Training

Friends Don't Let Friends Make Bad Graphs

Ploting a Microbial Genome with Circos

Visualisation with Circos

Visualisations in Galaxy

Calculating CHEK2 variant effect scores from MAVE data with CountESS

Pangenome variant calling with DeepVariant

Somatic Variant Discovery from WES Data Using Control-FREEC

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

Exome sequencing data analysis for diagnosing a genetic disease

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

Trio Analysis using Synthetic Datasets from RD-Connect GPAP

Calling variants in non-diploid systems

Calling variants in diploid systems

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

Visualization of RNA-Seq results with Volcano Plot in R

RNA-seq Alignment with STAR

RNA Seq Counts to Viz in R

Reference-based RNAseq data analysis (long)

RNA-Seq analysis with AskOmics Interactive Tool

Visualization of RNA-Seq results with CummeRbund

Genome-wide alternative splicing analysis

3: RNA-seq genes to pathways

Visualization of RNA-Seq results with heatmap2

Differential abundance testing of small RNAs

1: RNA-Seq reads to counts

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

Network analysis with Heinz

2: RNA-seq counts to genes

RNA-Seq data analysis, clustering and visualisation tutorial

GO Enrichment Analysis

RNA-RNA interactome data analysis

Small Non-coding RNA Clustering using BlockClust

De novo transcriptome assembly, annotation, and differential expression analysis

Visualization of RNA-Seq results with Volcano Plot

De novo transcriptome reconstruction with RNA-Seq

Pathway analysis with the MINERVA Platform

Reference-based RNA-Seq data analysis

Introduction to Transcriptomics

Set up a Galaxy for Training

Galaxy Admin Training

Hybrid training

Teaching experiences

Live Coding is a Skill

Asynchronous training

Training Infrastructure as a Service

Course Builder

Organizing a workshop

Teaching online

Running a workshop as an instructor

Workshop Kickoff

Overview of the Galaxy Training Material for Instructors

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

Designing plasmids encoding predicted pathways by using the BASIC assembly method

Evaluating and ranking a set of pathways based on multiple metrics

Introduction to Machine Learning using R

Supervised Learning with Hyperdimensional Computing

Fine tune large protein model (ProtTrans) using HuggingFace

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

Text-mining with the SimText toolset

Basics of machine learning

Unsupervised Analysis of Bone Marrow Cells with Flexynesis

Galaxy Tabular Learner - Building a Model using Chowell clinical data

Identifing Survival Markers of Brain tumor with Flexynesis

Modeling Breast Cancer Subtypes with Flexynesis

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

Comparing ligand-binding site predictions across different protein structure modalities using SIMORGH

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

Image classification in Galaxy with fruit 360 dataset

Prepare Data from CbioPortal for Flexynesis Integration

Age prediction using machine learning

Regression in Machine Learning

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

Interval-Wise Testing for omics data

GLEAM Image Learner - Validating Skin Lesion Classification on HAM10000

GTEx Tissue Modeling with Galaxy Image Learner

Classification in Machine Learning

Introduction to deep learning

PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis

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

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

Clustering in Machine Learning

Machine learning: classification and regression

GO Enrichment Analysis on Single-Cell RNA-Seq Data

Spatial transcriptomics analysis of a primary dermal melanoma section from Xenium

