Digital lab notebook: why and how

Why was this one of the most upvoted topics?

  • Why is it important for you to maintain a lab notebook
  • Why do it digitally?

General principles

  • Your commitment|discipline|habits are the primary determinant of how “good” your lab notebook

  • The best lab notebook is one that you update regularly.

  • We’ll go some options today, but above all, whatever system allows you to consistently add to the lab notebook is the best system

Background reading

Adoption of digital lab notebooks

NIH’s policy regarding electronic lab notebooks (ELN)

As with paper lab notebooks, ELNs serve as the complete research record, documenting why specific experiments were initiated, how they were performed, what data and observations were produced, where the data are stored, and how the data were analyzed and interpreted, in sufficient detail so the research can be reproduced by others.

This means that a scientifically literate person with no prior knowledge of the project should be able to use the documentation provided in the ELN to navigate the rationale, methods, experimental samples, results, analysis, and basis for the major conclusions entirely from the ELN.

Adopting common platforms for ELNs

  • In some cases, this is as simple as maintaining detailed notes in a Google doc or similar platform.

  • Software like Evernote can also be adopted for maintaining ELNs

  • There are pros and cons – e.g. setup is easy, but maintaining code becomes difficult

Commercial ELNs

  • Primarily designed for molecular biology-type labs

  • Especially important if dealing with sensitive data, e.g. health records, …

https://www.youtube.com/watch?v=YTp0W0i2eD4

Open-source software that can be adopted for ELNs

  • MediaWiki to create own “personal” wiki
  • Obsidian as a markdown-friendly note-taking framework
  • Treating your gitlab account as an unstructed lab notebook.

How to choose from many options?

Digital lab notebooks with Quarto?

  • A lot of us are going to have daily workflows that rely on RStudio, Git, and Quarto
  • Can we use this to set up a digital lab notebook?
    • (of course!)

An attempt at creating an ELN workflow through Quarto

This template and workflow is very much under development, and open to feedback!

  • Template and instructions available at https://labnotebooktemplate.gklab.org/, we will go through some steps together in class.

  • To use this template, also install a small R package with utility functions:

install.packages("pak")
library(pak)
pak("gitlab::gklab/quartoutils")

Using the template

Using the template

  1. Using the terminal in your Rstudio client, navigate to the location where you wish to create the lab notebook.

  2. Execute the following command: quarto use template https://gitlab.com/gklab/templates/lab-notebook-template-2/-/archive/main/lab-notebook-template-2-main.zip

  3. Open this up as an RStudio project and verify that it builds

Following features will be shared in RStudio.