4.1 Reproducible Research - CodeRefinery March 2023
Channel: CodeRefinery
Date: 2023-03-28

If you can't get your code to do the same thing again, is it really science?  Or more practically, are you able to do your work?  Reproducibilty is a big deal, but we don't always learn how to do it.  In this lesson, we cover the basics, how to organize projects, record computational steps with Snakemake or other workflow managers, how to record environments with conda (and docker a bit), and sharing code and data (FAIR).

https://coderefinery.github.io/reproducible-research/

00:20 Motivation
10:38 Organizing projects
21:48 Recording dependencies
28:55 Exercise: explore dependency management in conda/Python/R/Matlab
32:49 Exercise discussion
35:39 Recording computational steps
43:03 Exercise: Snakemake
53:52 Q&A and summary about the exercise
58:03 Recording environments (containers)
1:00:14 Sharing code and data
1:02:28 Demonstration of Zenodo

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This is part of the CodeRefinery March 2023 workshop.  The videos are available to everyone, but may be most useful to the people who attended the workshop and want to review later.

Playlist: https://www.youtube.com/playlist?list=PLpLblYHCzJACsZllghoLA4JBMjkTk0eq4

Workshop webpage: https://coderefinery.github.io/2023-03-21-workshop/

CodeRefinery: https://coderefinery.org/