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Lab Notebooks (2020)

sambleckley.com

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Re: Lab Notebooks (2020)

#41

Post by chaxor »

j0k3r_85 wrote: post #30
analog31 wrote: post #5

The article mentions, but doesn't elaborate, on the purpose of the notebook as a legal document. This was much more important when notebooks could be used to show priority in patent disputes, but only if well kept. My parents were both research scientists. Where my dad worked, the company patent lawyer read and critiqued your notebooks, and maintained the discipline. Many of those rules became unnecessary when the US…

Have you tried quarto markdown? It’s similar to rmarkdown but language agnostic and allows me to think in code in a way that can easily be added to notebooks. To work with them in notebook fashion I can work through one file a day and save the rendered pages in a folder.

Quarto is fantastic for making presentations as well!

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.

Re: Lab Notebooks (2020)

#42

Post by DarkSucker »

analog31 wrote: post #5

The article mentions, but doesn't elaborate, on the purpose of the notebook as a legal document. This was much more important when notebooks could be used to show priority in patent disputes, but only if well kept. My parents were both research scientists. Where my dad worked, the company patent lawyer read and critiqued your notebooks, and maintained the discipline. Many of those rules became unnecessary when the US…

> Notebooks are still a great way to preserve the little details of "what the hell was I thinking?"

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.

Re: Lab Notebooks (2020)

#43

Post by PNewling »

crispyambulance wrote: post #36

I have seen meticulous, beautiful lab notebooks before. Paper ones. With numbered oversize greenish pages, faintly quadrille ruled, filled with exceptional INK penmanship, paragraph after paragraph of cogent technical observations, theoretical musings, responses to papers, thought-experiments and real experiments, taped graphs and images. Everything dated and signed. I've seen stacks of them spanning YEARS of work. I…

>Perhaps these are becoming a relic of a lost era? Paper is too much of an "air-gap" when everything is done on computer. Moreover, the standard 2-week Agile "sprint" leaves no time for careful thinking and writing. One can't put epiphanies gained from writing up notes into "the deliverable" for a freaking Jira Ticket

So, I get what you're getting at here (I think), especially as someone who came from research labs and then moved into computer science, but teams should be building doco into the tickets and pushing back on anything that doesn't have some meaningful documentation built in.

Easier said than done in some organizations, I know, but I still think we need to be the ones to push back.

Re: Lab Notebooks (2020)

#44

Post by arminiusreturns »

analog31 wrote: post #5

The article mentions, but doesn't elaborate, on the purpose of the notebook as a legal document. This was much more important when notebooks could be used to show priority in patent disputes, but only if well kept. My parents were both research scientists. Where my dad worked, the company patent lawyer read and critiqued your notebooks, and maintained the discipline. Many of those rules became unnecessary when the US…

I honed my lab notebook taking during my time working under a brilliant geneticist, (I actually used raw yaml before I got into emacs org-mode) and really enjoyed the daily detail... and then when I got more into the startup world I kept getting "don't write that down because it's then discoverable!" but in shaded language from the in house counsels... and it was very off-putting. I ended up CYA'ing at some of those by sending slack/etc messages to myself of things like that.

Let's just say I much prefer working with scientist heavy companies and teams.

Re: Lab Notebooks (2020)

#45

Post by BasilPH »

karencarits wrote: post #8

I wonder if we soon will get wearable lab cameras/microphones that can log what you do while keeping your hands free. More than once, I have been working with both hands and suddenly been distracted for a brief moment just to discover that I no longer remember if I really added stuff to that well. Also, having more exact timestamps at each stage of an experiment might be useful for later

A former colleague of mine left to work at a company that builds a voice-controlled lab assistant[^0]. The idea is that you can record data and ideas while your hands are busy dealing with samples or a microscope.

I don't know how well it works, but I've always found it to be an interesting niche. Pharmaceutical companies have deep pockets and security, compliance and specific requirements let you build a moat from more generic voice assistants.

[^0]: https://www.labtwin.com/

Re: Lab Notebooks (2020)

#46

Post by ac50hz »

100% yes.

And a new page per day (paper is cheap), with the date always on top outer corner of the page. Never share a page across dates.

Thoughts, however bizarre, around the topics are very useful. Elaborate where possible. Names, keywords and classifications will be useful later, so do consider the future as you write.

Re: Lab Notebooks (2020)

#47

Post by ac50hz »

DarkSucker wrote: post #42
analog31 wrote: post #5

The article mentions, but doesn't elaborate, on the purpose of the notebook as a legal document. This was much more important when notebooks could be used to show priority in patent disputes, but only if well kept. My parents were both research scientists. Where my dad worked, the company patent lawyer read and critiqued your notebooks, and maintained the discipline. Many of those rules became unnecessary when the US…

> Notebooks are still a great way to preserve the little details of "what the hell was I thinking?" 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…

Record keeping, for better or worse, is essential.

Memories fade. Ink fades but rarely corrupts.

Re: Lab Notebooks (2020)

#48

Post by physicles »

The main problem with paper is that it's not searchable, so I've been using [0] since 2018. Each invocation just appends a timestamped line of text. I have a crontab that pops up a box every hour and I type in what I'm working on. Sometimes I'll add extra notes if I'm working through a particularly thorny problem. It's always right there on the terminal.

I'd say it's saved my ass at least a dozen times over the years, where I hit a problem that I've seen before but can't quite remember how to solve it. I also page through it quarterly to get a good summary of what I've worked on for that quarterly 1:1 with the boss.

[0]: https://gist.github.com/mfischr/f1ee2967ec0181b934639c30f4e6...

Re: Lab Notebooks (2020)

#49

Post by ac50hz »

crispyambulance wrote: post #37
j0k3r_85 wrote: post #30

Earlier quoted context omitted.

Have you tried quarto markdown? It’s similar to rmarkdown but language agnostic and allows me to think in code in a way that can easily be added to notebooks. To work with them in notebook fashion I can work through one file a day and save the rendered pages in a folder.

Quarto, I think, is definitely a step in the right direction. It allows for publication quality rendering into pdf, and various html flavors including Confluence. You can write fluently in it, mix-in actual running code, and you've got options for sophisticated graphics, tables and mathematics. I do hope the Quarto project makes it and survives. It's a cut above the other notebook solutions like jupyter.

I’ve been heading in this direction, and Quarto continues to be the end point, on the road from pandoc.

Re: Lab Notebooks (2020)

#50

Post by ac50hz »

physicles wrote: post #48

The main problem with paper is that it's not searchable, so I've been using [0] since 2018. Each invocation just appends a timestamped line of text. I have a crontab that pops up a box every hour and I type in what I'm working on. Sometimes I'll add extra notes if I'm working through a particularly thorny problem. It's always right there on the terminal. I'd say it's saved my ass at least a dozen times over the years…

Whilst i agree with all of this, I like paper, and to set time aside (with coffee) to review batches of notes.
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