Principles

The core guiding principle is simple: Someone unfamiliar with your project should be able to look at your computer files and understand in detail what you did and why. This “someone” could be any of a variety of people: someone who read your published article and wants to try to reproduce your work, a collaborator who wants to understand the details of your experiments, a future student working in your lab who wants to extend your work after you have moved on to a new job, your research advisor, who may be interested in understanding your work or who may be evaluating your research skills. Most commonly, however, that “someone” is you. A few months from now, you may not remember what you were up to when you created a particular set of files, or you may not remember what conclusions you drew. You will either have to then spend time reconstructing your previous experiments or lose whatever insights you gained from those experiments.

This leads to the second principle, which is actually more like a version of Murphy's Law: Everything you do, you will probably have to do over again. Inevitably, you will discover some flaw in your initial preparation of the data being analyzed, or you will get access to new data, or you will decide that your parameterization of a particular model was not broad enough. This means that the experiment you did last week, or even the set of experiments you've been working on over the past month, will probably need to be redone. If you have organized and documented your work clearly, then repeating the experiment with the new data or the new parameterization will be much, much easier.

To see how these two principles are applied in practice, let's begin by considering the organization of directories and files with respect to a particular project.