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Keeping a Lab Notebook [pdf] (nih.gov)
327 points by Tomte 64 days ago | hide | past | web | favorite | 170 comments

I've been keeping a paper notebook since I started my MS in computer science, which I graduated from about 10 years ago. It's something that really helps in software development work too. It's amazing how often the same stuff comes up over and over again, and keeping it all written down really helps. I've got them all going back to 2004 except for one which I seem to have misplaced.

Some things I'd recommend:

- Keep it chronological, don't try to keep a half dozen notebooks for different subjects or projects (unless you have to for privacy/secrecy/etc. reasons.)

- Number and/or date all of your pages. I date at the start of each day, and number all pages, although I don't date all the pages.

- Number your pages sequentially across multiple notebooks. This is nice for when you want to write a reference to a previous page, even when it's in an older notebook it's not a problem. I started doing that about 3 years ago, before that I'd start back at page 1 for each notebook. I'm at page 1947 right now, I think I'll be lucky to get to more than 20,000 pages before I die.

- A few pages in the back for a simple index is nice.

- Use ink, not pencil, and don't actually scribble out or erase, just a simple line through is good. Sometimes you want those wrong ideas after all.

- Put a Tile or similar tracker on your notebook. They are pretty cheap now, and losing your notebook can really suck.

I've used notebooks for decades. I buy a kind that is pre-numbered, and in which the pages larger than 8.5x11 inches, so I can tape in graphs and printouts of US letter size.

During my PhD, when I was scared of losing things, I made photocopies of my books when I completed them, and kept the copies in a separate location ... now I can scan them.

I have a simple cross-reference scheme. To refer to a result on page N of book M, I write [M.N]. If it's a certain figure or equation on that page, I just write e.g. [M.N.f3] or [N.M.e5].

So far, I think this is all quite conventional. But I do one more thing that's simple but has proved to be very helpful. I write forward references in the top margin of pages. So, if book 10 page 3 refers to book 2 page 9, I write <10.3> in the top margin of page [2.9]. This simple scheme makes it really easy to take care of ripple effects of errors.

Oh, and you've got to use pen, and you've got to use clean cross-outs when you find errors. Otherwise you'll get hopelessly lost.

Now I'm curious. From an archival standpoint, wouldn't a pencil be better than a pen unless you're using some really high quality ink? I find that ink degrades much faster than graphite when it is exposed to light and moisture.

India ink is a good solution to this problem. Koh-I-Noor Rapidograph pens are good for this application because they have a nice mechanism for breaking through dried ink on the tip of the pen. Even a ballpoint pen is quite good for being moisture resistant, although I don't use them so I don't know much about fade resistance except a guess that black is best.

The idea of not using a pencil is to prevent changes later. It's really important not to make changes that cannot be tracked. The best is to cross out, write in new text, and sign+date in the margin. Leaving lots of space helps in this. Frankly, though, I've seldom found small changes. When an analysis turns out to be wrong, I simply make a new entry. With my forward- and backward-referencing notation, it won't matter if the new entry corrects an error later in the day, or a decade later.

I've never worried about sunlight because my books remain closed on a shelf, when not in use. As for water, choosing a good ink helps a lot (even my fountain pen scrawls can resist quickly-dabbed-up tea stains), but making copies/scans is really a great solution.

An addendum to my earlier post -- it helps to title each entry (which often corresponds to a day or two of work), and to type those entries (plus dates, book number and page number, and also some keywords) into a file that can be searched. I recommend one line per entry, and a format that is uniform enough that you can use grep (or similar) actions to produce specialized tables of contents for individual projects, years, etc.

I'll occasionally take a scan (actually usually a photo with my iphone) as a super quick way to share a diagram. I'd love to get them all scanned in and indexed somehow. That would be the best of both worlds.

I started using leuchtturm1917 notebooks recently and love them. Mine come with page numbers and several pages of index at the beginning of the book. The paper feel is great.

If you are doing fountain pens (which I highly recommend!) then leuchtturm is the only way to go, every since moleskin downgraded their paper quality!

leuchtturm has every feature of moleskin and costs less and better paper quality.

