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by georgiev
3294 days ago
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What format do you use? I was searching for scientific​ notebook templates and examples but didn't find any so I just made my own: pandoc tags on the top and the rest is GitHub Markdown. Python cells when data need to be processed. |
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My typical notebook is mostly Python with a bit of Markdown, rather than vice versa. I'm rarely creating a linear narrative, so I often go back and add explanatory text after the fact but before I forget.
It's worth noting that I'm a lone wolf in terms of maintaining my own lab data and results. Nobody else cares how I do it, and I'm not in a regulated field. I'm in industry, so I don't publish. So it's mostly so I can figure out later what I did. At home, I've put some really obscure Jupyter notebooks on my GitHub page, which so far appears to have received exactly zero views. GitHub renders Jupyter notebooks automatically.
Alongside Jupyter, I've often got a regular Python IDE running, with programs or scripts that I use for data gathering. Most of my lab equipment is accessible via pySerial (a requirement for anything that I buy new). If you're really careful, you can script your data collection within the same Jupyter notebook that you use for analysis, but there are some hidden dangers, such as losing data stored in variables when you terminate the kernel, or over-writing files. My habit with data files is to use str(time.tim()) for file naming, so it's impossible to overwrite a file by accident.