Schedule

The course will take place online via Zoom. We will follow the approximate schedule below:

Day 1 - 2021-04-19
Time	Topic
09:00	Setting up
10:00	Introduction to Reproducible Research
10:30	Break
10:45	Data management and project organization
11:15	Break-out rooms and ice breaker session
11:30	Distributing and version tracking your code - Introduction to version control and Git - Practical tutorial: Git
12:00	Lunch
13:00	... continued: Git tutorial
14:30	Wrap-up day 1
Day 2 - 2021-04-20
Time	Topic
09:00	Master your dependencies - environments and reproducibility - Introduction to the package and environment manager Conda - Practical tutorial: Conda
10:15	Break
10:30	... continued: Conda tutorial
11:00	Wrap up - Conda tutorial
11:15	Organize your analysis using workflow managers - Introduction to Snakemake - Practical tutorial: Snakemake
12:00	Lunch
13:00	... continued: Snakemake tutorial
14:30	Wrap-up day 2
Day 3 - 2021-04-21
Time	Topic
09:00	... continued: Snakemake tutorial
10:00	Wrap-up - Snakemake tutorial
10:15	Break
10:30	Computational notebooks and reproducible reports - Introduction to R Markdown - Practical tutorial: R Markdown
12:00	Lunch
13:00	Computational notebooks and reproducible reports - Introduction to Jypyter - Practical tutorial: Jupyter
14:30	Wrap-up day 3
Day 4 - 2021-04-22
Time	Topic
09:00	Containerization - Introduction to containers - Practical tutorial: docker - Practical tutorial: singularity
10:30	Break
10:45	... continued: Docker & Singularity
12:30	Wrap-up day 4
Day 5 - 2021-04-23
09:00	Putting the pieces together - How to put all the tools and procedures together - How to implement these procedures on a day-to-day basis - Practical tutorial: Making a project reproducible
10:15	Break
10:30	... continued: Making a project reproducible
12:15	Wrap-up day 5
12:30	End of course!

Teachers: John Sundh, Verena Kutschera, Erik Fasterius, Tomas Larsson