Lab Notebooks
We have been using online lab notebooks since 2007 and the platforms and workflows have certainly changed over the years. Below is a compendium of best practices based on our experience and the particular research we do. This is intended for those in our lab group, however comments and suggestions are welcome.
An online lab notebook is required of all lab members. Entries need to be organized by date and in reverse chronological order, and Updated daily.
Notebooks
| Person | Notebook | Commitment |
|---|---|---|
| Steven Roberts | sr320.github.io |  |
| Sam White | robertslab.github.io |  |
| Matt George | mattgeorgephd.github.io |  |
| Aspen Coyle | aspencoyle.github.io |  |
| Olivia Cattau | ocattau.github.io |  |
| Delaney Lawson | drlawson.github.io |  |
| Ariana Huffmyer | ahuffmyer.github.io |  |
| Chris Mantegna | chrismantegna.github.io/cmlabsite |  |
| Zach Bengtsson | zbengt.github.io |  |
| Celeste Valdivia | valeste.github.io |  |
| Larken Root | larkenr.github.io |  |
| Laura Spencer | laurahspencer.github.io |  |
| Yaamini Venkataraman | yaaminiv.github.io |  |
| Grace Crandall | grace-ac.github.io |  |
| Shelly Trigg | shellytrigg.github.io/notebook |  |
| Kathleen Durkin | shedurkin.github.io |  |
| Megan Ewing | meganewing.github.io/mewing-notebook |  |
Platforms
The current recommendation is Quarto in Rstudio.
See this page for a tutorial on how to set up.
Make sure it is reproducible
Document in a fashion where someone could replicate your work.
Document daily
A record of your work should be published the day of activity. Yep, daily! Even if you feel like you did nothing, post something to describe what you did that day. Did you read some papers? Great! Make a post that lists the papers you read. Did you spend all day searching the web? Also great! Make a post about what you were searching for and how successful you were in finding what you wanted.
Maintain backup
Have a copy of your notebook in another location. This could be done in several ways. - composing in text editor and hosting on GitHub - using IFTTT to post/save entries elsewhere - run script (i.e. wget) to archive contents
Periodically, you will be asked to show where your backup is and demonstrate that it is functional.
All GitHub-based notebooks are also backed up to Gannet: https://gannet.fish.washington.edu/github_backups/notebooks/