kfaizi / poo

biogeochemical nutrient cycling with a focus on feces

a template electronic lab notebook

with a little help from jupyter

overview

[what project is this repo for?]

structure

by default, we divide this repository into several subdirectories which you're likely to find useful.

.
├── experiments/
│   └── YYYYMMDD_experiment_name/
│       ├── notebook.ipynb
│       └── data/
│           └── results.csv
├── data/
│   └── master.csv
├── code/
│   └── script.py
├── protocols/
│   └── sample_prep.md
├── tests/
│   └── testing.py
├── README.md
└── LICENSE

• experiments is home to notebooks describing daily progress on experiments, alongside any (smallish) raw data they've generated. musings, rants, observations, logs, and hypotheses all live here.
• data is for bigger datasets, especially any that have been transformed, concatenated, or are otherwise widely used.
• code hosts custom modules, scripts, and pipelines created for this project.
• protocols contains template files describing oft-repeated experimental procedures for easy reference.
• tests is for the unit tests that you will definitely, um, get around to writing someday.
• every high-level directory ought to have descriptive README.
• an appropriate LICENSE should be chosen to protect your work as needed.

instructions

1. click 'use this template'
2. add a title and description
3. adjust licensing as needed
4. go do transparent, reproducible science!

acknowledgements

all this is heavily inspired by (and forked from!) Griffin Chure's template for reproducible research. you can make your own ASCII filetrees at tree.nathanfriend.io.