I've been using the Moleskine Cahier XL for 3 or 4 years now, and I love them. Soft cover is flexible for folding back, they're lightweight, a comfortable size for carrying with my laptop, and hold up well. Each book is roughly 8 months of working life.

I don't use page numbers though - I do date every single entry.


Those look awesome, mostly I've used the ones from Eureka Lab Book[1] which seem similar, although I'm a big fan of mixed graph paper and lined. Which paper rule do you use from Leuchtturm1917?

[1] https://www.eurekalabbook.com/lab-engineering-notebooks/

Dotted. Even better than graph paper if you draw a lot of diagrams/figures, in my opinion.

I use Fabriano dotted saddle-stitch as a cheaper and lighter alternative to the Leuchtturm1917, for instance when I'm traveling or at a conference. The paper holds up to any non-calligraphic fountain pen I use.

I'm using one from Fiorentina, it's hardbound with a dragon and a griffin on the cover, I've been using them for a while now. They are really well made, but I mostly like them for the cover :)

To save the next person 30 seconds of googling around: http://www.fiorentinaltd.com/index.php?option=com_virtuemart...

I like it. I'll still stick with my Leuchtturm :)

That's not it, but I like that one too. That's the right brand though.

It's this one:


Came here to say this. The included spine and cover labels are a nice touch.

All this is party of the bullet journal system. For those curious: http://bulletjournal.com/

I love it and use it as my main journalling system.

Yeah, bulletjournal (w/ some ui stolen from sliceplanner) works great for me.

That’s the first I’ve heard of sliceplanner which looks interesting. Are you using an official sliceplanner journal so you can benefit from the cloud ‘sync’, or just copying the radial calendar idea into a regular paper journal? The one way manual sync seems a bit gee-whiz since the biggest issue for most would be getting calendar invites from the cloud back onto paper.

Yeah I did buy one actual sliceplanner but didn’t like the form factor and never integrated it digitally. Agreed it’s a “gee-whiz”/ meh feature, for my uses anyway. But I loved its visual time-tracking idea and lifted that into my custom bulletjournal system. I use terrific little paper journals (Moleskine Cahir quad-ruled 5x8, one per month.) I crafted a circular clockface template which I stash in the back cover flap, and use to draw a 12h clock for each day, in pen. (I put am stuff inside the circle, and pm outside, to account for overlap in my ~15h days in a single clockface.) Having the paper journal completely offline and separate from phone or laptop is ideal for me - not just for time-tracking and planning, but also for ideas and misc notes. There’s something special about a graph notebook and a good pencil (GraphGear 1000 0.5mm, best $11 I ever spent).

I'm assuming you're doing a radial daily plan in a regular notebook. I'm curious about: 1) Why you felt this would help you? (Do you have a lot of tasks in a typical day? Or did structure help you stay on track?, etc...) and 2) To hear a little more about how you're using it. Is it in place of the daily module? Or alongside it?

Yep. I just replied at some length in a peer comment. As an entrepreneur, consultant, father and musician I have an extraordinarily busy life and multifaceted set of active priorities, and bulletjournal was a revelation for me. I do a new quad-ruled journal for each month, w/ simple structure: index, future log, month page (w/ a row for ea day, and columns for tracking key items: sleep, run, zen, code, music). I use a nice fine-tipped felt pen to number the odd pages. Then use about a page or maybe a full spread per day, w/ sliceplanner-style 12h clockface in pen (drawn w/ a template I keep in the journal’s back flap). Moleskine Cahir 5x8 quad-ruled (80 pgs) and a GraphGear 1000 0.5mm pencil are both indispensable to me. Having some empty pages at the end of a month means not stressing about writing too much. I can always reference things across journals (eg “bj8p37” or by date). Truly important stuff I retype in markdown docs organized by week. Sometimes I’ll reference docs from journal entries (“cf ~/docs/we171125.md”). It’s not a perfect system but it keeps evolving and so far it’s been instrumental in helping me achieve things in mylife that matter to me — including self-care (sleep 7h, run 1-2mi, meditate 10min) etc.

PS To answer your 2nd Q, a given day has both the radial planner (sized almost 1/2 the page height, used to track passage of time and hard stops / events) and my variation on “standard” bullet journal signifiers (., -, x, >, <, *, $, !, //, o, etc).