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

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

Clustering 3K PBMCs with Seurat

Scanpy Parameter Iterator

Converting NCBI Data to the AnnData Format

Evaluating Reference Data for Bulk RNA Deconvolution

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

Multi-sample batch correction with Harmony and SnapATAC2

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

Combining single cell datasets after pre-processing

Comparing inferred cell compositions using MuSiC deconvolution

Removing the effects of the cell cycle

Clustering 3K PBMCs with Scanpy

Downstream Single-cell RNA analysis with RaceID

Single-cell ATAC-seq standard processing with SnapATAC2

Importing files from public atlases

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

Bulk RNA Deconvolution with MuSiC

Converting between common single cell data formats

Pre-processing of Single-Cell RNA Data

Generating a single cell matrix using Alevin

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

Pre-processing of 10X Single-Cell RNA Datasets

Single-cell quality control with scater

Quality and contamination control in bacterial isolate using Illumina MiSeq Data

Quality Control

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

Clean and manage Sanger sequences from raw files to aligned consensus

Screening assembled genomes for contamination using NCBI FCS

Mapping

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

Biomarker candidate identification

MaxQuant and MSstats for the analysis of TMT data

Neoantigen 5a: Predicting HLA Binding

DIA Analysis using OpenSwathWorkflow

Neoantigen 5b: IEDB binding Validated Neopeptides

Neoantigen 1b: Non-Reference-Database-Generation

Mass spectrometry imaging: Loading and exploring MSI data

Clinical Metaproteomics 5: Data Interpretation

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

metaQuantome 3: Taxonomy

MaxQuant and MSstats for the analysis of label-free data

Protein FASTA Database Handling

Multiomics data analysis using MultiGSEA

Label-free data analysis using MaxQuant

Peptide Library Data Analysis

Metaproteomics tutorial

Neoantigen 4: Variant Annotation

Clinical Metaproteomics 3: Verification

EncyclopeDIA

Clinical Metaproteomics 1: Database-Generation

Single Cell Proteomics data analysis with bioconductor-scp

metaQuantome 2: Function

Proteogenomics 1: Database Creation

Neoantigen 2: Database merge and FragPipe discovery

Peptide and Protein ID using SearchGUI and PeptideShaker

Peptide and Protein ID using OpenMS tools

Neoantigen 1a: Fusion-Database-Generation

Clinical Metaproteomics 4: Quantitation

Proteogenomics 2: Database Search

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

Neoantigen 3: PepQuery2 Verification

metaQuantome 1: Data creation

Proteogenomics 3: Novel peptide analysis

Clinical Metaproteomics 2: Discovery

Secretome Prediction

Peptide and Protein Quantification via Stable Isotope Labelling (SIL)

Machine Learning Modeling of Anticancer Peptides

Library Generation for DIA Analysis

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

M. tuberculosis Variant Analysis

Pox virus genome analysis from tiled-amplicon sequencing data

16S Microbial Analysis with mothur (short)

16S Microbial Analysis with mothur (extended)

Indexing and profiling microbes with MetaSBT

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

QIIME 2 Cancer Microbiome Intervention

QIIME 2 Moving Pictures

Metatranscriptomics analysis using microbiome RNA-seq data (short)

Binning of metagenomic sequencing data

Identifying Mycorrhizal Fungi from ITS2 sequencing using LotuS2

Detection of shared microbial strains with SameStr

Calculating α and β diversity from microbiome taxonomic 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

Antibiotic resistance detection

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

Remove contamination and host reads

Introduction to Metabarcoding using QIIME 2

16S Microbial analysis with Nanopore data

Taxonomic Profiling and Visualization of Metagenomic Data

Metatranscriptomics analysis using microbiome RNA-seq data

Assembly of metagenomic sequencing data

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

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

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

Predicting EI+ mass spectra with QCxMS

Mass spectrometry: LC-MS analysis

Mass spectrometry imaging: Examining the spatial distribution of analytes

Molecular formula assignment and mass recalibration with MFAssignR package

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

Mass spectrometry imaging: Finding differential analytes

Introduction to Metabolomics

Finding the muon stopping site with pymuon-suite in Galaxy

Upload data to Galaxy

Introduction to the Dataverse Integration in Galaxy

IGV Introduction

Best Practices for Citing Galaxy

Options for using Galaxy

Data Manipulation Olympics

How to reproduce published Galaxy analyses

Introduction to Genomics and Galaxy

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

Nucleoli segmentation and feature extraction using CellProfiler

Object tracking using CellProfiler

Segmentation of Anatomical Structures in Medical 3-D Images

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

Voronoi segmentation

Tracking of mitochondria and capturing mitoflashes

Parameter tuning and optimization - Evaluating nuclei segmentation with Galaxy

Use Pycytominer in Galaxy for processing high dimensional image-based readouts

Using BioImage.IO models for image analysis in Galaxy

Quantification of electrophoresis gel bands using QuPath and Galaxy imaging tools

