Galaxy for Translational Research

Galaxy for Translational Research

Monday6th –Wednesday 8thFebruary 2017

final vs 170125

Introduction

The course will focus on using the Galaxy platform ( to analyse data from DNAseq and RNAseq experiments and provide the scientist a platform to communicate the output of an analysis back to the research team using iReport in Galaxy.

Audience

This training of is aimed at giving the clinical research scientists who is non-bioinformatician the necessary skills to understand and successfully work with next-generation sequencing (NGS) data.

This course will be in held in computer room Ee-15.28, on the 15th floor of the Ee-building, Bioinformatics dept., Medical Faculty, Erasmus MC. Note: participants from outside need a pass because the Ee tower will be closed for people not working at Erasmus MC. We will give their names in advance to the guard and you can pick up your pass with your name every morning at the 3rd floor in the Ee tower, at the porter’s lodge.

ECTS

After completing the course, signing the attendance list every morning and handing in the evaluation form at the end of the course you will get a certificate for 1,0 ECTS.

Course objectives

The course will be given as a series of lectures and practical’s designed such that by the end of the course the participant will expected to know:

What is and how to use Galaxy for data analysis
How to analyse DNAseqandRNAseq experiments
How to create and interpret an integrative cancer study (SNV, CNV and SV)
How to analyse microbiota NGS
FAIR Data Management and Analysis
Bring Your Own Data (BYOD) – analyse your own data

Attendance fees

Fee for commercial participants is available upon request.

The subscription fee of non-commercial participants for this 3-day course is € 550. Discounts are handled as followed:

All PhD students get a discount of 50% and pay €275,00.
All participants from the Postgraduate school MolMed and of the Bio Informatics Dept. get a discount of 100% and pay €0.
For research master students the invoice is €100,- based on €100 per ECTS as agreed between the research master programs.
All research master students who have to pay themselves receive 75% discount, and pay €137,50.

Day 1–Monday 6th - Galaxy NGS Foundations and DNAseq (room: Ee-1528)
Time / Description / Presenter
9:30 / Welcome and Agenda / Andrew Stubbs
9:35 / Galaxy Ecosystem / Andrew Stubbs
10:00 / Practical Intro: Galaxy 101: Introduction to Galaxy / Saskia Hiltemann
10:30 / PRACTICAL: Galaxy 101: Introduction to Galaxy / Saskia Hiltemann / David van Zessen
11:00 / BREAK
11:15 / PRACTICAL: Galaxy 101: Introduction to Galaxy / Saskia Hiltemann / David van Zessen
11:45 / LECTURE: Variation analysis / Saskia Hiltemann
12:00 / PRACTICAL: Variation analysis / Saskia Hiltemann / David / Yunlei
13:00 / LUNCH
13:30 / ELIXIR-NL / Celia van Gelder
14:00 / Practical Intro: Enhanced RNAseq / Youri Hoogstrate
14:30 / PRACTICAL: Enhanced RNAseq / Youri Hoogstrate / Yunlei Li
15:30 / BREAK
15:45 / PRACTICAL: Enhanced RNAseq / Youri Hoogstrate / Yunlei Li
16:45 / END Day 1
Day 2 –Tuesday 7th – RNAseq and FAIR Data Analysis (room: Ee-1528)
Time / Description / Presenter
9:30 / LECTURE: Cancer analysis from Research Scientist to Galaxy / Guido Jenster
10:00 / Practical Intro: Cancer Analysis in GalaxyReporting / Saskia Hiltemann
10:30 / PRACTICAL: Cancer Analysis in Galaxy & Reporting / Saskia Hiltemann / Yunlei / David
11:00 / BREAK
11:15 / PRACTICAL: Cancer Analysis in Galaxy & Reporting / Saskia Hiltemann / Yunlei / David
13:30 / Practical Intro: Galaxy workbooks / Saskia
13:00 / LUNCH
14:00 / PRACTICAL: Galaxy workbook for R / Andrew Stubbs / Saskia
14:45 / Lecture: FAIR data – Why, What and How? / Andrew Stubbs
15:00 / Practical Intro: Galaxy “Do it yourself” FAIR Data Analysis and workbooks / Andrew Stubbs/
15:30 / BREAK
15:45 / PRACTICAL: Galaxy “Do it yourself” FAIR Data Analysis / Andrew Stubbs/Rick Jansen
16:45 / END Day 2
Day 3–Wednesday 8th – Metagenomics and BYOD (room: Ee-1528)
Time / Description / Presenter
9:30 / Microbial Analysis – “end to end” (Lecture) / Stefan Boers
10:15 / 16S rRNA analysis in Galaxy (Lecture and Practical Intro) / Saskia Hiltemann
11:00 / BREAK
11:15 / MothurSOP in Galaxy (Practical) / Saskia, Stefan, Andrew
13:00 / LUNCH
13:30 / MYcrobiota (Lecture and Demo) / Stefan or Saskia
14:00 / BYOD: Outline projects (Practical Intro)
14:30 / BYOD: Work through Projects (Practical) / Saskia Hiltemann / Andrew Stubbs/ Youri / David
15:30 / BREAK
15:45 / BYOD: Work through Projects (Practical) / Saskia Hiltemann / Andrew Stubbs/ Youri / David
16:45 / END Day 3