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."
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.
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.
Let's just say I much prefer working with scientist heavy companies and teams.
I tried. Mine look like shit. If it's in ink, it's peppered ALL OVER with correction after correction after correction. Perhaps it's a matter of practice, but then I've not been at one place long enough where projects weren't constantly re-shuffled, killed, or lasted long enough to get a grip (sometimes the job and the company itself doesn't even last long enough).
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.
FWIW, some do structure a "data review" state prior to closure of a ticket where the deliverable is some type of report (often with a presentation). Obviously, this can't be done for every ticket but it's appropriate for periodic "capstone" tickets.
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...
The other thing is to date every page accurately. Notes are a time series.
Apart from the format of the headings, it is deliberately informal and unstructured. I've found it very useful.
That said, I don't use lab notebooks for coding/software development. I tend to use Markdown files in a Git repository for that. That setup serves the same purpose, since I write down what I intend to do and whether I was able to achieve it or not, but it is much easier to use when coding in my experience.
I plan to get it bound and call it my “real” thesis.
Rule #1. Every thing gets a date (And more an aspiration than reality a time.) I am truely an oddball and have my own date format 2023_12Dec_26Tue_1312. Rational, when used a a corresponding file name, it sorts naturally assuming you used 0 prefix on one digit numbers. Day of week, just another memory clue to try to recall specific thought experiment.
Rule #2. It is a process, not end product. Like the article mentions, no erasure. Point is re remember mistakes, not hide them.
Rule #3. Take you time to write neatly. It is for your future you, and you will thank yourself. May feel like a debt due to slowness, but really an investment for your future self.
Pros. reMarkable likes: feels like nice inkflow. Can get a fine line not quite comperable to a Pilot G-Tec-C 0.25 pen, but fine enought. I write small to increase information density per page. NeoSmart pen: doesn't just feel like ink flow, it is inflow
Cons. NeoSmart pen: notebooks are expensive. Cheapskate in me, writes less than I should. Remarkable tablet: Miss the real estate of two pages open in a labnote book. Also, miss the leafthrough feel of physical notebook. Can't as easily binary seach to find something like one can in paper notebook
Just saw Smart Plate at neosmartpen site, resisting urge for impulse purchase
Edit - update to expand
Additional cons or NeoSmartpen: Very limited number of pen widths.
Note: When I worked for a living, it was much more likely to be greenfield project, not a repetition of a existing workflow. Even on repetitive projects, debugging is a good match for a notebook. Now my projects are for learning, never finished product. As always, your mileage may vary.
Try to formalize your process and have repeatable actions done in repeatable ways. I have a collection of tokens. Before starting I write down a #GOAL, useful for climbing out of rabbit holes. Of course, the all important #ASSUMPTIONS. If the goal is not likely achievable in one session, write down a #PLAN. If need motivation to pursue a path, I write #BABYSTEPS for an action to start with. If I have a thought that would distract from present pursuit, I write a #STASH. If I do have a distraction I pursue, I note #DETOUR. End of day gets a few #LESSONSLEARNED and a #WRAPUP.
I have a target audience of one, me. Thru trial and error I know what I'll want to know in the future, usually from stuff I regreted not having written down. From time to time, recall, revise, and document "process" currently in use in notebooks. Date_Time are links to other notes in notebook, Date_Time_Notebook are references to other notebooks. Date_Time and Date_Time_Notebook are also typed as comments in associated computer files, be they source code or what serves as documentation.
To re-emphasize importance of Rule#1: Truth value of things changes with time. Time, usually, but not always, serves as a shortcut description of context, or at least provides enough hints to re-build the context
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/
https://www.muji.eu/product/recycling-paper-notebook-dark-gr...
1. Scientific Notebook Company <https://snco.com/>
2. BookFactory <https://www.bookfactory.com/>
Of the two, I slightly prefer BookFactory's offerings. Note that there are many, many variants. Unless you are employed somewhere that mandates a particular type – and if you do, they are likely available from your office supply closet – pick one you like. Do go with the bound hardcover style, though. They're much more durable than spiral or softbound.
Preserving a record in detail seems like a natural fit, we're used to doing the same for our source code, I'm surprised it's not more common to do the same for the source of the source code.
That said, I usually try to preserve the results of my "experimentation" in documentation with the software, so I can share it with others. It's a good sign when people never talk about X to me, and I end up asking them if they ever used X and they tell me "I just used your documentation". Best feeling ever.
