Lab Notebooks for Computational Science

Question

Many grants require an official record be kept of day-to-day research activities. For experimental research groups, this is often accomplished with a bound paper notebook in which the experimental details, troubles, and possibly a few key results can be written (or sometimes even printed off and taped in).

Some electronic lab notebook options exist, which may be better suited to work done entirely on the computer (or maybe not!), but these are still less common. Plain text files may not satisfy the requirement of immutable entries. Furthermore, some institutions and groups with a tradition of experimental work may not take to an electronic format at all.

What methods have you tried to keep an official log of your computational research activities?

Answer 1

As Paul mentioned in his comment, git and public hosting sites like Github and Gitlab are invaluable for keeping track of the development history of computational projects. A few concrete examples of where I've found that history useful:

• US federal grants require you to fill out yearly progress reports and I can never remember exactly what I did, but I can always look through the commit history.
• Finding exactly where bugs have crept into the code I write, sometimes manually and sometimes automatically with git bisect.
• I like to remind the students I work with that it's ok to make mistakes, the important part is being circumspect in testing, so I go through the commit history of projects I've worked on to show them some of my more idiotic mistakes.

You also mentioned electronic notebooks; I'm guessing you're already familiar with Jupyter notebooks then. I use these a lot for computational experiments, especially when I'm messing around with new methods that I don't quite understand yet. Usually the experimental notebooks would get lost on my hard drive somewhere. What I've started doing lately is keeping these notebooks in a git repository and publishing them online using the static site generator nikola, which can generate posts from Jupyter notebooks. Along with the code I also add explanations of the mathematics with references to other useful sources. This is helpful for future me to remember exactly what I was doing and to be able to show things to colleagues and students. Both github and gitlab offer free static site hosting. You can use continuous integration tools to automatically execute notebooks (so you can keep them in their much smaller purely textual pre-execution form in version control) and build a website with them. The same tools are also helpful in hosting documentation for software projects.

Your usage / mileage my vary, just speaking from personal experience here.