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

Date

17-19 October 2018

Venue

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

Logistics & route

Organizers

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

Target audience

This course consists of two parts, each of which you could register separately in the application form.

Part 1 (Day 1 and 2): biomedical & translational medicine researchers/students who are keen on bioinformatics
Part 1 and 2 (Day 1, 2 and 3): 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, each of which you could register separately. 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 recognized researchers in the fields of biomedicine, bioinformatics education, and Galaxy workflows. The confirmed speakers include Remond Fijneman (Day 1), a researcher in oncology from NKI; Björn Grüning (Day 2), the leader of Galaxy training network, who is also actively involved in Bioconda, and Jaap Heringa (Day 3), the scientific director of the Netherlands Bioinformatics Centre.

Prerequisite knowledge

The attendees of Part I are assumed to have the basic knowledge of biomedicine (molecular biology and genomics) and be interested in analyzing 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 

Find detailed programme here

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.
  • How to prepare training material development.

 

Day 1 – Wed Oct 17Day 2 – Thu Oct 18Day 3 – Fri Oct 19
MorningIntroduction to GalaxyNetwork analysis with microbiota metatranscriptomeTeaching bioinformatics workflows
Saskia HiltemannChao ZhangAnton Feenstra
KeynoteI: About bioinformatics workflowsII: About Galaxy and ELIXIRIII: About bioinformatics teaching
Remond FijnemanBjörn GrüningJaap Heringa
AfternoonRNAseq16S rRNA sequencing with mothurGalaxy training material development
Björn GrüningSaskia 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), Björn Grüning, Chao Zhang (VU), Leon Mei (LUMC), Ruben Vorderman (LUMC) and Sanne Abeln (VU).

Please note:  You 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 (celia.van.gelder@dtls.nl)

How to apply?

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