Overview

The course "High Performance Computing for genomic applications" is organized for the D-BIOL researchers (including PhD students) by Scientific IT Services on 26-27 November 2018. The main goal of the course is to increase IT competences of researchers and encourage them to use Euler cluster for bioinformatic analyses: independently or together with a bioinformatician in a co-analysis mode.

Some modules include hands-on exercises, so the participants are expected to bring own laptops. On Tuesday, Nov 27th there is planned a time slot, when the participants can discuss or work on solutions for their own data analysis issues with the instructors.

The course will include on the second day also a module related to cluster use for personalized medicine: "Data & Computing Services for Personalized Health Research"

Application

The classes of the course can be attended or skipped in a "pick-and-mix" mode, depending on the need and skills of the participant, however a registration is required for the full course by filling the form:

https://goo.gl/forms/J6thSjAKjWGwMnDI3

The course is limited to 20 participants, confirmations will be sent after the registration process on first-come-first-served basis, preference for DBIOL ETH.

Location

ETH Zurich; Department of Biology; Honggerberg Campus

Additional information

Coordination: Michal Okoniewski, Scientific IT Services ETH

Instructors

Michal Okoniewski, Samuel Fux, Diana Coman-Schmid

Schedule

====> High Performance Computing for genomic applications

Day 1, 26 Nov 2018, HIT F 32

9:00 - 9:40 Linux command line re-fresh

9:40 - 10:20 Basics of shell scripting

10:20 -10:30 Coffee break

10:30 - 11:00 Introduction to the Euler cluster and HPC

11:00- 12:00 LSF queueing system

12:00- 12:30 Genomic formats

12:30- 13:30 Lunch break

13:30- 14:15 Working with genomic data using AWK

14:15 -15:00 Basics of useful R

15:00 -15:30 Basic R scripts for RNA-seq statistics

15:30- 15:45 Coffee break

15:45- 17:00 Genomic software on the Euler cluster

Day 2, 27 Nov 2018, HIT F 32

9:00 - 9:30 Data & Computing Services for Personalized Health Research

10:00-11:30 Workflow orchestration with snakemake - demo

11:30 -13:00 Hackaton: participants' own problems and data