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Just bash it – An intro to the unix command line
Provider: Faculty of Health and Medical Sciences

Activity no.: 3934-23-00-00 
Enrollment deadline: 22/05/2023
Date and time05.06.2023, at: 09:00 - 06.06.2023, at: 16:00
Regular seats25
Course fee2,040.00 kr.
LecturersAnders Krogh
ECTS credits1.30
Contact personEleonora Nigro    E-mail address: eleonora.nigro@sund.ku.dk
Enrolment Handling/Course OrganiserPhD administration     E-mail address: phdkursus@sund.ku.dk

Aim and content

This is a generic course. This means that the course is reserved for PhD students at the Graduate School of Health and Medical Sciences at UCPH.

Anyone can apply for the course, but if you are not a PhD student at the Graduate School, you will be placed on the waiting list until enrolment deadline. After the enrollment deadline, available seats will be allocated to the waiting list.

The course is free of charge for PhD students at Danish universities (except Copenhagen Business School), and for PhD students at NorDoc member universities. All other participants must pay the course fee.

Learning objectives

A student who has met the objectives of the course will be able to:

1. Understand what a terminal is, how to use it, how to get help and handle errors.
2. Set up a good directory structure for computational projects.
3. Perform basic unix operations on files.
4. Automate their workflow through scripts and workflow language.
5. Navigate on unix-based HPC environments (servers) such as computerome 2.0.


The course will introduce how to interact with the computer via the unix terminal, detail its strengths and use cases and demonstrate how to obtain a terminal on Windows. The course will provide an overview of the fundamental unix commands such as sort, cut, grep and sed which are used to perform essential file operations with ease. We will further address how to chain commands and build simple pipelines in bash, as well as introduce the concept of workflow language.

Lastly, participants will learn how to set up a good directory structure for their computational projects and hear about options for backup which will benefit their workflow and make it easier to collaborate on projects or pass them on to other researchers.


The course is intended for PhD students at SUND who are interested in learning how to operate on the command line and use it to execute scientific programs that do not have a graphic user interface or to navigate on HPC environments. It requires no prior knowledge of unix. It is specifically targeted towards medical and biological researchers who are looking to strengthen their computational skills, though PhD students from all disciplines are welcome.

Relevance to graduate programmes

The course is relevant to PhD students from the following graduate programmes at the Graduate School of Health and Medical Sciences, UCPH:

All graduate programs.




Lectures, interactive presentations using the terminal (code along) and exercises.

Course director

Anders Krogh,
Professor, Head of Center for Health Data Science,
Center for Health Data Science,


Henrike Zschach,
PhD, Data Scientist,
Center for Health Data Science,

David Galligani,
IT specialist,
NNF Center for Protein Research,

Christian B. Knudsen
Data Scientist,
Copenhagen University Library,

Daniel Pryn
Data Scientist,
Copenhagen University Library,


5 - 6 June 2023, 09:00 - 16:00

Course location

KUB Lighthouse Learning space,
Ground floor to the right from the entrance,
Copenhagen University Library North,
Nørre Allé 49, 2200 København


Please register before 22 May 2023

Expected frequency

We do not know yet.

Seats to PhD students from other Danish universities will be allocated on a first-come, first-served basis and according to the applicable rules. Applications from other participants will be considered after the last day of enrollment.

Note: All applicants are asked to submit invoice details in case of no-show, late cancellation or obligation to pay the course fee (typically non-PhD students). If you are a PhD student, your participation in the course must be in agreement with your principal supervisor.

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