysis with Roary

Bacterial pangenomics

Bacterial genome quality control

Creating an Official Gene Set

Comparison of two annotation tools - Helixer and Braker3

Identification of AMR genes in an assembled bacterial genome

Refining Genome Annotations with Apollo (prokaryotes)

Bacterial Genome Annotation

Genome annotation with Helixer

Genome annotation with Braker3

From small to large-scale genome comparison

Secondary metabolite discovery

Genome annotation with Prokka

CRISPR screen analysis

Long non-coding RNAs (lncRNAs) annotation with FEELnc

Refining Genome Annotations with Apollo (eukaryotes)

Functional annotation of protein sequences

Genome annotation with Maker

Essential genes detection with Transposon insertion sequencing

Genome annotation with Maker (short)

Comparative gene analysis in unannotated genomes

Genome annotation with Funannotate

Introduction to Genome Annotation

Masking repeats with RepeatMasker

Exporting to Onedata remote

Importing (uploading) data from Onedata

Using dataset collections

RStudio in Galaxy

Use Jupyter notebooks in Galaxy

Understanding Galaxy history system

Group tags for complex experimental designs

Name tags for following complex histories

Rule Based Uploader

Downloading and Deleting Data in Galaxy

Searching Your History

Getting started with Onedata distributed storage

Annotate, prepare tests and publish Galaxy workflows in workflow registries

Rule Based Uploader: Advanced

Onedata user-owned storage

JupyterLab in Galaxy

Extracting Workflows from Histories

Accessing IIIF from within Galaxy

Creating high resolution images of Galaxy Workflows

Getting data into Galaxy

Galaxy workflows in Dockstore

Using Workflow Parameters

InterMine integration with Galaxy

Workflow Reports

Creating, Editing and Importing Galaxy Workflows

Uploading Data to Zenodo from Galaxy

Integrating InvenioRDM-compatible Repositories with Galaxy

An earth-system RO-Crate

Data management in Medicinal Chemistry

FAIRification of an RNAseq dataset

Persistent Identifiers

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

FAIR Bioimage Metadata

Access

Submitting workflows to LifeMonitor

Best practices for workflows in GitHub repositories

Data Registration

FAIR Galaxy Training Material

Exporting Workflow Run RO-Crates from Galaxy

RO-Crate in Python

Metadata

FAIR data management solutions

DataPLANT ARCs

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

FAIR and its Origins

FAIR in a nutshell

Workflow Run RO-Crate Introduction

Sequence data submission to ENA

Making clinical datasets FAIR

RO-Crate - Introduction

Phylogenetic analysis for bacterial comparative genomics

Tree thinking for tuberculosis evolution and epidemiology

Identifying tuberculosis transmission links: from SNPs to transmission clusters

Phylogenetics - Back to Basics - Phylogenetic Networks

Phylogenetics - Back to Basics - Estimating trees from alignments

Phylogenetics - Back to Basics - Building Trees

Phylogenetics - Back to Basics - Multiple Sequence Alignment

Phylogenetics - Back to Basics - Terminology

Phylogenetics - Back to Basics - Introduction

Phylogenetics - Back to basics

CUT&RUN data analysis

DNA Methylation data analysis

Identification of the binding sites of the Estrogen receptor

Hi-C analysis of Drosophila melanogaster cells using HiCExplorer

Infinium Human Methylation BeadChip

ATAC-Seq data analysis

Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)

Formation of the Super-Structures on the Inactive X

Introduction to ChIP-Seq data analysis

Introduction to DNA Methylation data analysis

Foundational Aspects of Machine Learning using Python

Motivation and Demotivation

Training techniques to enhance learner participation and engagement

Assessment and feedback in training and teachings

Train-the-Trainer: putting it all together

Regulations/standards for AI using DOME

Optimizing DNA Sequences for Biological Functions using a DNA LLM

Generating Artificial Yeast DNA Sequences using a DNA LLM

Deep Learning (without Generative Artificial Intelligence) using Python

Predicting Mutation Impact with Zero-shot Learning using a pretrained DNA LLM

Neural networks using Python

Fine-tuning a LLM for DNA Sequence Classification

Pretraining a Large Language Model (LLM) from Scratch on DNA Sequences

Cleaning GBIF data using OpenRefine

Visualize EBV cube data with Panoply netCDF viewer

QGIS Web Feature Services

Audio data annotation with NEAL (Nature + Energy Audio labeler)

Creating FAIR Quality assessment reports and draft of Data Papers from EML metadata with MetaShRIMPS

