[HN Gopher] Lab Notebooks (2020)
___________________________________________________________________
Lab Notebooks (2020)
Author : momonga
Score : 105 points
Date : 2023-12-26 07:53 UTC (15 hours ago)
(HTM) web link (sambleckley.com)
(TXT) w3m dump (sambleckley.com)
| OldGuyInTheClub wrote:
| Lab notebooks have saved me many times. The days run together in
| experimental work and having a record of what I tried or saw and
| on what day has paid off weeks or months later when a collection
| of observations snapped into focus. Never been able to keep a
| table of contents, though.
| qetuo13579 wrote:
| We call them "Engineering Notebooks" and after 5 years at a
| company they tell an interesting story of the projects worked on.
| I'm often reviewing notes from the past couple of months and
| occasionally have to go back a year or two to dig up some
| information that I know is there somewhere.
| eternityforest wrote:
| I'll probably just use an app, rather than real paper, but I'll
| definitely keep this in mind next time I'm doing something
| experimental and not just "Stuff copilot could probably do".
|
| 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.
| analog31 wrote:
| 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 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."
| doctorpangloss wrote:
| To your specific point, the legal issues are so idiosyncratic.
| You can't write an article about them. You can't tease out the
| difference between "this is a best practice everyone should
| follow" and "the patent lawyer is selling the holistic social
| experience of compliance," which is the non-trial attorney's
| primary product. It's the same energy as DocuSign: when your
| biggest competitor is a pen, you know all the bullshit they
| peddle about timestamps and tracking and custody is just that,
| bullshit.
|
| 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.
| j0k3r_85 wrote:
| 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.
| crispyambulance wrote:
| 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.
| ac50hz wrote:
| I've been heading in this direction, and Quarto continues
| to be the end point, on the road from pandoc.
| chaxor wrote:
| 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.
| DarkSucker wrote:
| > 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.
| ac50hz wrote:
| Record keeping, for better or worse, is essential.
|
| Memories fade. Ink fades but rarely corrupts.
| arminiusreturns wrote:
| 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.
| fireynis wrote:
| I have started using Obsidian for daily notes (which you can
| categorize better than the default so it's more findable) and you
| can tag / create back links. I am thinking that these tips plus
| the tools Obsidian provides would make an excellent combo. Then
| the files can also be placed in git and backed up for protection!
| nolamark wrote:
| Habit of lab notebook has stuck with me since college. Shoutout
| to reMarkable tablets and Neo Smartpens, for helping combine the
| analog process of handwriting with digital search. Likely a
| personal thing, just like to take hands off keyboard from time to
| time. Seen hints of research re benefits of handwriting, but
| never really dug into it.
| maCDzP wrote:
| Haven't heard of Neo before but it looks amazing. Could you
| explain your process and likes/dislikes with the
| Neo/reMarkable?
| nolamark wrote:
| Here is a first draft. I'll expand if I have more time and
| energy.
|
| 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
| pimlottc wrote:
| > Rational, when used a a corresponding file name, it sorts
| naturally assuming you used 0 prefix on one digit numbers.
|
| Minor bit, but I think you meant "rationale" here, as a
| noun. "Rational" as an adjective is a bit of a different
| meaning than you intended, I think.
| nolamark wrote:
| you are correct. (Note from grade school report card:
| Mark missed 39 of the 81 spelling words this month).
|
| But it does point to another issue with handwritten
| notes. Sloppy spelling and dislexia (sic)
| maCDzP wrote:
| Thanks for the write up. I am seriously considering the
| NeoSmartpen since it's cheaper in the beginning and I
| really like the feeling of ink flow.
|
| I looked at their website and if you buy the idea pads you
| get 5 for 20 USD, seems reasonable.
| karencarits wrote:
| 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
| BasilPH wrote:
| 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/
| atrettel wrote:
| One advantage of lab notebooks that the article does not mention
| is that by design, the pages are firmly bound to the book, so you
| cannot lose them. I started to use lab notebooks because I would
| otherwise just write thoughts on loose-leaf paper and have a
| difficult time keeping track of the pages and their order. The
| lab notebook (or any notebook with firmly bound pages) solves
| that problem.
|
| 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.
| stanford_labrat wrote:
| As a grad student I have an "official" lab notebook which sits
| on my lab bench and has all my technical details etc. I also
| have what I affectionately call my "real" lab notebook which is
| a stack of loose printer paper at my office desk, full of
| scribbles, designs, math, random planning and thoughts.
|
| I plan to get it bound and call it my "real" thesis.
| robertlacok wrote:
| A huge downside of writing this down on paper is team
| collaboration. Imagine that instead this is kept in a tool like
| Notion which the entire team can access. At first this feels
| incredibly uncomfortable - your notes are there for everyone to
| see. However it's a massive force multiplier because often the
| work is picked up by someone else later on, and instead of asking
| you they can self-serve. It's pretty common that by the time they
| need it you would no longer be at the company.
|
| 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.
| oslem wrote:
| I agree that it's useful for the rest of the team to have
| access to your notes, but I find that it's far more useful to
| write my notes with a pen and paper rather than typing them
| out. It forces me to slow down and think through what I'm
| doing, in addition to aiding in memorizing the parts of my
| notes that I find important.
| nolamark wrote:
| Discussion prompted me to find NeoSmartpen accessory, seems
| like it could help with the sharing.