This looks really interesting, thanks for mentioning it. I make use of a notebook daily(ish). Bullet looks like a lightweight formalized process that can help me get a little more out of my notebook while keeping things simple.

Do you attempt to group your notes by subject and project within the higher-level chronology?

I also keep a paper notebook for software engineering, but I find it less convenient than my old chemistry lab notebooks were. The problem is that in my software engineering job, I must alternate between tasks and meetings many times a day. So either I keep things strictly chronological and have a difficult time maintaining a usable table of contents, or I have a new page for each of the day's projects, at the cost of constantly jumping from page to page and inefficient use of the notebook's space. I've yet to find a happy solution.

I'm experimenting with a combination of loose sheets of paper in a binder, and re-writing. I tend to favor rewriting to summarize coupled with archiving as I find I rarely actually go back and review the notes otherwise, and rewriting them tends to lead to summarizing and compacting and excising unnecessary information, while I can keep the old pages.

(This is especially relevant for things like task lists, plans etc., where things often change substantially over time, though it's important not to overdo it and "lose" context etc.)

Recently I've tried something similar, using paper notes as a temporary store and every few days rewriting into my wiki and agenda. The process is similar to a GTD inbox that gets processed regularly. Lots of the TODO items can be handled while rewriting(e.g. email Casey about the widgets).

Exactly - I think one of the great benefits of rewriting is that it creates work that makes it pointless to defer small tasks, while it also lets you weed out a lot of things that have become irrelevant since you wrote it first time.

TODO lists in particular, I feel gets stale very quickly and accumulates obsolete info.

Nope, purely chronological. I do a short index in the back, that's as close as I get to subjects.

Thanks, I'll give that a try!

I've used https://www.rekonect.com/ (magnetic notebook & paper) for solving precisely this problem. New page for each project/meeting and then just pull it out and slot it in to the correct spot. Can be done cheaper with a 3 ring binder but cheaper isn't always the goal.

On paper notebooks -- I keep one, too, and I tried subject grouping which always failed for me within a few months.

I now write clearly visible headings and maintain chronological order. I often color code the headings: just underlining or highlighting the title with subject color makes it easy to find. Thid, with chronological order ingeneral, works well for me in lieu of a table of contents. YMMV.

I keep one, too. I don't bother with keeping subjects. I thread them - there are references pointing to different page numbers everywhere - just like computers do.

The way this was approached with paper back in the day was a chronological journal + subject files.

I find that this works for me. I keep the journal in hand-writing form, and subject files digital. This also has the advantage from my perspective of keeping my thought process on an analog medium that is easier to control.

Some type of disc bound notebook might be good, unless of course you require something bound. I like the Arc from Staples.

What sort of things do you put in them? I don't know about you, but I'm not exactly running experiments. Do you have a format that differs from purpose, procedure, results?

I'll start with the date and a big horizontal line.

For meetings I'll put the start time and a quick header, then some quick notes, usually not even complete sentences, I'm just scribbling things down to remember.

In deep coding, debugging, or infrastructure stuff: I'll keep short notes on infrastructure stuff, URLs, hostnames, ports, function names, file names, lots of breadcrumbs basically. This is often great the next day, where I might not really remember how I got from A to B, but all of a sudden need to make a document describing it for other people to repeat. This is the part that is most like a "lab notebook."

If I'm designing something new or exploring something, I'll often sketch system diagrams or the like. I'll maybe try to diagram flow between components, user steps, basic algorithm steps, etc. Think design document, version -1.

I'll often intersperse TODOs as well, which I'll try to quickly migrate to something real (Jira here at work, or my iPhone tasks list.) I don't use it for task tracking, although I used to do that.

Exactly my scheme! You are going at about the same rate too: I’m on about page 1500 since 2009.

My one difference is that I don’t keep my notebooks. I scan them then discard the originals. I’ve got so much material hoarded that the only way I can afford the storage is to keep digital copies only.

I would love to hear thoughts on digital vs hardcopy notebooks

I have an ipad pro specifically to use as a digital notebook. I use notability, and discovered I prefer to write on black background with white, red, and blue ink. I skip green as I'm colorblind and will mix it up with red.

