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 faculties. 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.

Content
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.

Participants
Seats: 20
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.

Language
English

Form
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,
anders.krogh@sund.ku.dk

Teachers
Henrike Zschach,
PhD, Data Scientist,
Center for Health Data Science,
henrike.zschach@sund.ku.dk

Thilde Terkelsen
PhD, Data Scientist
Center for Health Data Science
thilde.terkelsen@sund.ku.dk

Valentina Sora
PhD, Postdoc
Center for Health Data Science
vaso@di.ku.dk

Dates
23 & 24 September 2024, 08:45 – 15:30

Course location
23 September 2024: Universitetsparken 13 – Und.lokale 14, pavillonen – stuen
24 September 2024: Universitetsparken 13 – Und.lokale 8, pavillonen – stuen

Registration
Please register before 24 August 2024.

Expected frequency
Twice per year.

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.

Disclaimer:
DDSA has explicit permission from Arcanic and the owners of the https://phdcourses.dk/ website to display the courses on ddsa.dk.