Training

Visualisations in Galaxy

Friends Don't Let Friends Make Bad Graphs

Ploting a Microbial Genome with Circos

Visualisation with Circos

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)

Calculating CHEK2 variant effect scores from MAVE data with CountESS

Trio Analysis using Synthetic Datasets from RD-Connect GPAP

Mapping and molecular identification of phenotype-causing mutations

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

Calling variants in non-diploid systems

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

Calling variants in diploid systems

Exome sequencing data analysis for diagnosing a genetic disease

Somatic Variant Discovery from WES Data Using Control-FREEC

Calling very rare variants

Introduction to Variant analysis

De novo transcriptome reconstruction with RNA-Seq

Pathway analysis with the MINERVA Platform

Reference-based RNA-Seq data analysis

RNA Seq Counts to Viz in R

Visualization of RNA-Seq results with Volcano Plot in R

Reference-based RNAseq data analysis (long)

RNA-seq Alignment with STAR

Introduction to Transcriptomics

Visualization of RNA-Seq results with CummeRbund

RNA-Seq analysis with AskOmics Interactive Tool

Visualization of RNA-Seq results with Volcano Plot

Visualization of RNA-Seq results with heatmap2

Network analysis with Heinz

Differential abundance testing of small RNAs

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

Small Non-coding RNA Clustering using BlockClust

RNA-Seq data analysis, clustering and visualisation tutorial

De novo transcriptome assembly, annotation, and differential expression analysis

2: RNA-seq counts to genes

Genome-wide alternative splicing analysis

GO Enrichment Analysis

3: RNA-seq genes to pathways

1: RNA-Seq reads to counts

RNA-RNA interactome data analysis

Galaxy Admin Training

Training Infrastructure as a Service

Set up a Galaxy for Training

Teaching experiences

Hybrid training

Asynchronous training

Running a workshop as an instructor

Live Coding is a Skill

Teaching online

Organizing a workshop

Course Builder

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

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

Interval-Wise Testing for omics data

GLEAM Image Learner - Validating Skin Lesion Classification on HAM10000

Galaxy Tabular Learner - Building a Model using Chowell clinical data

Basics of machine learning

Identifing Survival Markers of Brain tumor with Flexynesis

GTEx Tissue Modeling with Galaxy Image Learner

PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis

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

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

Regression in Machine Learning

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

Introduction to deep learning

Modeling Breast Cancer Subtypes with Flexynesis

Unsupervised Analysis of Bone Marrow Cells with Flexynesis

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

Text-mining with the SimText toolset

Image classification in Galaxy with fruit 360 dataset

Prepare Data from CbioPortal for Flexynesis Integration

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

Age prediction using machine learning

Classification in Machine Learning

Clustering in Machine Learning

Machine learning: classification and regression

Automated Cell Annotation

Trajectory analysis

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

Inferring single cell trajectories with Monocle3

Inferring single cell trajectories with Monocle3 (R)

Single-cell Formats and Resources

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

Inferring single cell trajectories with Scanpy

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

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

Evaluating Reference Data for Bulk RNA Deconvolution

Multi-sample batch correction with Harmony and SnapATAC2

Scanpy Parameter Iterator

Converting NCBI Data to the AnnData Format

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

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

Downstream Single-cell RNA analysis with RaceID

Understanding Barcodes

Comparing inferred cell compositions using MuSiC deconvolution

Combining single cell datasets after pre-processing

Importing files from public atlases

Clustering 3K PBMCs with Scanpy

Removing the effects of the cell cycle

Single-cell ATAC-seq standard processing with SnapATAC2

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

An introduction to scRNA-seq data analysis

Generating a single cell matrix using Alevin

Single-cell quality control with scater

Pseudobulk Analysis with Decoupler and EdgeR

Converting between common single cell data formats

Bulk RNA Deconvolution with MuSiC

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

Pre-processing of 10X Single-Cell RNA Datasets

GO Enrichment Analysis on Single-Cell RNA-Seq Data

Pre-processing of Single-Cell RNA Data

Screening assembled genomes for contamination using NCBI FCS

Mapping

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

Quality and contamination control in bacterial isolate using Illumina MiSeq Data

Quality Control

Clean and manage Sanger sequences from raw files to aligned consensus

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

Introduction to proteomics, protein identification, quantification and statistical modelling