I don't know if it is my color deficiency or generally applicable, but the colored ink really pops on a black background. So if I have little annotations that I want to point out on a diagram, that helps.

The iPad Pro with the Pencil is almost a perfect device. I use GoodNotes rather than Notability, but I think the capabilities are roughly the same. It's great to be able to write by hand most of the time, type when I need to, paste images, insert snapshots of white boards, etc...

The OCR is very good too and even my handwritten notes are indexed. I'm not sure if it indexes the text in images though. I used to use Evernote and it did an amazing job of that.

I used to use text files exclusively, then I moved to Microsoft Word so I could paste in images and other non-text items. I missed the handwriting part of it. Something about using those muscles and going slow helps me absorb the material better.

What size of iPad are you using (you and parent post)? I've been considering getting a pro+pencil for this purpose. I like to scribble on paper, but I'd really like archived, searchable copies that don't take up physical space.

I have the 10.5" one.

The rumor for next year's model is that it will get face id and that's something I definitely want.

The one big downside to note taking with an iPad is that it turns itself off frequently. Having to authenticate frequently with the home button is a pain and I think face id would be a lot less intrusive.

FWIW, I still scribble on paper, but that tends to be for very ephemeral things (like a number I need to remember for the next 5 minutes).

Thanks, I ended up going with the 10.5" one. It's the size of the steno pads I scribble on and weighs less than the bigger on. Not a lot of space on my desk either.

I'm gonna give Notes a try for a while and also Notability, because it appears I purchased it years ago.

I use the 12.9" (?) whatever the bigger size is. The screen is just about as big as a sheet of paper.

For what it's worth, I don't think notability has OCR. GoodNotes appears to though. I might have to give it a try.

I have switched away from all apps and mobile devices for anything note-related. I feel like it's not worth trying to adapt my note habits I've had since graduate school just to appease the latest iOS or App idiosyncrasies. I also need to switch between computers and operating systems frequently, so the most reliable device I have is a notebook sitting next to my desk.

I prefer digital because...

1. It can be searched

2. It can be backed up

3. It is accessible from nearly anywhere

It's also incredibly easy to misplace files and forget that you wrote notes altogether. I've lost many notes.txt throughout the years. I've recently forced myself to use Evernote, which for me is better than any file-based system, but it is a bottomless pit with poor discoverability. A physical object doubles as a reminder.

With respect, that seems like less of a problem of digital note-taking in general, and more of a problem of the specific digital note-taking systems you have tried. Using notes.txt files is a bit like writing notes on napkins and leaving them scattered about. I don't know anything about Evernote, but I'd be interested to hear what issues you had.

What works for me is taking notes via email. Backing up, organizing, searching, and distributing email is more-or-less a solved problem, and my note-taking inherits those solutions. I can read and add notes from my phone and from my computer, with the ability to choose from a plethora of applications. I have multiple backups of my email around the world via standard email syncing. My email host has been 100% reliable in not losing my emails, as well. If I want to migrate to a different email host, that is trivial.

That's a solution I might want to try. But how do you differentiate between your notes and the dozens of emails you receive every day? You can filter by sender, but then you often get your sent mail, depending of how filtering is set up in the email client.

I have my notes at work as org files, and simply added them to a git repository.

And in my case, it can be read. Important, as my hand writing is atrocious!

I keep it paper for various reasons. I've played around with digital notes, the main problem is it's hard to sketch stuff quickly, even though I have a nice wacom tablet, and it's horrible with just a mouse or trackpad. And there's always a need it seems to try to edit existing stuff. That's why I use ink. I can't erase and "fix" it.

Digital lets me find things much more easily, but for maths-heavy notes, I prefer hardcopy. I'm not as quick with LaTeX as I am writing, and I couldn't get the hang of using a stylus for maths. Wish I could more easily get the best of both worlds.

Have you tried TeXmacs for math-heavy notes? Thanks to copy/paste, I find I'm quicker in it than on paper, as long as the work isn't too diagram heavy. For simple diagrams, there's a vector image editor built in.

I have lost countless notebooks and other notes on paper. For those I haven't lost, I find it really hard to find what I'm looking for. I started consolidating my note-taking in google docs and haven't looked back.