Content Tracking and Verification in Galaxy Workflows with ISCC-SUM

Introduction to Image Analysis using Galaxy

Analyse HeLa fluorescence siRNA screen

Training Custom YOLO Models for Segmentation of Bioimages

Quantitative Analysis of Histological Staining Using Color Deconvolution

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

Where to start with bioimage analysis in Galaxy

Execute a BiaPy workflow in Galaxy

Genomic Data Visualisation with JBrowse2

Genomic Data Visualisation with JBrowse

Microbial Variant Calling

Bacterial genome quality control

Genome Annotation

Dataset construction for bacterial comparative genomics

Pangenome analysis with Roary

Bacterial pangenomics

Creating an Official Gene Set

Bacterial Genome Annotation

Refining Genome Annotations with Apollo (prokaryotes)

Identification of AMR genes in an assembled bacterial genome

Comparison of two annotation tools - Helixer and Braker3

From small to large-scale genome comparison

Genome annotation with Helixer

Genome annotation with Braker3

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)

Genome annotation with Funannotate

Comparative gene analysis in unannotated genomes

Introduction to Genome Annotation

Masking repeats with RepeatMasker

Onedata user-owned storage

Understanding Galaxy history system

RStudio in Galaxy

Accessing IIIF from within Galaxy

Rule Based Uploader

Importing (uploading) data from Onedata

Group tags for complex experimental designs

Use Jupyter notebooks in Galaxy

Using dataset collections

Creating high resolution images of Galaxy Workflows

Extracting Workflows from Histories

Getting started with Onedata distributed storage

Downloading and Deleting Data in Galaxy

Name tags for following complex histories

Searching Your History

Rule Based Uploader: Advanced

Annotate, prepare tests and publish Galaxy workflows in workflow registries

JupyterLab in Galaxy

Exporting to Onedata remote

Galaxy workflows in Dockstore

Getting data into Galaxy

Workflow Reports

Creating, Editing and Importing Galaxy Workflows

InterMine integration with Galaxy

Using Workflow Parameters

Integrating InvenioRDM-compatible Repositories with Galaxy

Uploading Data to Zenodo from Galaxy

An earth-system RO-Crate

FAIRification of an RNAseq dataset

Persistent Identifiers

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

Access

FAIR Bioimage Metadata

Submitting workflows to LifeMonitor

Data Registration

Best practices for workflows in GitHub repositories

FAIR data management solutions

Metadata

RO-Crate in Python

Exporting Workflow Run RO-Crates from Galaxy

DataPLANT ARCs

RO-Crate - Introduction

Sequence data submission to ENA

Workflow Run RO-Crate Introduction

Making clinical datasets FAIR

FAIR and its Origins

FAIR in a nutshell

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

Phylogenetic analysis for bacterial comparative genomics

Identifying tuberculosis transmission links: from SNPs to transmission clusters

Tree thinking for tuberculosis evolution and epidemiology

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

Infinium Human Methylation BeadChip

Identification of the binding sites of the Estrogen receptor

CUT&RUN data analysis

ATAC-Seq data analysis

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

DNA Methylation data analysis

Hi-C analysis of Drosophila melanogaster cells using HiCExplorer

Formation of the Super-Structures on the Inactive X

Introduction to DNA Methylation data analysis

Introduction to ChIP-Seq data analysis

Training techniques to enhance learner participation and engagement

Assessment and feedback in training and teachings

Motivation and Demotivation

Train-the-Trainer: putting it all together

Foundational Aspects of Machine Learning using Python

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

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

Cleaning GBIF data using OpenRefine

Visualize EBV cube data with Panoply netCDF viewer

QGIS Web Feature Services

Marine Omics identifying biosynthetic gene clusters

Preparing genomic data for phylogeny reconstruction

Checking expected species and contamination in bacterial isolate

Taxonomic Analysis of eDNA

