Schedule
The course will take place in the room 10:an (see travel info).
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| Time | Topic | |
| 10:00 | Coffee and fika available from 10.00. Welcome! | |
| 10:30 | Introduction to Reproducible Research - Introduction slides |
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| 11:15 | Data management and project organization - Data management slides |
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| 11:45 | Lunch | |
| 12:45 |
Master your dependencies - environments and reproducibility
- Introduction to the package and environment manager Conda - Practical tutorial: Conda - Conda slides |
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| 14:30 | Fika | |
| 14:45 |
Distributing and version tracking your code
- Introduction to version control and git - Practical tutorial: Git - Git slides |
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| 16:45 | Wrap-up day 1 (slides) | |
| 17:00 | Free time! | |
| 17:30 | Joint departure for dinner | |
| 18:00 | Course dinner | |
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| Time | Topic | |
| 09:00 |
Organize your analysis using workflow managers
- Introduction to Snakemake - Practical tutorial: Snakemake - Snakemake slides Fika break ~10:15 |
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| 11:45 | Lunch | |
| 12:45 |
...continued: Practical tutorial: Snakemake |
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| 13:45 |
Computational notebooks and reproducible reports
- Introduction to Jupyter and R Markdown - Practical tutorial: Jupyter - Practical tutorial: R Markdown - Computational notebooks slides Fika break ~14:30 |
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| 16:45 | Wrap-up day 2 (slides) | |
| 17:00 | Free time! | |
| 17:30 | Social event! | |
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| Time | Topic | |
| 09:00 |
Containerization
- Introduction to containers (slides) - Practical tutorial: Docker - Practical tutorial: Singularity Fika break ~10:15 |
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| 11:45 | Lunch | |
| 12:45 |
Wrap-up - putting the pieces together
- Overview - Using the tools in concert (slides) - Practical tutorial: Making a project reproducible |
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| 14:30 | Fika | |
| 15:00 |
Open discussion - Reproducible research in practice Tips and tricks on how to implement these procedures on a day-to-day basis |
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| 16:30 | All done! | |
Teachers:
Leif Wigge
John Sundh
Verena Kutschera
Tomas Larsson