Seems like you might need a better indexing system -- table of contents in the start of notebooks, and perhaps a directory consisting of copies of those ToCs in a loose-leaf binder for the entire set?

That... sounds like a lot of work

It's part of an ongoing process.

It's a bit of systemic investment which provides future payoffs.

How valuable is your past journaling in the absence of such a system?

How valuable is your past journaling with such a system?

I use a mixture of Vim with text files, and the Windows Sticky Notes app, for my notes. The text files go into a folder related to what I'm taking notes on, and are for longer storage. There's usually other file types in there too, and the folder can be backed up and/or version controlled.

Short-term and quick-access notes are in Sticky Notes, which plaster the desktop on one of my monitors. That's where I keep meeting notes, TODO lists for the next day or two, time-tracking if I'm not putting it directly into my time-tracking app, etc. Generally, none of that is worth saving beyond its immediate usage.

I've rarely needed to refer back to any of this stuff beyond the few days where I'm using it (Sticky Notes) or the duration of a project (text files). I don't delete the text files, but I hardly ever need to refer back to them.

I've been relying very heavily on index cards and finding it well-suited to my needs


Various other methods are also in use. I've found journals less than intuitive, as there's a distinction between keeping a notebook vs organising/recording routine activities and events that I find difficult to span and/or separate.

Online/electronic systems remain insufficiently flexible for daily activities, though I've gone through several iterations of shell / vim / org-mode systems.

I use both where each excels - paper for capture, org files or what-have-you for persistence.

Interesting. I find paper to be far more "persistent". I have notebooks I kept in high school and college, but have lost most of the digital files from that time, or can no longer read them due to their being in a file format long dead. Corruption also plays a role, as they've moved through a variety of storage media in that time. I find digital works best for me for keeping shopping lists (that sync up with my wife, so we both know what we need and can add things), giving me reminders of appointments and time sensitive tasks, immediate communications, or as a tool for projects I'm currently on (I use org-mode heavily and particularly like its linking features for getting back to config files on remote servers, emails with instructions, etc.). All quite transitory.

I keep a small moleskin book with me with a pen loupe I added as a part of my every day carry. I jot down projects I am working on and it’s great.

I use Quo Vadis notebooks with unlined creamy French-milled thick paper that is absolutely wonderful to write upon with a fountain pen.

> Use ink, not pencil

Ink will run when wet. I recommend taking notes with a pencil.

Not all inks. This for example withstands pretty much any liquid (yes, including industrial strength solvents -- I've checked): https://www.amazon.com/Noodlers-Black-Waterproof-Fountain-Pe...

Get better pens. There are waterproof ones that I use, they are the anti-fraud ones that they market for use with paper checks.

I was reading through some of my journals that I wrote a few years ago and noticed that the ones written with a pencil are much more readable than the ones written with a fountain pen. I guess picking the right kind of paper and ink is very important for a notebook not to lose its quality.

I use Staedtler pigment liner pens (http://a.co/i0tN5Bz) and they have never run on me. The different widths really help for sketching vs writing vs annotating too.

It may not last for long on the paper, that's why it is suggested to use ink.

I have 20 year old notebooks that are mostly filled with pencil and I refer to them occasionally. They are all perfectly legible still and I used a wide variety of pencils.

For true lab notebooks pencil is unacceptable because of their erasability, not longetivity. A formal lab notebook is used in such a way to provide a nearly immutable record. That's why corrections are done with a single line, blank space is blocked out, the notebook is bound with numbered pages and used chronologically, etc.

In a college chemistry class I took our lab notebooks had carbon(less) copy paper for every page. It made handing work in easier, but it also made an unerasable copy of the original record. Quite handy.

Why are your notebooks wet?

Stuff spills, rain, etc... accidents happen.

Use the cheap bic ballpoints. They don't run or smudge.

Keeping notes and notebooks is a critical skill for any top-tier engineer. I love to share this quote for that very reason:

  For this you keep a lab notebook. Everything gets written down, formally,
  so that you know at all times where you are, where you’ve been, where you’re
  going and where you want to get. In scientific work and electronics technology
  this is necessary because otherwise the problems get so complex you get lost
  in them and confused and forget what you know and what you don’t know and
  have to give up.
  Zen and the Art of Motorcycle Maintenance: An Inquiry Into Values
  Robert M. Pirsig

Starting this week I've been keeping a development diary, inspired by another post [1] on HN.

