High Performance Computing for genomic applications

Date 13 - 14 December 2017
Speaker(s) Michal Okoniewski, Samuel Fux, Daniel Spies, Christophe Chabbert, Hans-Joachim Ruscheweyh, Enkelejda Miho
Cancellation deadline 10 Dec 2017
Application Closed
City Zurich

Overview

The course "High Performance Computing for genomic applications" is organized for the D-BIOL researchers by Scientific IT Services on 13-14th December 2017. 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 Thursday, Dec 14th there is planned a "hackaton" time slot, when the participants can discuss or work on solutions for their own data analysis issues with the instructors.

Final part of the course is a module "Bioinformatic analysis of immune repertoires from high-throughput sequencing data" delivered by Enkelejda Miho and her colleagues from the Reddy lab from the D-BSSE department.

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/KyQCrKaATvS4Bn7j1

The course is limited to 20 participants, with preference for DBIOL, confirmations will be sent after the registration process.

Location

Zurich

Additional information

Coordination: Michal Okoniewski, Scientific IT Services ETH

Instructors

Michal Okoniewski, Samuel Fux, Daniel Spies, Christophe Chabbert, Hans-Joachim Ruscheweyh, Enkelejda Miho

Schedule

====> High Performance Computing for genomic applications

Day 1, 13 Dec 2017 (HPL D 34):

9:00 - 9:30 Introduction to the Euler cluster and HPC

9:30 -10:15 Linux re-fresh

10:15 -11:00 Basics of shell scripting

11:00 -11:15 Coffee break

11:15- 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- 15:45 Genomic software on the Euler cluster

16:00- 16:15 Coffee break

16:15- 17:30 RNA-seq software tools

Day 2, 14 Dec 2017, (HIL E 5):

9:00 - 9:30 Workflow orchestration with snakemake - demo

9:30 -10:15 Basics of useful R

10:15 -11:00 Basic R scripts for RNA-seq statistics

11:00 -11:15 Coffee break

11:15 -12:45 Hackaton: participants' own problems and data

====> Bioinformatic analysis of immune repertoires from high-throughput sequencing data (HCI E 2):

15:00 - 15:30 Introduction

15:30 - 16:15 Preprocessing data

16:15 - 16:30 Coffee break

16:30 - 17:15 Immune repertoire analysis