|
| 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
| cratermoon wrote:
| The important point is that the raw notes are for the note-
| taker. They not only document what you thought, they are
| themselves a part of and tool for the thinking process.
| Writing is thinking[1], and the initial results aren't going
| to be very useful for someone else, because they'll be
| rambling and messy, with lots of false starts, errors, and
| just wrong ideas. They're for the author to remember the path
| to the outcome[2], they are not the outcome itself.
|
| 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...
| kijin wrote:
| > instead of asking you they can self-serve. It's pretty common
| that by the time they need it you would no longer be at the
| company.
|
| 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.
| tomjakubowski wrote:
| Absolutely not. My working / lab notes capture raw thoughts,
| often abbreviated and with shortcuts taken. Others would have
| trouble gleaning much meaning from them, with so many scratched
| out words, wildly drawn arrows, and peculiar diagrams.
|
| 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.
| diracs_stache wrote:
| I agree with having shared team documentation but this has
| always been gray for me. My notebook ( and my softcopy log for
| the week) are incredibly raw (one-lines through mistakes, my
| personal commentary/snark, "napkin math",etc.). I am willing to
| share them with teammates/our lead/ or whoever may benefit but
| this has backfired on me. We perform analytical verification
| work and I've seen middling performers on our team look to
| avoid performing thorough work by copying from the notes of
| someone else ( I get this is work and not school so typical
| academic rules don't apply but our work is very
| investigative/exploratory in it's nature, performing
| derivations to ensure our approach is correct is encouraged and
| not considered a waste of time. Also contexts change quickly
| and a deep understanding is necessary) Thus when someone is
| trying to take a shortcut it leaves a bad taste in my mouth.
| Also "micro-managers" see pages of notes open and treat it as
| fair game to pull up to my desk and expect immediate updates
| instead of requesting reasonably or waiting for the appropriate
| forum. I get this is a culture/staff issue more so than other
| things.
| distortionfield wrote:
| I recommend the Leuchtturm 1917 Notebook for this kind of stuff.
| It comes with spine labels and a table of contents pages in the
| notebook already, and the paper is extremely high quality.
| They're the perfect daily-use notebook, IMO.
| bayindirh wrote:
| I do this for my personal software projects, research or
| otherwise. I have more stricter rules about paper and pen I use
| though.
|
| 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.
| shcheklein wrote:
| It reminds me an approach to data science and ML. It's way more
| common and essential for ML teams to log their attempts
| (experiments). There is a whole set of tools for this -
| experiments trackers. Primarily to even being able to compare and
| pick the best direction, but also to ensure reproducibility (in
| some areas it might be required).
|
| 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).
| cratermoon wrote:
| I know of two places to buy genuine engineering lab notebooks,
| for anyone interested.
|
| 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.
| jcpst wrote:
| I always have one of more pages of loose-leaf on my desk. It's
| messy, but basically the lowest barrier to entry. And if I'm
| somewhere else and write something down, it goes in the pile with
| the other notes when I get back.
|
| 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.
| charred_patina wrote:
| I started working at a lab where I am the only SWE and everyone
| else is a scientist. I have a lab notebook, but I don't use it
| properly (thankfully nobody gets on my case about it). I usually
| just use it as a short-term working memory, but it helps me keep
| track of the progress I've made. It's nice to look back on
| something I was working on two months ago and see all my thoughts
| written down about which library to use or architecture to use.
| Looking back at my past struggles gives me a sense of
| accomplishment and progress.
|
| 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.
| devsda wrote:
| Does anybody have a reference/example of a lab notebook for
| software engg ?
|
| 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.
| iancmceachern wrote:
| I get these, modified to be regular notebooks, from
| https://snco.com/
|
| 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.
| Fomite wrote:
| A good reminder to get back to keeping lab notebooks - they are
| extremely useful for being able to look back in time and go "What
| was I thinking and where did that number come from?"
| photochemsyn wrote:
| One issue is whether to organize lab notebooks by project, or by
| time. In the latter case, this means the notebook is a record of
| your day-to-day activity, which has certain advantages (like
| having a single record to refer to), and disadvantages
| (reconstructing a project's timeline can be time-consuming if
| you're working concurrently on different projects). A decent
| compromise is to have a daily notebook, but never put work on two
| projects on the same page. Then if you really want to reconstruct
| a project's history from the daily journal, you can at least just
| copy pages.
|
| 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.
| carrozo wrote:
| Highly recommend Muji's gridded notebooks (EUR1.95 for A5-size,
| 30 sheets):
|
| https://www.muji.eu/product/recycling-paper-notebook-dark-gr...
| crispyambulance wrote:
| 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 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.
| PNewling wrote:
| >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.
| bobek wrote:
| I use lab notebook inspired process to share information across
| our engineering organization. It is like your daily standup, but
| written throughout the day.
|
| https://bobek.cz/blog/2021/written-standup/
| bobek wrote:
| I use lab notebook inspired process to share information across
| our engineering organization. It is like your daily standup, but
| written throughout the day.
|
| https://bobek.cz/blog/2021/written-standup/
| jstanley wrote:
| I've started writing a markdown file every day, with a separate
| heading for each project, and a tool that automatically creates
| an index page that says what topics (based on headings) were
| present each day.
|
| Apart from the format of the headings, it is deliberately
| informal and unstructured. I've found it very useful.
| ac50hz wrote:
| 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.
| physicles wrote:
| 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...
| ac50hz wrote:
| 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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