I'd been hesitant to do so until now, thinking everything I wrote would go to waste as I'd never look at it or even remember what I had written.

But after giving it a go, I think that even if I never look at my logs again, I'll continue to write them.

The key for me has been to continuously write to it almost as if it were an extension to my brain, rather than just writing things up after the fact.

I'm only on day 4, but so far some benefits I've noticed:

- Writing down what I'm about to do before I do it helps me stay focused.

- I can quickly grep to find a command I ran in the past, along with my stream of consciousness when I ran it.

- I can pick up where I left off in no time. The ramp up time after distractions has diminished to almost nothing.

- I have tangible output at the end of every day, where otherwise it would have felt like I accomplished nothing. Specifically, when working on those problems that don't seem to have any tangible output, like debugging some tricky bug. At the end of the day, instead of just telling myself "I fixed this issue", I now have hard evidence (for myself) that I actually spent the day working through a long rigorous debugging process to fix the issue. This helps me stay motivated and ward off that imposter syndrome.

- I feel less stressed when I'm stuck on something. I have a hunch that it's similar to how keeping a personal journal helps to process emotions.

- Writing out my process makes me less likely to go off on a tangent, or at least to be more aware that I am in fact going off on a tangent.

- It helps me keep the bigger picture in mind, sort of like rubber duck debugging.

Amazingly, I've been writing about 5000 words per day (though that includes pasted code and command output) and yet I'm getting more work done each day.

[1] https://news.ycombinator.com/item?id=14382965

I'd love to hear some thoughts about keeping a "lab notebook" for ML experiments. I use Jupyter Notebooks when playing around with different ML models, and I find that it really helps to document my thought process with notes and comments. It also seems that the ML workflow is very 'experiment' driven. I'm always thinking "Hm, I think if I tweak this hyperparameter this way, or adjust this layer this way, then I'll get a better result because X". Thus, I have a bit of a hypothesis and proposed experiment. I run that model, and see if it improved or not.

Then, I run into an issue where I can either: 1. overwrite the original model with my new hyperparameters/design and re-run and analyze or 2. keep adding to the same notebook "page" with a new hypothesis/test/analysis loop, thus making the notebook pretty large. With number 1, I often want to backtrack and re-reference how a previous experiment went, but I lose that history. With number 2, it seems to get big pretty quickly, and coming back to the same notebook requires more setup, and "searching" the history gets more cumbersome.

Does anyone try using a separate notebook page for each experiment, maybe with a timestamp or "version"? Or is there a better way to do this in a single notebook? I am thinking that something like "chapters" could help me here, and it seems like this extension might help me: https://github.com/minrk/ipython_extensions#table-of-content...

My process is to separate numbered "scratch" notebooks in which I do one-off analysis from "pipeline" notebooks/code that process data for use in later analysis/modeling. Pipeline notebooks are made to take input/output locations from environment variables and run with nbconvert.

The pipeline code is run by a DAG-like runner (sort of like Make) that is aware of the parameters and what level of the pipeline they are used at so that I can trace back outputs to the parameters and files used at every stage of the model. For stages that are notebooks I can also see the HTML generated by that run of the notebook.

Unfortunately I've looked far and wide and there's no real open source version of what I've described, but I'm hoping to open source it once I've worked through the kinks.

I'm interested in something like this more generically - like a task runner that creates maybe creates a branch for a particular job/training run on a remote server that you can monitor/trace source for.

You could export the results of the models to a file and reference those. With tensorflow you can do this quite easily.

I think notebooks are crucial for ML research, especially in teams. It's how we've been sharing our research with each other(i.e. https://github.com/DanburyAI/SG_DLB_2017 ). Wolfram calls these computational essays ( http://blog.stephenwolfram.com/2017/11/what-is-a-computation...). He was actually one of the pioneers in these types of notebooks. Distil.pub has a similar ethos. I think the whole notebook way of doing research is central to reducing research debt ( https://distill.pub/2017/research-debt/ ).