Biodiversity data exploration

RAD-Seq de-novo data analysis

Preparing genomic data for phylogeny reconstruction

Sentinel 2 biodiversity

Visualization of Climate Data using NetCDF xarray Map Plotting

Species distribution modeling

SAM3 – AI-based Semantic Segmentation of marine biodiversity Images and Videos

Creating metadata using Ecological Metadata Language (EML) standard with EML Assembly Line functionalities

Cleaning GBIF data for the use in Ecology

Regional GAM

Ecoregionalization workflow tutorial

Life Traits Ecoregionalization workflow

Checking expected species and contamination in bacterial isolate

Marine Omics identifying biosynthetic gene clusters

Phylodiversity analysis quick tutorial

Metabarcoding/eDNA through Obitools

Taxonomic Analysis of eDNA

Obis marine indicators

Compute and analyze biodiversity metrics with PAMPA toolsuite

Champs blocs indicators

RAD-Seq to construct genetic maps

Data submission using ENA upload Tool

From NDVI data with OpenEO to time series visualisation with Holoviews

RAD-Seq Reference-based data analysis

Object detection with YOLO

Text-Mining articles with GROBID

Text-Mining Differences in Chinese Newspaper Articles

Montreal Forced Aligner

OpenRefine Tutorial for researching cultural data

Transcribing Audio and Video files with Automated Speech Recognition

Introduction to Digital Humanities in Galaxy

ToolFactory: Generating Tools From More Complex Scripts

Adding and updating best practice metadata for Galaxy tools using the bio.tools registry

Data source integration

Galaxy Interactive Tools

Writing Automated Tests for Galaxy

Setting up a dev Onedata instance

Contributing to BioBlend as a developer

Debugging Galaxy

nb2workflow: Generating Galaxy Tools From Jupyter Notebooks

Creating Galaxy tools from Conda Through Deployment

Contributing a New Feature to Galaxy Core

Prerequisites for building software/conda packages

Architecture 15 - Galaxy Production Deployment

Architecture 03 - Galaxy Architecture Principles

Architecture 08 - Galaxy Application Components: Models, Managers, and Services

Architecture 06 - Dependency Injection in Galaxy

Generic plugins

Architecture 07 - Galaxy Task Management with Celery

Tool Shed: sharing Galaxy tools

Tool development and integration into Galaxy

Architecture 04 - Galaxy Files and Directory Structure

Tool Dependencies and Conda

Architecture 09 - Galaxy Plugin Architecture

Architecture 12 - Galaxy Client Architecture

Architecture 10 - Galaxy File Sources Architecture

Galaxy Interactive Tours

Tool Dependencies and Containers

Galaxy Interactive Environments

ToolFactory: Generating Tools From Simple Scripts

Galaxy Webhooks

Scripting Galaxy using the API and BioBlend

Architecture 02 - Galaxy Project Management and Contribution

Architecture 13 - Galaxy Dependencies Management

Architecture 16 - Galaxy Testing

Architecture 05 - Galaxy Web Frameworks

JavaScript plugins

Architecture 01 - Galaxy Ecosystem and Projects

Architecture 11 - Galaxy Markdown Architecture

Architecture 14 - Galaxy Startup Process

SQL with R

Introduction to SQL

Basics of using Git from the Command Line

Make & Snakemake

SQL with Python

Variant Calling Workflow

Advanced SQL

Version Control with Git

Advanced CLI in Galaxy

CLI Educational Game - Bashcrawl

One protein along the UniProt page

SQL Educational Game - Murder Mystery

CLI basics

Learning about one gene across biological resources and formats

Data Manipulation Olympics

Python - Multiprocessing

Python - Coding Style

Python - Subprocess

Python - Globbing

Python - Type annotations

Virtual Environments For Software Development

Conda Environments For Software Development

Python - Argparse

Python - Testing

Python - Introductory Graduation

Python - Try & Except

Versioning your code and data with git

Python - Files & CSV

Data manipulation with Pandas

Python - Loops

Python - Flow Control

Introduction to sequencing with Python (part four)

Python - Lists & Strings & Dictionaries

Introduction to sequencing with Python (part three)

Data Manipulation Olympics - JQ

Introduction to sequencing with Python (part two)

dplyr & tidyverse for data processing

Data Manipulation Olympics - SQL

Plotting in Python

Python - Basic Types & Type Conversion

Data visualisation Olympics - Visualization in R

Introduction to sequencing with Python (part one)

