Explore our curated collection of training materials covering a wide range of topics in cloud computing, bioinformatics, and data science. These tutorials are designed for hands-on learning and support both beginners and advanced users.
Lesson materials are all available online, under a CC BY license, for self-directed study or for adaptation and re-use in your own training sessions.
Unix
Tutorials focused on basic Unix / Linux commands and shell usage.
| Tutorial | Versions | Slides | Description | Contributors | Estimated Time |
|---|---|---|---|---|---|
| Introduction to basic Unix commands |
main spring-school-2024 |
This is the introduction to the basic shell commands. | 2H |
Cloud computing
Tutorials focused on using the de.NBI Cloud infrastructure and project types.
| Tutorial | Versions | Slides | Description | Contributors | Estimated Time |
|---|---|---|---|---|---|
| SimpleVM Workshop | main | Tutorial shows how to identify pathogenic bacteria within publicly available metagenomic datasets and scale up a bioinformatics workflow using SimpleVM. | 2H | ||
| BiBiGrid Hands-on | main | Tutorial shows how to provision and operate a small HPC cluster on OpenStack using BiBiGrid | 2H |
Cloud application deployment
Tutorials in this group offer hands-on experience in building, containerizing, and deploying applications from local development environments to the cloud.
| Tutorial | Versions | Slides | Description | Contributors | Estimated Time |
|---|---|---|---|---|---|
| Build a Simple Dataset Web App on EMBL Cloud Infrastructure | main | Learn to create and deploy a web application using Python, Streamlit, Docker/Podman, and Kubernetes on EMBL cloud computing infrastructure | 2H |
Machine Learning on Cloud infrastructure
Tutorials focused on setting up machine learning toolkits and applications on cloud infrastructure.
| Tutorial | Versions | Slides | Description | Contributors | Estimated Time |
|---|---|---|---|---|---|
| Deploying ML workflow using FastAPI | main | FIXME | 3H | ||
| Setting up ML project in the cloud infrastructure | main | Transform a trained model into an online service with a UI using Streamlit. | 5H |
PATCH Tutorials
Tutorials in this group contain learning material about the tools contained inside the pangenomics toolbox PATCH
| Tutorial | Versions | Slides | Description | Contributors | Estimated Time |
|---|---|---|---|---|---|
| PanBench | main | Introduction to using the web interface of panbench.eu |
Andreas Rempel
|
10m |
Genomics and Metagenomics
Tutorials focused on handling of genomics and metagenomics sequencing data
| Tutorial | Versions | Slides | Description | Contributors | Estimated Time |
|---|---|---|---|---|---|
| Metagenome Assembly: concepts and hands-on comparison of assemblers | main | This tutorial introduces the principles and challenges of metagenome assembly, including de Bruijn graph-based approaches, k-mer selection, and metagenome-specific assembly strategies. You will apply several assemblers, including Velvet, MEGAHIT, metaSPAdes, IDBA-UD, and Ray, and compare their assembly performance. | 6H | ||
| Basics of Amplicon Quality Processing | main | Basic steps to do manually quality processing of 16S data step by step with individual tools instead of using integrated solutions like qiime2 / dada2 / deblur. | 2H | ||
| Basecalling and QC of ONT data | main | This tutorial introduces the preprocessing workflow for Oxford Nanopore Technologies (ONT) sequencing data, from raw signal files to quality-controlled reads for downstream analysis. | 2H | ||
| Introduction to Long-Read Metagenomics using the Metagenomics-Toolkit | main | This tutorial will guide you through the first steps to run the Metagenomics-Toolkit on ONT data | 1H | ||
| Prokaryotic Genome Annotation (hands-on) | main | Learn the steps of prokaryotic genome annotation by generating and comparing annotations with Prokka and Bakta. The tutorial also introduces EDGAR for comparative genome analysis, including core-genome, pan-genome and ortholog identification. | 2H | ||
| Assembly and assembly evaluation (hands-on) | main | This tutorial demonstrates how to assemble a prokaryotic genome using Oxford Nanopore and Illumina sequencing data, evaluate assembly quality, improve assemblies through polishing and hybrid assembly approaches, and assess the final results. | 2H |
Data Management on the Cloud
Tutorials focused on data management best practices, solutions on the Cloud, including how to adapt a solution to the cloud (Kubernetes and S3 storage)
| Tutorial | Versions | Slides | Description | Contributors | Estimated Time |
|---|---|---|---|---|---|
| Basic Data Management in the de.NBI Cloud | main | Basic Data Management in the de.NBI Cloud. Intended for a cloud-naive audience. | 8H | ||
| Using the cross-domain Data-Management Platform repository | main | A step-by-step overview of how to use the repository. | 40M |
Incubator
Tutorials in this group are under review.
| Tutorial | Versions | Slides | Description | Contributors | Estimated Time |
|---|---|---|---|---|---|
| FIXME | main | FIXME | FIXME |