Mass spectrometry imaging: Loading and exploring MSI data

Metaproteomics tutorial

Peptide Library Data Analysis

EncyclopeDIA

metaQuantome 2: Function

Clinical Metaproteomics 1: Database-Generation

Clinical Metaproteomics 2: Discovery

Single Cell Proteomics data analysis with bioconductor-scp

Biomarker candidate identification

Peptide and Protein ID using OpenMS tools

Peptide and Protein Quantification via Stable Isotope Labelling (SIL)

Clinical Metaproteomics 5: Data Interpretation

Proteogenomics 2: Database Search

Neoantigen 2: Database merge and FragPipe discovery

Machine Learning Modeling of Anticancer Peptides

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

Neoantigen 4: Variant Annotation

Clinical Metaproteomics 3: Verification

DIA Analysis using OpenSwathWorkflow

Neoantigen 5a: Predicting HLA Binding

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

metaQuantome 3: Taxonomy

Neoantigen 5b: IEDB binding Validated Neopeptides

Neoantigen 3: PepQuery2 Verification

Proteogenomics 1: Database Creation

Label-free data analysis using MaxQuant

Neoantigen 1b: Non-Reference-Database-Generation

Library Generation for DIA Analysis

MaxQuant and MSstats for the analysis of TMT data

Peptide and Protein ID using SearchGUI and PeptideShaker

Protein FASTA Database Handling

Secretome Prediction

Neoantigen 1a: Fusion-Database-Generation

Proteogenomics 3: Novel peptide analysis

Clinical Metaproteomics 4: Quantitation

MaxQuant and MSstats for the analysis of label-free data

metaQuantome 1: Data creation

Multiomics data analysis using MultiGSEA

Statistical analysis of DIA data

Analysis of plant scRNA-Seq Data with Scanpy

NCBI BLAST+ against the MAdLand

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

Whole transcriptome analysis of Arabidopsis thaliana

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)

Indexing and profiling microbes with MetaSBT

QIIME 2 Moving Pictures

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

QIIME 2 Cancer Microbiome Intervention

Assembly of metagenomic sequencing data

Clinical Metaproteomics 1: Database-Generation

MGnify v5.0 Amplicon Pipeline

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

Clinical Metaproteomics 2: Discovery

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

Clinical Metaproteomics 5: Data Interpretation

Remove contamination and host reads

Antibiotic resistance detection

Metatranscriptomics analysis using microbiome RNA-seq data (short)

Binning of metagenomic sequencing data

Clinical Metaproteomics 3: Verification

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

Metatranscriptomics analysis using microbiome RNA-seq data

Calculating α and β diversity from microbiome taxonomic data

Taxonomic Profiling and Visualization of Metagenomic Data

Identifying Mycorrhizal Fungi from ITS2 sequencing using LotuS2

16S Microbial analysis with Nanopore data

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

Clinical Metaproteomics 4: Quantitation

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

Introduction to Metabolomics

Mass spectrometry: LC-MS preprocessing with XCMS

Predicting EI+ mass spectra with QCxMS

Mass spectrometry imaging: Finding differential analytes

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

Mass spectrometry: LC-MS analysis

Mass spectrometry imaging: Examining the spatial distribution of analytes

Molecular formula assignment and mass recalibration with MFAssignR package

Finding the muon stopping site with pymuon-suite in Galaxy

Very Short Introductions: QC

Introduction to Galaxy as an RDM platform

Galaxy Basics for everyone

Galaxy Basics for genomics

A short introduction to Galaxy

Upload data to Galaxy

IGV Introduction

Best Practices for Citing Galaxy

Introduction to the Dataverse Integration in Galaxy

Options for using Galaxy

Introduction to Galaxy

How to reproduce published Galaxy analyses

NGS data logistics

Data Manipulation Olympics

Introduction to Genomics and Galaxy

From peaks to genes

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

Analyse HeLa fluorescence siRNA screen

Introduction to Image Analysis using Galaxy

Execute a BiaPy workflow in Galaxy

Training Custom YOLO Models for Segmentation of Bioimages

Object tracking using CellProfiler

Using BioImage.IO models for image analysis in Galaxy

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

Quantification of electrophoresis gel bands using QuPath and Galaxy imaging tools