From NDVI data with OpenEO to time series visualisation with Holoviews

Compute and analyze biodiversity metrics with PAMPA toolsuite

Visualization of Climate Data using NetCDF xarray Map Plotting

Ecoregionalization workflow tutorial

RAD-Seq de-novo data analysis

Data submission using ENA upload Tool

Biodiversity data exploration

Regional GAM

Sentinel 2 biodiversity

Metabarcoding/eDNA through Obitools

Obis marine indicators

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

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

RAD-Seq to construct genetic maps

Species distribution modeling

Phylodiversity analysis quick tutorial

Cleaning GBIF data for the use in Ecology

RAD-Seq Reference-based data analysis

Life Traits Ecoregionalization workflow

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

Champs blocs indicators

Object detection with YOLO

Text-Mining articles with GROBID

Transcribing Audio and Video files with Automated Speech Recognition

Montreal Forced Aligner

Text-Mining Differences in Chinese Newspaper Articles

Analysing Solar Eclipse Frequency with a Galaxy Workflow

OpenRefine Tutorial for researching cultural data

Introduction to Digital Humanities in Galaxy

Contributing a New Feature to Galaxy Core

ToolFactory: Generating Tools From More Complex Scripts

nb2workflow: Generating Galaxy Tools From Jupyter Notebooks

Writing Automated Tests for Galaxy

Debugging Galaxy

Galaxy Interactive Tools

Data source integration

Contributing to BioBlend as a developer

Understanding Galaxy Data Managers

Creating Galaxy tools from Conda Through Deployment

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

Setting up a dev Onedata instance

Scripting Galaxy using the API and BioBlend

Generic plugins

Architecture 01 - Galaxy Ecosystem and Projects

Architecture 02 - Galaxy Project Management and Contribution

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

Architecture 12 - Galaxy Client Architecture

Architecture 06 - Dependency Injection in Galaxy

Tool development and integration into Galaxy

Tool Shed: sharing Galaxy tools

Architecture 03 - Galaxy Architecture Principles

Architecture 16 - Galaxy Testing

Galaxy Webhooks

Galaxy Interactive Environments

Galaxy Interactive Tours

Architecture 09 - Galaxy Plugin Architecture

Tool Dependencies and Containers

Architecture 04 - Galaxy Files and Directory Structure

Prerequisites for building software/conda packages

Architecture 11 - Galaxy Markdown Architecture

Architecture 05 - Galaxy Web Frameworks

Tool Dependencies and Conda

Architecture 13 - Galaxy Dependencies Management

JavaScript plugins

Architecture 07 - Galaxy Task Management with Celery

ToolFactory: Generating Tools From Simple Scripts

Architecture 10 - Galaxy File Sources Architecture

Architecture 14 - Galaxy Startup Process

Architecture 15 - Galaxy Production Deployment

Make & Snakemake

Introduction to SQL

SQL with R

Variant Calling Workflow

SQL Educational Game - Murder Mystery

Advanced CLI in Galaxy

Advanced SQL

Basics of using Git from the Command Line

One protein along the UniProt page

Version Control with Git

CLI basics

SQL with Python

CLI Educational Game - Bashcrawl

Learning about one gene across biological resources and formats

Python - Multiprocessing

Python - Coding Style

Python - Subprocess

Python - Globbing

Conda Environments For Software Development

Python - Argparse

Python - Type annotations

Python - Testing

Virtual Environments For Software Development

Python - Introductory Graduation

Python - Try & Except

Python - Files & CSV

Versioning your code and data with git

Data manipulation with Pandas

Python - Loops

Python - Flow Control

Introduction to sequencing with Python (part four)

Introduction to sequencing with Python (part three)

Data Manipulation Olympics - JQ

Python - Lists & Strings & Dictionaries

Python - Basic Types & Type Conversion

Plotting in Python

dplyr & tidyverse for data processing

Data Manipulation Olympics - SQL

Introduction to sequencing with Python (part two)

Data visualisation Olympics - Visualization in R

Advanced R in Galaxy

Introduction to sequencing with Python (part one)

