ELIXIR-NL Course:

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



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: 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).

Course page (incl. Application Form): https://www.biosb.nl/education/course-portfolio/bioinformatics-for-translational-medicine-using-galaxy/



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:





Day 1 - Wed Oct 17

Day 2 - Thur Oct 18

Day 3 - Frid Oct 19

Morning

Galaxy 101 + Variant detection

Network analysis with microbiota metatranscriptome

Teaching bioinformatics workflows

Saskia Hiltemann

Chao Zhang

Anton Feenstra

Keynote Speech*

I: About bioinformatics workflows

II: About Galaxy and ELIXIR

III: About bioinformatics teaching

TBD

Björn Grüning

Jaap Heringa

Afternoon

BWA + RNAseq

16S rRNA sequencing with mothur

Galaxy training material development

Saskia Hiltemann

Saskia Hiltemann

Saskia Hiltemann

Evening


Social dinner



About the instructors:  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 (celia.van.gelder@dtls.nl)





Dr. Celia W.G. van Gelder

Programme Manager DTL Learning

Training Coordinator ELIXIR-NL

ELIXIR Training Platform Leader

tel. +31613375327

e-mail: celia.van.gelder@dtls.nl

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.