ReproNim Reproducible Basics Module: Reference

Efficient practices are the (more) reproducible ones

There are a number of incompatible shells; different neuroimaging tools may use specific shells and thus provide instructions that are not compatible with your current shell.

A command line shell is a powerful tool and learning additional ‘tricks’ can help make its use much more efficient, less error-prone, and thus more reproducible.

Shell scripting is the most accessible tool to automate execution of arbitrary set of commands; this avoids manual retyping of the same commands and in turn avoids typos and erroneous analyses.

Environment variables play a big role in defining script behavior.

You can write automated tests for your commands to ensure correct execution.

Shell scripts are powerful, but – if misused – can cause big problems.

Using VCS not only improves sharing and collaboration, but is integral for guaranteeing reproducibility

VCS can be used directly or can serve as a foundation for domain-specific tools

Package managers and distributions allow for the efficient creation of tightly version-controlled computation environments

Clear up any legal as early as possible in the timeline of a project

Choose a standard license for your materials to ease dissemination

If you can’t reproduce it, it’s likely that nobody else can

Having open sharing in mind from the beginning can simplify future reproducibility

“Push yourself to incorporate these practices into your daily workflow.”