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

training Elixir

From 2018-10-17 to 2018-10-19 - Add to your Calendar

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.

For more information and the application form, please see the course page

TARGET AUDIENCE

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

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 bioinformatics.

COURSE SCHEDULE

The course consists of six modules, as the table above 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 17 Day 2 - Thu Oct 18 Day 3 - Fri Oct 19
Morning Galaxy 101 + Variant detection
(Saskia Hiltemann)
Network analysis with microbiota metatranscriptome
(Chao Zhang)
Teaching bioinformatics workflows
(Anton Feenstra)
Keynote I: About bioinformatics workflows (TBD) II: About Galaxy and ELIXIR
(Björn Grüning)
III: About bioinformatics teaching
(Jaap Heringa)
Afternoon BWA + RNAseq
(Saskia Hiltemann)
16S rRNA sequencing with mothur
(Saskia Hiltemann)
Galaxy training material development
(Saskia Hiltemann)
Evening   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), 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.

EXPENSE

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)

To apply for this course, please see the course page

Organiser

Elixir-NL, VU Amsterdam, Erasmus Medical Center
Email

Location

VU
O|2 Lab Building, Gustav Mahlerlaan 665,
1082 MK, Amsterdam,
The Netherlands