It really comes down to, what is your role? Are you making discoveries or working for people who do? Both are very worthy. In my experience, the PIs - and their subordinates who become PIs - they aren’t thinking very hard about lab notebooks and their tactics vary widely. No best practices. However they are focused on maximizing the amount of serendipity they can have per unit time, which tends to devalue how you’re documenting stuff for patent lawyers.
Does Benchling have a manifesto about why you should care about lab notebooks? No. It has a ton of little reactive opinions that are relevant to its sales pipeline. But nothing like “Agile, except for life sciences” which incorporates their software. It’s everything to all people, like most life science software. I know people receive huge grants on promising discoveries in life sciences, and some of their labs have Benchling licenses and don’t use them. The people first authoring the papers use lab notebooks of course, but see this as a small part of their process.
Where I think software like that gains its use is when you have multiple people working on similar research or processes, and trying to manage that kind of research and the data that it generates. At the extreme, I see job openings like this:
Wanted, quality control chemist for third shift...
On the other hand, I work in a "small lab" setting. I'm often the only person working on a project. No two of my projects resemble one another, though there are themes that progress through my work, and tools that I re-use and share. My choice of a notebook system, if you can grace it with such a description, is almost solely for my own benefit.
I do hope the Quarto project makes it and survives. It's a cut above the other notebook solutions like jupyter.
Instead, everything is markdown and you can interleave codeblocks (or inline code statements) anywhere you like to generate plots/tables, etc.
I haven't had a need to generate markdown programmatically, though I imagine there's probably at least a "hard way" to do that. FWIW, quarto is still in its early stages. The quarto devs on github are very nice and responsive to questions if you ever look into again.
If you're a developer and want to have your presentations amenable to being tracked in git, with all of the figures made from code and so on, Quarto is the absolute best you can do.
It's phenomenal and every developer should be using it.
But... the first thing I'll do is try quarto for my passive web page, which I presently generate using nbconvert.
Here here. WWIT (what was I thinking) is so valuable. I'm spending much more time now writing notes that provide context in addition to a bare description of what I did. I hate it when I look at old notes, have a million questions, and curse myself for not writing more.
Also, thank you for making the point about the US patent system. I recall somewhere around 1990, where people silently didn't bother to issue notebooks for me to record ideas (i.e. inventions) in favor of electronic disclosure forms.
Memories fade. Ink fades but rarely corrupts.
Seems a forgotten thing in the modern world.
Let's just say I much prefer working with scientist heavy companies and teams.
Many of those rules became unnecessary when the US patent system joined the rest of the world by adopting "first to file" priority. Rules such as: Always writing in pen, and crossing things with a single strike-through.
Notebooks are still a great way to preserve the little details of "what the hell was I thinking?" A colleague told me a good notebook prevents you from having to repeat a study because you can't figure out what you did the first time.
There are still industries that require legally defensible record management -- you'll know if you're in that boat. If not, you can DIY whatever method works for you. The success metric is if you actually use it. On paper, I write in pencil because I'm more concerned about readability than a precise narrative. On the computer, Jupyter, just because nothing else really lets me document "thinking in code."