Linux for Scientists [GE14]

Course highlights

EC points

0.6

Months

October

Course days

Monday and Tuesday (full days)

Faculty

Lennart Karssen, PhD

Course fee

€ 370

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.

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

Attendance, Assignment(s)


Reduction on fees

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

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

Institute of Medical Education Research Rotterdam (iMERR)

Netherlands Cancer Institute/Antoni van Leeuwenhoek Hospital

  • Department of Cancer Epidemiology

25% reduction on our fees for partner institutes of NIHES

For participants formally appointed at the following departments, institutes:

  • Departments of Erasmus MC (except the departments mentioned above)
  • Addiction Research Institute (IVO)
  • Integraal Kankercentrum Zuid (IKZ)
  • Pallas Health Research and Consultancy
  • Municipal Health Service Amsterdam (GGD Amsterdam)
  • Municipal Health Service Rotterdam (GGD Rotterdam)
  • Havenpolikliniek
  • Admiraal De Ruyter Ziekenhuis

25% reduction for all (international) PhD students
Please state your tutor’s name and email address on the application form (remarks field).

25% reduction on our course fees (maximum 3 EC points per academic year) for all NIHES alumni
Please state that you are a NIHES alumnus/alumna and the academic year you graduated (remarks field).