Fwd: [BBC] Registration Open for ELIXIR-NL Course Bioinformatics for Translational Medicine using Galaxy - 17- 19 October 2018, Amsterdam

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Fwd: [BBC] Registration Open for ELIXIR-NL Course Bioinformatics for Translational Medicine using Galaxy - 17- 19 October 2018, Amsterdam

Dave Clements
Hi All,

The second part of this workshop is about using Galaxy in courses as an introduction to bioinformatics.

Space is limited.


Dave C

---------- Forwarded message ---------
From: Celia van Gelder <[hidden email]>
Date: Sat, Sep 15, 2018 at 10:47 PM
Subject: [BBC] Registration Open for ELIXIR-NL Course Bioinformatics for Translational Medicine using Galaxy - 17- 19 October 2018, Amsterdam
To: <[hidden email]>

ELIXIR-NL Course: Bioinformatics for Translational Medicine using Galaxy


Please circulate this email to those who might be interested.


Date: 17-19 October, 2018

Location: VU Amsterdam (O|2 Lab Building, Gustav Mahlerlaan 665, 1082 MK, 1082 MK Amsterdam)

Organizers: Chao (Cico) Zhang (VU), Sanne Abeln (VU), Anton Feenstra (VU), Saskia Hiltemann (ErasmusMC), Mateusz Kuzak (DTL) and Celia van Gelder (DTL).

Course page: https://www.biosb.nl/education/course-portfolio/bioinformatics-for-translational-medicine-using-galaxy/

Application form: https://www.biosb.nl/education/course-portfolio/bioinformatics-for-translational-medicine-using-galaxy/enrollment-galaxy-workshop-2018/




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.




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 scientist 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.




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.)




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 17

Day 2 - Thu Oct 18

Day 3 - Fri Oct 19


Introduction to Galaxy

Network analysis with microbiota metatranscriptome

Teaching bioinformatics workflows

Saskia Hiltemann

Chao Zhang

Anton Feenstra


I: About bioinformatics workflows

II: About Galaxy and ELIXIR

III: About bioinformatics teaching

Remond Fijneman

Björn Grüning

Jaap Heringa



16S rRNA sequencing with mothur

Galaxy training material development

Björn Grüning

Saskia Hiltemann

Saskia Hiltemann


Social 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).

Correction: An earlier version of this announcement mentioned that you don’t need to bring your own laptop, this is NOT TRUE. We regret the error. You do need to bring your own laptop.




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 ([hidden email])



Dr. Celia W.G. van Gelder

Programme Manager DTL Learning

Training Coordinator ELIXIR-NL

ELIXIR Training Platform Leader

tel. +31613375327

e-mail: [hidden email]

websites:  www.dtls.nl, www.biosb.nl

skype: celia.van.gelder

Office: DTL | Jaarbeurs Innovation Mile (JIM) | 6th floor Beatrixgebouw | Jaarbeursplein 6 | 3521 AL Utrecht
Postal address: Postbus 8500 | 3503 RM Utrecht

While I may be sending this email outside my normal office hours, I have no expectation to receive a reply outside yours.


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