In the past, it is common to throw away the ladder in mathematical research and write nice lean formal papers. This often produces a type of debt. In a team, the ladder is vitally important. Notebooks help retain the ladder.

I have the same problem. In time, I found notebooks to be rather useless as lab notebooks for this reason.

I now use notebooks only transiently, for running a few experiments, but not as lasting documentation. Instead, I copy a summary of my experiments and findings into a journal, and delete the notebook once it has done its job.

The journal is then my true research notebook. It contains experiments, results, code examples, future tasks, ideas, and a daily summary of how I spent my time. Particularly, I use org-journal on Emacs, but any old journal would do.

There is http://sacred.readthedocs.io/en/latest/collected_information..., but I haven't used it and it doesn't integrate with Jupyter as far as I know

", I often want to backtrack and re-reference how a previous experiment went, but I lose that history"

Have you considered using Git or some other control version system? I'm not sure about the practicality in your case, but it seems like something to try.

Don't overwrite. It's so valuable to go back when you run into an evolutionary dead end.

These are ASCII-sortable:



ISO8601 w/ UTC is also ASCII sortable.

# Jupyter notebooks as lab notebooks

## Disadvantages

### Mutability

With a lab notebook, you can cross things out but they're still there.

- [ ] ENH: Copy cell and mark as don't execute (or wrap with ```language\n``` and change the cell type to markdown)

- [ ] ENH: add a 'Save and {git,} Commit' shortcut

CoCalc (was: SageMathCloud) has (somewhat?) complete notebook replay with a time slider; and multi-user collaborative editing. ("Time-travel is a detailed history of all your edits and everything is backed up in consistent snapshots.")

### Timestamps

You must add timestamps by hand; i.e. as #comments or markdown cells.

- [ ] ENH: add a markdown cell with a timestamp (from a configurable template) (with a keyboard shortcut)

### Project files

You must manage the non-.ipynb sources separately. (You can create a new file or folder. You can just drag and drop to upload. You can open a shell tab to `git status diff commit` and `git push`, if the Jupyter/JupyterHub/CoCalc instance has network access to e.g. GitLab or GitHub)

## Advantages

### Reproducibility Executable I/O cells

The version_information and/or watermark extensions will inline the software versions that were installed when the notebook was last run

Dockerfile for OS config

Conda environment.yml (and/or pip requirements.txt and/or pipenv Pipfile) for further software dependencies

BinderHub can rebuild a docker image on receipt of a webhook from a got repo, push the built image to a docker image repository, and then host prepared Jupyter instances (with Kubernetes) which contain (and reproducibly archive) all of the preinstalled prerequisites.

Diff: `git diff`, `nbdime`

### Publishing

You can generate static HTML, HTML slides with RevealJS, interactive HTML slides with RISE, executable source with comments (e.g. a .py file), LaTeX, and PDF with 'Save as' or `jupyter-convert --to`. You can also create slides with nbpresent.

MyBinder.org and Azure Notebooks have badges for e.g. a README.md or README.rst which launch a project executably in a docker instance hosted in a cloud. CoCalc and Anaconda Cloud also provide hosted Jupyter Notebook projects.

You can template a gradable notebook with nbgrader.

GitHub renders .ipynb notebooks as HTML. Nbviewer renders .ipynb notebooks as HTML.

There are more than 90 Jupyter Kernels for languages other than Python.


The "Lab Notebook" was once an important legal document: it showed the date of invention for US Patents. Several years ago, the United States moved to "First to File" in determining the date of invention, and so much of the legal need for notebooks vanished.

That said, there are specific notebook tricks every developer should know: 1. Write the date and subject neatly in the upper corner. For some reason, this makes your writing on the rest of the page significantly cleaner. 2. Use your notebook instead of scratch paper whenever possible. I often find myself looking for a scribbled package name or search term that I remember when I had the problem without remembering the incantation. 3. Use detailed bug logs occasionally. That is, keep a list all programming errors with tally marks or a list of minutes spent. Usually, your repeated, trivial errors will disappear over a few sessions.

Notebooks can be of real value to you. Pulling out electronics in a meeting disrupts exactly like paper does not; you appear more organized because you are; and it can be habit that builds in fits and starts and lost notebooks. The real downside is that a notebook increases your workload as follow-ups and investigations are remembered.