Advanced Python

Python - Functions

Python - Math

Python - Warm-up for statistics and machine learning

R basics in Galaxy

Introduction to Python

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

Submitting sequence data to ENA

Automating Galaxy workflows using the command line

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

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

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

Contributing with GitHub via its interface

GTN Metadata

Principles of learning and how they apply to training and teaching

Teaching Python

Creating Interactive Galaxy Tours

Adding auto-generated video to your slides

Updating diffs in admin training

Adding Quizzes to your Tutorial

Design and plan session, course, materials

Tools, Data, and Workflows for tutorials

Generating PDF artefacts of the website

Including a new topic

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

High Throughput Molecular Dynamics and Analysis

Data management in Medicinal Chemistry

Running molecular dynamics simulations using GROMACS

Running molecular dynamics simulations using NAMD

Protein-ligand docking

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

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

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

Make your tools available on your subdomain

Creation of resources listing Galaxy workflow for your community

Creation of a Galaxy tutorial table for your community

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

Creating a Special Interest Group

What's a Special Interest Group?

Creating community content

Collaboration with JupyterGIS

Ocean Data View (ODV)

Visualize Climate data with Panoply netCDF viewer

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

Getting your hands-on earth data

Functionally Assembled Terrestrial Ecosystem Simulator (FATES)

Pangeo Notebook in Galaxy - Introduction to Xarray

Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools

Analyse Argo data

Getting your hands-on climate data

Sentinel 5P data visualisation

Ocean's variables study

Nitrate DMQC for autonomous platforms such as Argo floats

Introduction to climate data

Genome assembly and assembly QC - Introduction short version

Deeper look into Genome Assembly algorithms

An introduction to get started in genome assembly and annotation

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

Large genome assembly and polishing

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

Chloroplast genome assembly

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

Unicycler Assembly

De Bruijn Graph Assembly

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

Decontamination of a genome assembly

ERGA post-assembly QC

Hybrid genome assembly - Nanopore and Illumina

Genome assembly using PacBio data

Genome Assembly Quality Control

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

Assembly of the mitochondrial genome from PacBio HiFi reads

Making sense of a newly assembled genome

An Introduction to Genome Assembly

Contribute to the BioImage.IO models

BioImage Model Zoo: Advanced models in one-click

Welcome to the BioImage Model Zoo

Enable upload via FTP

Adding file-sources to Galaxy

Upgrading Galaxy

Performant Uploads with TUS

Training Infrastructure as a Service (TIaaS)

Automation with Jenkins

Galaxy Database schema

Create a subdomain for your community on UseGalaxy.eu

Deploying a Beacon v1 in Galaxy

Use Apptainer containers for running Galaxy jobs

Galaxy Monitoring with Reports

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

How I learned to stop worrying and love the systemd

Mapping Jobs to Destinations using TPV

Reference Data with CVMFS without Ansible

Monitoring Galaxy and Pulsar with Sentry

Customizing the look of Galaxy (Manual)

Customizing the look of Galaxy

Alternative Celery Deployment for Galaxy

Server Maintenance: Cleanup, Backup, and Restoration

Distributed Object Storage

Connecting Galaxy to a compute cluster

Galaxy Tool Management with Ephemeris

uWSGI

Galactic Database

Controlling Galaxy with systemd or Supervisor

Reference Data with CVMFS

Server: Other

Docker and Galaxy

External Authentication

Galaxy Interactive Tools

Empathy

Reference Data with Data Managers

Galaxy Troubleshooting

Running Jobs on Remote Resources with Pulsar

Setting up Celery Workers for Galaxy

Data Libraries

User, Role, Group, Quota, and Authentication managment

Galaxy Monitoring with Telegraf and Grafana

Gearing towards production

Ansible

Galaxy Monitoring

Galaxy Installation with Ansible

Galaxy Administrator Time Burden and Technology Usage

Galaxy Monitoring with gxadmin

Advanced customisation of a Galaxy instance

Deploying a compute cluster in OpenStack via Terraform

Deploying Tailscale/Headscale for private mesh networking

Deploying Wireguard for private mesh networking

Pulsar usage on SURF Research Cloud

Galaxy usage on SURF Research Cloud

Managing Galaxy on Kubernetes

Galaxy Installation on Kubernetes

Galaxy from an administrator's point of view

Galaxy on the Cloud