Linux for Scientists [GE14]
Monday and Tuesday (full days)
Lennart Karssen, PhD
Erasmus MC, Rotterdam NL
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.
- Genetic Epidemiology
Detailed information about this course:
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.
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.
Participants of Genetic Epidemiology (GE02) will automatically be subscribed for this course.
Reduction on fees
PLEASE NOTE THIS DOES NOT APPLY TO THE RESEARCH MASTERS (120 EC points)
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:
- 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)
- 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).