Lab Notebooks
We have used online lab notebooks since 2007; platforms and workflows have changed over the years. This page covers expectations for everyone in the lab. Comments and suggestions are welcome.
An online lab notebook is required for all lab members. Entries should be organized by date in reverse chronological order and updated daily. Document so that you or a stranger could reproduce the work years later. Monthly goals and meeting prep belong in the notebook; see Project Management and Environment and Expectations.
Platforms
The current recommendation is Quarto in RStudio.
Setup tutorial: course-fish521 websites lecture.
Document daily
Publish a record of your work the day of activity. If you did little hands-on science, post what you did anyway (papers read, troubleshooting, planning). See Environment and Expectations for how notebooks fit with writing and project goals.
Backups
Keep a copy of your notebook in another location, for example:
- compose in a text editor and host on GitHub
- use IFTTT to post or save entries elsewhere
- run a script (e.g.
wget) to archive contents periodically
You may be asked to show that your backup works. GitHub-based notebooks are also mirrored on Gannet: https://gannet.fish.washington.edu/github_backups/notebooks/
Member notebooks
Directory of current and past notebooks (may be out of date — open an issue to add or update a link).
| Person | Notebook | Activity |
|---|---|---|
| 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 |  |
| 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 Wanamaker | shellywanamaker.github.io/notebook |  |
| Kathleen Durkin | shedurkin.github.io |  |
| Megan Ewing | meganewing.github.io/mewing-notebook |  |