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

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

Segmentation of Anatomical Structures in Medical 3-D Images

Parameter tuning and optimization - Evaluating nuclei segmentation with Galaxy

Content Tracking and Verification in Galaxy Workflows with ISCC-SUM

Tracking of mitochondria and capturing mitoflashes

Voronoi segmentation

Nucleoli segmentation and feature extraction using CellProfiler

Quantitative Analysis of Histological Staining Using Color Deconvolution

Where to start with bioimage analysis in Galaxy

Genomic Data Visualisation with JBrowse2

Genomic Data Visualisation with JBrowse

Microbial Variant Calling

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

Bacterial pangenomics

Dataset construction for bacterial comparative genomics

Pangenome analysis with Roary

Genome Annotation

Bacterial genome quality control

Creating an Official Gene Set

Introduction to Genome Annotation

Identification of AMR genes in an assembled bacterial genome

Genome annotation with Helixer

Genome annotation with Braker3

From small to large-scale genome comparison

Secondary metabolite discovery

Bacterial Genome Annotation

Refining Genome Annotations with Apollo (prokaryotes)

Masking repeats with RepeatMasker

Comparison of two annotation tools - Helixer and Braker3

Genome annotation with Prokka

Group tags for complex experimental designs

Onedata user-owned storage

Importing (uploading) data from Onedata

Annotate, prepare tests and publish Galaxy workflows in workflow registries

Rule Based Uploader

Name tags for following complex histories

Extracting Workflows from Histories

JupyterLab in Galaxy

Getting started with Onedata distributed storage

Exporting to Onedata remote

Understanding Galaxy history system

Creating high resolution images of Galaxy Workflows

Accessing IIIF from within Galaxy

Rule Based Uploader: Advanced

Using dataset collections

RStudio in Galaxy

Downloading and Deleting Data in Galaxy

Use Jupyter notebooks in Galaxy

Searching Your History

Galaxy workflows in Dockstore

Getting data into Galaxy

Using Workflow Parameters

InterMine integration with Galaxy

Creating, Editing and Importing Galaxy Workflows

Workflow Reports

FAIRification of an RNAseq dataset

Persistent Identifiers

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

Access

Submitting workflows to LifeMonitor

FAIR Bioimage Metadata

FAIR Galaxy Training Material

Data Registration

Best practices for workflows in GitHub repositories

FAIR data management solutions

Exporting Workflow Run RO-Crates from Galaxy

RO-Crate in Python

Metadata

DataPLANT ARCs

Uploading Data to Zenodo from Galaxy

Integrating InvenioRDM-compatible Repositories with Galaxy

Sequence data submission to ENA

Workflow Run RO-Crate Introduction

RO-Crate - Introduction

FAIR in a nutshell

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

FAIR and its Origins

Making clinical datasets FAIR

An earth-system RO-Crate

Data management in Medicinal Chemistry

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

Phylogenetic analysis for bacterial comparative genomics

Phylogenetics - Back to Basics - Introduction

Tree thinking for tuberculosis evolution and epidemiology

Identifying tuberculosis transmission links: from SNPs to transmission clusters

Phylogenetics - Back to basics

Introduction to DNA Methylation data analysis

Introduction to ChIP-Seq 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

Identification of the binding sites of the Estrogen receptor

CUT&RUN data analysis

Infinium Human Methylation BeadChip

Hi-C analysis of Drosophila melanogaster cells using HiCExplorer

Formation of the Super-Structures on the Inactive X

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

Train-the-Trainer: putting it all together

Assessment and feedback in training and teachings

Motivation and Demotivation

Training techniques to enhance learner participation and engagement

Foundational Aspects of Machine Learning using Python

