Bioinformatics for Translational Medicine using Galaxy: see it, do it, teach it!


17-19 October 2018


Vrije Universiteit Amsterdam (O|2 Lab Building, Gustav Mahlerlaan 665, 1082 MK, 1082 MK Amsterdam


This course is an ELIXIR-EXCELERATE course and is organised by ELIXIR-NL by Chao Zhang (VU), Sanne Abeln (VU), Anton Feenstra (VU), Saskia Hiltemann (ErasmusMC), Mateusz Kuzak (DTL) and Celia van Gelder (DTL)

Target audience

1) Biomedical & translational medicine researchers/students who are keen on bioinformatics and 2) educators in the “bio” domain who would like to start using Galaxy in their courses as an introduction to Bioinformatics.

Course description

Analysing molecular data in translational medicine involves a multitude of computational steps. Here, we introduce the basics of how to design and run these steps within Galaxy, a free and easy-to-use web platform that enables users to connect bioinformatics tools into a workflow without any prior programming expertise.

This course consists of two parts. Part 1 will let you get familiar with Galaxy; it will introduce some bioinformatics workflows used for RNAseq, variant detection and metagenomics; and how to easily connect different computational steps in Galaxy. Part 2 will focus on how to teach bioinformatics with Galaxy and to design bioinformatics courses using Galaxy. Participants can register for both parts separately.

This course is also interspersed with a few keynotes, from recognised researchers in the fields of Biomedicine, Bioinformatics education and Galaxy workflows. The confirmed speakers include Jaap Heringa, who is the scientific director of the Netherlands Bioinformatics Centre; and Björn Grüning, who is the leader of Galaxy training network, also actively involved in Bioconda.

Prerequisite knowledge

The attendees of Part I are assumed to have the basic knowledge of biomedicine (molecular biology and genomics) and be interested in analysing patient derived sequencing data. The attendees of Part II are assumed to have some teaching experience in the relevant field (e.g., bioinformatics, computational biology, systems biology, quantitative biology, etc.).

Course schedule 

The course consists of six modules, as the table below shows, covering a list of topics as follows:

  • Introduction to Galaxy. Run bioinformatics tools and workflows in Galaxy without the need for any programming expertise.
  • Reference-based RNA-Seq data analysis.
  • Module detection in differential gene expression in meta transcriptomics samples.
  • Microbiota Analysis: 16S rRNA sequencing analysis in Galaxy.
  • How to teach bioinformatics workflows.
  • Galaxy setup for teaching and training material development.
Day 1 – Wed Oct 17Day 2 – Thur Oct 18Day 3 – Frid Oct 19
MorningGalaxy 101 + Variant detectionNetwork analysis with microbiota metatranscriptomeTeaching bioinformatics workflows
Saskia HiltemannChao ZhangAnton Feenstra
Keynote Speech*I: About bioinformatics workflowsII: About Galaxy and ELIXIRIII: About bioinformatics teaching
TBDBjörn GrüningJaap Heringa
AfternoonBWA + RNAseq16S rRNA sequencing with mothurGalaxy training material development
Saskia HiltemannSaskia HiltemannSaskia Hiltemann
EveningSocial dinner

About the instructor: Each session is led by one instructor listed in the table above but strongly supported by multiple co-instructors, including, but not limited to, Saskia Hiltemann (ErasmusMC), Chao Zhang (VU), Leon Mei (LUMC), Ruben Vorderman (LUMC) and Sanne Abeln (VU).

Note: The course is held in a computer classroom, so you don’t need to bring your own laptop.

Course fee

Course participation is free of charge.
A workshop dinner will be organized on Thursday (at participants’ own expenses)

Should you have any question about this course, please contact Celia van Gelder (

How to apply?

You can register for the course via the application form. We will accept a maximum of 30 participants.