High Performance Computing for genomic applications

Date 13 - 14 December 2018
Speaker(s) Michal Okoniewski, Samuel Fux, Diana Coman-Schmid
Cancellation deadline 23 Nov 2018
City Basel

Overview

The course "High Performance Computing for genomic applications" is organized for the D-BIOL researchers (including PhD students) by Scientific IT Services on 13-14 December 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 Friday, Dec 14th 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/tscMb9TAURIlWtFI2

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

Location

BSSE ETH in Basel

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, 13 Dec 2018, Erasmus Room

13:00- 13:40 Linux command line re-fresh

13:40- 14:20 Basics of shell scripting

14:20- 14:30 Coffee break

14:30- 15:00 Introduction to the Euler cluster and HPC

15:00- 16:00 LSF queueing system

16:00- 16:30 Genomic formats

16:30- 17:15 Working with genomic data using AWK

Day 2, 14 Dec 2018, Erasmus Room

9:30 - 10:00 Basics of useful R

10:00- 10:30 Basic R scripts for RNA-seq statistics

10:30- 10:45 Coffee break

10:45- 12:00 Genomic software on the Euler cluster

12:00- 13:00 Lunch break

13:00- 13:45 Data & Computing Services for Personalized Health Research

13:45- 14:30 Workflow orchestration with snakemake - demo

14:30- 16:30 Hackaton: participants' own problems and data