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)
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.
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.
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.).
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 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|
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 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 (email@example.com)
How to apply?
You can register for the course via the application form. We will accept a maximum of 30 participants.