Advanced R in Galaxy

Advanced Python

Python - Functions

Python - Math

Python - Warm-up for statistics and machine learning

Introduction to Python

R basics in Galaxy

A (very) brief history of genomics

SARS-CoV-2 Viral Sample Alignment and Variant Visualization

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

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

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

Submitting sequence data to ENA

Automating Galaxy workflows using the command line

Removal of human reads from SARS-CoV-2 sequencing data

Adding Quizzes to your Tutorial

Adding auto-generated video to your slides

Updating diffs in admin training

Design and plan session, course, materials

Tools, Data, and Workflows for tutorials

Including a new topic

Principles of learning and how they apply to training and teaching

Generating PDF artefacts of the website

GTN Metadata

Creating Interactive Galaxy Tours

Teaching Python

Contributing with GitHub via its interface

Contributing to the Galaxy Training Network with GitHub

Updating tool versions in a tutorial

Creating Slides

Creating content in Markdown

FAIR Galaxy Training Material

Single Cell Publication - Data Plotting

Single Cell Publication - Data Analysis

Creating a new tutorial

FAIR-by-Design methodology

Preview the GTN website as you edit your training material

Overview of the Galaxy Training Material

Setting up molecular systems

Analysis of molecular dynamics simulations

Protein-ligand docking

High Throughput Molecular Dynamics and Analysis

Data management in Medicinal Chemistry

Running molecular dynamics simulations using NAMD

Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring

Running molecular dynamics simulations using GROMACS

Protein target prediction of a bioactive ligand with Align-it and ePharmaLib

Make your tools available on your subdomain

Creation of the labs in the different Galaxy instances for your community

Creation of resources listing all the tools and their metadata relevant to your community

Creation of resources listing Galaxy workflow for your community

Creation of a Galaxy tutorial table for your community

Creating a Special Interest Group

What's a Special Interest Group?

Creating community content

Visualize Climate data with Panoply netCDF viewer

Getting your hands-on earth data

Functionally Assembled Terrestrial Ecosystem Simulator (FATES) with Galaxy Climate JupyterLab

Collaboration with JupyterGIS

Ocean Data View (ODV)

Analyse Argo data

Sentinel 5P data visualisation

Pangeo Notebook in Galaxy - Introduction to Xarray

Nitrate DMQC for autonomous platforms such as Argo floats

Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools

Functionally Assembled Terrestrial Ecosystem Simulator (FATES)

Ocean's variables study

Getting your hands-on climate data

Introduction to climate data

An introduction to get started in genome assembly and annotation

Deeper look into Genome Assembly algorithms

Genome assembly and assembly QC - Introduction short version

Large genome assembly and polishing

Unicycler Assembly

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

Making sense of a newly assembled genome

Assembly of the mitochondrial genome from PacBio HiFi reads

De Bruijn Graph Assembly

Genome assembly using PacBio data

ERGA post-assembly QC

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

Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)

Genome Assembly Quality Control

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

Decontamination of a genome assembly

Chloroplast genome assembly

Assembly of metagenomic sequencing data

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

Hybrid genome assembly - Nanopore and Illumina

An Introduction to Genome Assembly

Welcome to the BioImage Model Zoo

BioImage Model Zoo: Advanced models in one-click

Contribute to the BioImage.IO models

Adding file-sources to Galaxy

Configuring the Onedata connectors (remotes, Object Store, BYOS, BYOD)

Alternative Celery Deployment for Galaxy

Deploying a Beacon v1 in Galaxy

Use Apptainer containers for running Galaxy jobs

Customizing the look of Galaxy (Manual)

Mapping Jobs to Destinations using TPV

Automation with Jenkins

Upgrading Galaxy

Customizing the look of Galaxy

Reference Data with CVMFS without Ansible

Galaxy Monitoring with Reports

Performant Uploads with TUS

Training Infrastructure as a Service (TIaaS)

Galaxy Database schema

Create a subdomain for your community on UseGalaxy.eu

Monitoring Galaxy and Pulsar with Sentry

How I learned to stop worrying and love the systemd

Enable upload via FTP

Empathy

Galaxy Monitoring with gxadmin

Galaxy Tool Management with Ephemeris

Galaxy Monitoring

Galaxy Administrator Time Burden and Technology Usage

uWSGI

Galactic Database

Galaxy Troubleshooting

Galaxy Monitoring with Telegraf and Grafana

Server: Other

User, Role, Group, Quota, and Authentication managment

Connecting Galaxy to a compute cluster

Distributed Object Storage

Ansible

External Authentication

Gearing towards production

Reference Data with Data Managers

Galaxy Interactive Tools

Advanced customisation of a Galaxy instance

Data Libraries

Galaxy Installation with Ansible

Server Maintenance: Cleanup, Backup, and Restoration