Course syllabus
October 2026, onsite week 19-23/10
Online and Stockholm
The aim of this workshop is to introduce the participants to the importance of the FAIR data management and the use of computational tools to perform scalable, reproducible and transparent research. The participants will get a theoretical foundation coupled with practical exercises where they will learn the tools and concepts and then apply them to their own research projects. This will increase the impact the course has on their continued daily-life research.
Audience: The course is open to members of the DDLS Research School. By accepting to participate in the course, you will agree to follow the NBIS Training Code of Conduct.
Location: The course is blended with some sessions online while the majority will take place onsite at SciLifeLab Solna. Individual work is also expected between the sessions.
Recommended credits: This course is equivalent to 3 ECTS credits and a certification of participation will be awarded to participants actively participating in the entire course.
Covered topics
- Data Management and FAIR in Practice
- Organising data, files and folders in research projects
- Describing data with metadata
- Publishing data and code to public data repositories
- Writing Data Management Plans
- Version control using Git
- Software management using Conda
- Reproducible workflows using Snakemake and Nextflow
- Writing documentation and reports using Quarto and Jupyter
- Containerization using Docker and Apptainer
Learning outcomes
Upon completion of this course, the participants will be able to:
- Organise their files and metadata in a structured way
- Clearly organise their bioinformatic projects
- Identify relevant metadata standards for their research project
- Select suitable public repositories for their data and code and have an understanding of how to submit data to them
- Construct a Data Management Plan and summarize their benefits
- Apply the version control system Git to track and collaborate on code
- Utilise the package and environment manager Conda
- Build workflows with Snakemake and Nextflow
- Make use of Quarto and Jupyter Notebooks to document and generate automated reports for their analyses
- Deploy and manage containerized computational environments with Docker and Apptainer
Application
This is a course for members of the DDLS research school and is recommended to participate in the course during the first year of the research school. The course material is open for anyone to use as self-study material.
Registration will open in April
Prerequisites
To successfully follow this course, participants should have:
- basic skills of using Unix systems (i.e. being able to work on the command and be familiar with commands such as ls, cd, touch, mkdir, pwd, wget, man, etc.)
- a basic knowledge of either R or Python
- a basic understanding of Open Science and the FAIR principles
Pre-course material
Pre-course material will be available and distributed before the course starts.
Course leaders
Elin Kronander
Elisavet Torstensson
Erik Fasterius
John Sundh
contact: edu.fair-rp@nbis.se