Learning Pathways

Learning pathways are sets of tutorials curated for you by community experts to form a coherent set of lessons around a topic, building up knowledge as you go. We always recommend to follow the tutorials in the order they are listed in the pathway.

For Scientists

Introduction to Galaxy and Sequence analysis

This learning path aims to teach you the basics of Galaxy and analysis of sequencing data. You will learn how to use Galaxy for analysis, and will be guided through the most common first steps of any genome analysis; quality control and a mapping or assembly of your genomic sequences.

beginner

Clinical metaproteomics workflows within Galaxy

This learning path aims to teach you the basics of how to perform metaproteomics analysis of the clinical data within the Galaxy platform. You will learn how to use Galaxy for analysis, and will be guided through the most common first steps of any metaproteomics database generation to searching the database, verifying the proteins/peptides, and data analysis.

beginner

Introduction to Galaxy and Single Cell RNA Sequence analysis

This learning path aims to teach you the basics of Galaxy and analysis of Single Cell RNA-seq data. You will learn how to use Galaxy for analysis, and an important Galaxy feature for iterative single cell analysis. You’ll tbe guided through the general theory of single analysis and then perform a basic analysis of 10X chromium data. For support throughout...

beginner

Detection of AMR genes in bacterial genomes

This learning path aims to teach you the basic steps to detect and check Antimicrobial resistance (AMR) genes in bacterial genomes using Galaxy.

amr bacteria microgalaxy one-health

Applying single-cell RNA-seq analysis

Gone is the pre-annotated, high quality tutorial data - now you have real, messy data to deal with. You have decisions to make and parameters to decide. This learning pathway challenges you to replicate a published analysis as if this were your own dataset. You will be introduced to a few more tools available for scRNA-seq in Galaxy. Finally, if...

intermediate

Discovering galaxy through climate analysis

How to have a complete overview of how Galaxy works going from the user welcome page to use batch tools and finishing by conducting interactive analysis. These set of 3 Climate tutorials allow you to understand and see plenty of the multiple features of Galaxy and learning about the cool subject of climate analysis.

Climate Overview

Genome annotation for eukaryotes

Learn how to annotate an eukaryotic genome sequence: identify repeated regions, find the position and function of genes, and even set up a manual curation environment with Apollo.

genome annotation eukaryote

Genome annotation for prokaryotes

Learn how to annotate a prokaryotic genome sequence: find the position and function of genes, and even set up a manual curation environment with Apollo.

genome annotation prokaryote

Introduction to Galaxy and Ecological data analysis

This learning path aims to teach you the basics of Galaxy and analysis of ecological data. You will learn how to use Galaxy for analysis, and will be guided through the common steps of biodiversity data analysis: download, check, filter and explore biodiversity data and analyze abundance data through modeling.

beginner

From R to Machine Learning; an introductory course

This learning path aims to teach you the basics of Machine Learning using R. Initially you will learn how to code in R within the Galaxy platform, gaining some familiarity into how to wrangle and analyze data. Then, you will be guided through the various types of Machine Learning techniques, developing some simple models using R.

beginner

Metagenomics data processing and analysis for microbiome

This learning path aims to teach you the basics of Galaxy and analysis of metagenomics data. You will learn how to use Galaxy for analysis, and will be guided through the common steps of microbiome data analysis: quality control, taxonomic profiling, taxonomic binning, assembly, functional profiling, and also some applications

microbiome

Introductory Python

This is an introductory course of Python, as it was taught in Avans Hogeschool in the Netherlands.

python real-course

Introductory SQL

This is an introductory course of SQL, as it was taught in Avans Hogeschool in the Netherlands.

python real-course

For Teachers, Developers and System Administrators

Building training material in Galaxy

This learning path aims to teach you the basics of navigating the Galaxy training Github repository, and turning your ace training materials and workflows into Galaxy sites. For support throughout these tutorials, join our Galaxy training network on Matrix to ask questions!

intermediate

Admin Training Course

Learn how to setup, configure, and maintain your own Galaxy server. This learning pathway will guide you through all the steps required to setup your own Galaxy server with Ansible, configuring it, and making it production ready.

Galaxy administrators 5-day course

FAIR Data Management

The FAIR data management training learning pathway teaches you how to organise, describe, and store research data according to the FAIR principles (Findable, Accessible, Interoperable, Reusable).

fair dmp data management data stewardship

Train the Trainers

This pathway introduces trainers to learning principles, training techniques, lesson, session, course, and material design as well as assessment and feedback. This is has been developed for by trainers in the bioinformatics but is suitable for all trainers and educators in higher education.

training trainers