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

Object detection with YOLO

QGIS Web Feature Services

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

Cleaning GBIF data using OpenRefine

Visualize EBV cube data with Panoply netCDF viewer

RAD-Seq Reference-based data analysis

Phylodiversity analysis quick tutorial

Compute and analyze biodiversity metrics with PAMPA toolsuite

Data submission using ENA upload Tool

Biodiversity data exploration

Metabarcoding/eDNA through Obitools

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

Ecoregionalization workflow tutorial

Regional GAM

Taxonomic Analysis of eDNA

Sentinel 2 biodiversity

RAD-Seq to construct genetic maps

Preparing genomic data for phylogeny reconstruction

Marine Omics identifying biosynthetic gene clusters

Visualization of Climate Data using NetCDF xarray Map Plotting

Cleaning GBIF data for the use in Ecology

Champs blocs indicators

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

Obis marine indicators

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

RAD-Seq de-novo data analysis

Checking expected species and contamination in bacterial isolate

Species distribution modeling

From NDVI data with OpenEO to time series visualisation with Holoviews

Life Traits Ecoregionalization workflow

Montreal Forced Aligner

Transcribing Audio and Video files with Automated Speech Recognition

Introduction to Digital Humanities in Galaxy

Text-Mining Differences in Chinese Newspaper Articles

OpenRefine Tutorial for researching cultural data

Debugging Galaxy

Data source integration

Galaxy Interactive Tools

Writing Automated Tests for Galaxy

Contributing a New Feature to Galaxy Core

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

Contributing to BioBlend as a developer

nb2workflow: Generating Galaxy Tools From Jupyter Notebooks

Setting up a dev Onedata instance

Creating Galaxy tools from Conda Through Deployment

ToolFactory: Generating Tools From More Complex Scripts

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

Scripting Galaxy using the API and BioBlend

Galaxy Interactive Tours

Architecture 16 - Galaxy Testing

Architecture 06 - Dependency Injection in Galaxy

Tool Dependencies and Conda

Galaxy Interactive Environments

Architecture 15 - Galaxy Production Deployment

Generic plugins

Architecture 12 - Galaxy Client Architecture

Architecture 04 - Galaxy Files and Directory Structure

Architecture 01 - Galaxy Ecosystem and Projects

Architecture 11 - Galaxy Markdown Architecture

Architecture 10 - Galaxy File Sources Architecture

Architecture 07 - Galaxy Task Management with Celery

Architecture 13 - Galaxy Dependencies Management

Architecture 09 - Galaxy Plugin Architecture

Architecture 14 - Galaxy Startup Process

Architecture 03 - Galaxy Architecture Principles

JavaScript plugins

Tool Dependencies and Containers

Galaxy Webhooks

Architecture 02 - Galaxy Project Management and Contribution

Tool Shed: sharing Galaxy tools

Architecture 05 - Galaxy Web Frameworks

Tool development and integration into Galaxy

Prerequisites for building software/conda packages

ToolFactory: Generating Tools From Simple Scripts

Python - Multiprocessing

Python - Coding Style

Python - Subprocess

Python - Globbing

Python - Argparse

Virtual Environments For Software Development

Python - Type annotations

Python - Testing

Conda Environments For Software Development

Python - Introductory Graduation

Python - Try & Except

Python - Files & CSV

Versioning your code and data with git

Python - Loops

Data manipulation with Pandas

Python - Flow Control

Introduction to sequencing with Python (part four)

Data Manipulation Olympics - JQ

Python - Lists & Strings & Dictionaries

Introduction to sequencing with Python (part three)

Data Manipulation Olympics - SQL

Python - Basic Types & Type Conversion

dplyr & tidyverse for data processing

Plotting in Python

Introduction to sequencing with Python (part two)

Advanced Python

Data visualisation Olympics - Visualization in R

Introduction to sequencing with Python (part one)

