Schedule
The course will take place online via Zoom. We will follow the approximate schedule below:
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| 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 |
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| 12:30 | Wrap-up day 1 | |
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| Time | Topic | |
| 09:00 | ... continued: Practical tutorial: Git |
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| 10:00 | Wrap-up - git tutorial | |
| 10:15 | Break | |
| 10:30 | Master your dependencies - environments and reproducibility
- Introduction to the package and environment manager Conda - Practical tutorial: Conda |
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| 12:15 | Wrap up - Conda tutorial | |
| 12:30 | Wrap-up day 2 | |
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| Time | Topic | |
| 09:00 | Organize your analysis using workflow managers
- Introduction to Snakemake - Practical tutorial: Snakemake |
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| 10:30 | Break | |
| 10:45 | ...continued - Practical tutorial: Snakemake | |
| 12:15 | Wrap-up - Snakemake tutorial | |
| 12:30 | Wrap-up day 3 | |
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| Time | Topic | |
| 09:00 | Computational notebooks and reproducible reports
- Introduction to Jupyter and R Markdown - Practical tutorial: Jupyter - Practical tutorial: R Markdown |
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| 10:15 | Wrap up - Notebook tutorial | |
| 10:30 | Break | |
| 10:45 | Containerization
- Introduction to containers - Practical tutorial: Docker - Practical tutorial: Singularity |
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| 12:30 | Wrap-up - Day 4 | |
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| 09:00 | ...continued - Practical tutorial: Docker & Singularity | |
| 10:15 | Wrap-up - Container tutorial | |
| 10:30 | Break | |
| 10:45 | Putting the pieces together
- Q&A: How to implement these procedures on a day-to-day basis |
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| 12:15 | Wrap-up | |
| 12:30 | All done! | |
Teachers: John Sundh, Verena Kutschera, Erik Fasterius, Tomas Larsson