The primary reason for having a lab bench notebook is that, if properly used, you can always reconstruct the process you were documenting. A lot of bench research involves protocol development, for example. In comparison with software engineering, a protocol is like an algorithm, only you're applying it to physical samples. In a well-run lab, once someone has developed a protocol, they 'publish' it (stick it in the lab's manual of protocols, where other people can have access to it). So, you don't share your lab notebooks with others, you share the completed protocol, and then if there's some question about if the protocol can be improved, you can go back to the lab notebooks to see what was already tried (this seems similar to software library or device driver development).
Some people don't like lab notebooks much, because properly recording what you did in enough detail that you can go back and repeat it eats up time and requires a certain discipline, and it often takes some unfortunate catastrophe (comparable to losing all your data backups) to learn the value of the practice.
Incidentally, if a research lab, public or private, has no guidelines at all on lab notebook practices, it's an indication they may be engaging in shady behavior (e.g. Theranos) - it's comparable to a crypto exchange outfit like FTX not having an accounting division, and should be a red flag for investors. This is also a reason for the ink-only rule, with pencil you can go back and fudge data more easily.
If I'm forced to log my thoughts/actions it comes out as either too terse(everthing feels obvious) or it's too verbose and it's often difficult to find the right balance.
I don’t have experience writing in a lab journal format, but for documents like growth experiments and how they worked, or RFCs, this is a godsend. It takes a lot of work to keep it tidy, but it’s worth it.
Take my raw notes, rewrite them for another audience, and post those on Notion? Maybe. But it's likely a different document (an essay, tutorial, FAQ) could be rewritten out of my notes, one which would be more useful for my teammates.
SIGNIFICANT
\* topic1
\* this happened
\* topic2
\* This project
\* Made this change
\* Made another change
\* Some training
\* Completed this section
I'm in a setting where I'm incredibly temporary. I could be tasked elsewhere tomorrow. Every day I reply to my previous email and work on the draft throughout the day as my notebook. At the end of the day I send it, received in the mailbox I'm attending. I title the email "Captain's Log" and my supervisor and peers can read it, as well as the draft, whenever. This keeps them clued in on where my head is at, what I'm working on, etc. Great for performance reviews mostly. Not as convenient as something like my Remarkable tablet.
All lab notebooks are company property. You don't keep them locked away in your desk or take them with you when you leave. Any current or future employee with the right clearances should be able to serve themselves to the entire archive. No need to ask the original author.
Searchability is by far the most significant advantage of electronic documents, but you can get pretty far with paper notebooks if you keep a decent table of contents. Even better if you regularly scan, OCR, and upload your pages to the archive. IMO the inconvenience of scanning is greatly outweighed by the paper notebook's guarantee of immutability. Tools like Notion make it too easy to erase information, either accidentally or not.
1. Email is good for sharable things like interview or meeting notes. It's searchable and you can dump it to Google Docs/Notion from the draft if that's appropriate. Using Gmail keeps you from trying to format it too much while writing.
2. My lab book is for me. Writing with pen/paper forces one to sort out ideas up front--not a lot but just enough for them to make sense and be readable later.
It seems as if everyone will have a different take on this.
For the rest of the team, those raw notes are source material. That can be the input into lightweight documents like technical memos and decision records.
1. https://www.insidehighered.com/blogs/higher-ed-gamma/writing...
2. https://posts.oztamir.com/the-opposite-of-forgetting-is-writ...
https://shop.neosmartpen.com/collections/accessories/product...
an impulse purchase I am fighting not make, not actual experience with the tablet. Do use Neo Smartpens
ML/DS always seemed to me closer to science in its nature vs software engineering. Can be because of its nature as well - in a lot of cases it's a process of incremental improvements (vs - simplifying this a lot - let's say in SE we do a button that just works or not).
Right, i have felt this way too (even though i am just a noob at ML/DS). For me it is the use of Statistics/Probability/Mathematics in driving understanding/intuition about the problem.
A single fountain pen, filled with the same permanent, pigment or cellulose reactive ink, on a hardcover, ink-safe notebook.
However, the rest “at the speed of thought” rules are almost the same. Theorize, design and detail on paper, implement, document results, GOTO 10.
It’s a greet speed regulator, clarifier and keeps everything documented. As a bonus, you get “That weird guy” merit badge, which I don’t care.
A few times a year, I open an org-mode file and start summarizing my notes. Those sheets then get put away, to help keep things a little less messy.
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.
You can get them custom printed with whatever paper you like, custom names, titles and numbering on the books, for no more cost than a regular notebook.