Python - Functions

Advanced R in Galaxy

Variant Calling Workflow

CLI Educational Game - Bashcrawl

Version Control with Git

SQL with R

Python - Math

SQL Educational Game - Murder Mystery

SQL with Python

Introduction to SQL

Make & Snakemake

Advanced SQL

Introduction to Python

R basics in Galaxy

Basics of using Git from the Command Line

Python - Warm-up for statistics and machine learning

One protein along the UniProt page

CLI basics

Advanced CLI in Galaxy

A (very) brief history of genomics

Learning about one gene across biological resources and formats

Data Manipulation Olympics

SARS-CoV-2 Viral Sample Alignment and Variant Visualization

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

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

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

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

Design and plan session, course, materials

Creating Interactive Galaxy Tours

Tools, Data, and Workflows for tutorials

Updating diffs in admin training

FAIR-by-Design methodology

Including a new topic

Preview the GTN website as you edit your training material

Adding auto-generated video to your slides

Adding Quizzes to your Tutorial

Principles of learning and how they apply to training and teaching

Teaching Python

GTN Metadata

Generating PDF artefacts of the website

Contributing with GitHub via its interface

Overview of the Galaxy Training Material

Contributing to the Galaxy Training Network with GitHub

Setting up molecular systems

Data management in Medicinal Chemistry

Running molecular dynamics simulations using NAMD

Running molecular dynamics simulations using GROMACS

High Throughput Molecular Dynamics and Analysis

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

Protein-ligand docking

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

Analysis of molecular dynamics simulations

Creating a Special Interest Group

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

Creating community content

Creation of resources listing Galaxy workflow for your community

Creation of a Galaxy tutorial table for your community

Make your tools available on your subdomain

What's a Special Interest Group?

Collaboration with JupyterGIS

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

Getting your hands-on earth data

Ocean Data View (ODV)

Visualize Climate data with Panoply netCDF viewer

Introduction to climate data

Analyse Argo data

Nitrate DMQC for autonomous platforms such as Argo floats

Getting your hands-on climate data

Ocean's variables study

Functionally Assembled Terrestrial Ecosystem Simulator (FATES)

Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools

Sentinel 5P data visualisation

Pangeo Notebook in Galaxy - Introduction to Xarray

Deeper look into Genome Assembly algorithms

Genome assembly and assembly QC - Introduction short version

An introduction to get started in genome assembly and annotation

Genome assembly using PacBio data

Assembly of metagenomic sequencing data

Unicycler Assembly

Genome Assembly Quality Control

Large genome assembly and polishing

De Bruijn Graph Assembly

Chloroplast genome assembly

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

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

Decontamination of a genome assembly

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

ERGA post-assembly QC

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

Making sense of a newly assembled genome

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

Hybrid genome assembly - Nanopore and Illumina

Assembly of the mitochondrial genome from PacBio HiFi reads

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

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

How I learned to stop worrying and love the systemd

Upgrading Galaxy

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

Automation with Jenkins

Create a subdomain for your community on UseGalaxy.eu

Customizing the look of Galaxy (Manual)

Reference Data with CVMFS without Ansible

Mapping Jobs to Destinations using TPV

Galaxy Monitoring with Reports

Deploying a Beacon v1 in Galaxy

Adding file-sources to Galaxy

Enable upload via FTP

Galaxy Database schema

Use Apptainer containers for running Galaxy jobs

Alternative Celery Deployment for Galaxy

Monitoring Galaxy and Pulsar with Sentry

Performant Uploads with TUS

Customizing the look of Galaxy

Training Infrastructure as a Service (TIaaS)

Galaxy Monitoring with Telegraf and Grafana

Controlling Galaxy with systemd or Supervisor

Data Libraries

Galaxy Administrator Time Burden and Technology Usage

Server Maintenance: Cleanup, Backup, and Restoration

Galaxy Interactive Tools

User, Role, Group, Quota, and Authentication managment

Galactic Database

Galaxy from an administrator's point of view

Empathy

Advanced customisation of a Galaxy instance

Setting up Celery Workers for Galaxy

Running Jobs on Remote Resources with Pulsar

Galaxy Monitoring

Docker and Galaxy

External Authentication