Linux for Scientists [EL016]

Course highlights

EC points

0.6

Start date

26-01-2022

End date

27-01-2022

Course days

Monday and Tuesday (full days)

Faculty

Lennart Karssen, PhD

Course fee

€ 390

Location

Erasmus MC, Rotterdam NL

Level

Introductory

Prerequisites

No previous Linux knowledge is expected, however, on order to gain most from the course it is recommended to have done a few analyses on a Linux server already.


This course is a prerequisite for the course GE02 Genetic-epidemiologic Research Methods.

Disciplines

  • Genetic Epidemiology

Application

How to apply

Detailed information about this course:

Description

This course aims to teach users of a Linux/UNIX system how to work with the command line interface. After an introduction to some history and basic concepts the basic commands for file and directory manipulation will be discussed. Subsequently, the students will learn how to manage processes as well as input and output redirection, followed by more advanced text processing utilities like 'sed' and 'gawk'.

The second half of the course shows how to write Bash shell scripts to automate tasks. This knowledge is then used when discussing the Sun Grid Engine job queue system in use on the epib-genstat servers.

The course will focus on providing hands-on experience, so those who have been using a Linux system for a longer time will be able to skip the parts they already feel comfortable with and move on to more advanced concepts like regular expressions, version control and advanced use of a text editor. 

Objectives

After completing this course, the students should be able to efficiently use a Linux system and its tools to:

  • manage your project data from the command line (i.e. without having to copy files back and forth to the server);
  • reformat output from previous analyses and use this as input for a subsequent analysis step;
  • write scripts that automate repetitive tasks;
  • efficiently run time-consuming analyses like a GWAS without overloading the server.

Participant profile

Participants of Genetic Epidemiology (GE02) will automatically be subscribed for this course.

Assessment

Assignment(s)


Reduction on fees

PLEASE NOTE THIS DOES NOT APPLY TO THE RESEARCH MASTERS (120 EC points)

No fees are charged for participation of Erasmus MC PhD candidates

Please note that in case of cancellation or no show, the cancellation policy applies based on the full course fee.

50% reduction on our fees for participating institutes of NIHES

This 50% reduction is offered to participants formally appointed at the departments or sections participating in NIHES.

University Medical Center Rotterdam/Erasmus University Rotterdam:

  • Department of Epidemiology
  • Department of Public Health
  • Department of Psychiatry, Section of Medical Psychology and Psychotherapy
  • Department of Child and Adolescent Psychiatry/Psychology
  • Department of Medical Informatics
  • Department of General Practice
  • Erasmus School of Health Policy & Management
  • Generation R

50% reduction on our fees for NIHES affiliated partners

This 50% reduction is offered to participants formally appointed at the following NIHES affiliated partners:

University Medical Center Rotterdam/Erasmus University Rotterdam, departments of:

  • Dermatology
  • General Paediatrics
  • Plastic and Reconstructive Surgery
  • Rehabilitation Medicine

UMIT, Department of Public Health, Health Services Research and Health Technology Assessment.

25% reduction on our fees for Erasmus MC employees

For participants formally appointed at all departments of Erasmus MC (except the departments mentioned above and Erasmus MC PhD candidates).

25% reduction for all (international) PhD students without formal appointment at Erasmus MC

Upon receipt of your application you will receive a request to upload proof of enrollment as a PhD student.