As a programmer, I struggle with the lab notebook. I'd like to keep it digitally along with my other notes, but the legal environment for IP in programming makes it scary for me.

I've been deposed before, and I'm completely terrified of my notes being used against me. Either as evidence of me somehow attempting to steal IP from my employer (because software patents are a fucking joke) or as evidence that I stole IP from somewhere else.

Curious if anyone has advice around this - thanks! I might just be irrationally afraid.

I've been deposed, in a case involving my employer of twenty years ago. The defendant was trying to invalidate a patent; one of several at play in a multi-billion-dollar infringement case.

The fraction that someone will spend on lawyers in order to avoid a multi-billion-dollar judgement buys a lot of research. The attorneys had everything I'd ever published, for a very loose definition of “published”. They had every article anyone else had published, that mentioned me or thanked me in the acknowledgements. They had papers I didn't know existed, where I'd been credited. I was asked about the content of all of these, and about the history and content of my communications with their authors.

I had also been asked to deliver all relevant documents from my time of employment. Nothing had survived all my de-clutterings / house-cleanings from the intervening years. I can only imagine that if I had been able to supply additional fodder for questioning, I would have been deposed for many days instead of just one. I would also have had a greater chance of accidentally giving contradictory answers somewhere in there, by trying to reconstruct events from twenty years ago instead of remembering always to say “I don't recall”. (Learning not to be helpful in conversation was the bulk of the “deposition training” that the plaintiff's attorney provided me, the day before the deposition.)

Fear of having any record used against you by a third-party is a completely rational fear, since as you noted, regardless of your intent, simply viewing third-party IP that is publicly viewable, such as an existing patent, introduces potential claims of theft regardless of the facts.

On the flip side, if done correctly, such records can provide supporting evidence that the claimed conflict did not occur.

For similar case law, see:


I'm a research scientist in industry and I'm mostly puzzled by your concern. I see this an excellent way to document what I have been working on in a rigorous way that could establish prior work.

I don't disagree that software patents are unnecessarily broad. The patenting system is largely a relic of the industrial era. Not that patents are not useful, but that the current system has been 'gamified.'

I think OP was referring to their preference for digital notes, which could be (mis?)construed as taking them out of the workplace.

Disclosure: I'm not a lawyer. This is based om my experience being sued by a previous employer. They was in the EU, laws may be different in other parts of the world.

If your (former) employer wants to sue you for IP theft, they must prove the damage you did to them, which is really, really hard.

They can't sue you over stuff you learned while you worked somewhere. Your contract may say so, but it wont hold up in court, because you wouldn't be able to do your work without that experience.

It's not clear to me why you are afraid of keeping them digitally rather than physically, but if the issue is using a private service then perhaps you can use a company storage option? I use OneNote and we use Office 365, so my digital work notebook is on work 'property' but still available to me everywhere.

If your process doesn't involve stealing IP, why would documenting it increase your risk?

Because you "stealing" IP does not require that you stole anything intentionally, it matters when you happened to do the same thing.

There are patents for things like paxos, TCP, "network servers" and everything else. If you write down that you looked up a wikipedia page about the topic, and then some notes about your implementation - it may look legally like you stealing IP even though you are doing nothing nefarious.

Maybe a patent lawyer can weigh in, but I think it does require intent.

Like if your notes demonstrated independent discovery, that wouldn't create any liability. You could be prevented from ongoing use of the IP though.

You might be thinking of wilful infringement, which in some jurisdictions can significantly increase the penalties for infringing some types of IP rights.

This in turn can lead to the perverse position that someone doing R&D in a certain field may be advised by their IP lawyer not to read existing research papers or patents, so that at least if they infringe and get sued, they can honestly say they didn't know and it wasn't wilful.

Of course this completely undermines the entire principle of publishing knowledge through academic papers, disclosing inventions through patents, and so on.

Not really. The patent is filed with details so that when the patent expires, the design is ready to be disseminated freely without risk of legal challenge.

And in the meantime, it is openly disclosed so that others can learn from it and potentially it is available for licensing if it or later inventions based on it are valuable enough.

If you weren't going to do that, and you wanted to have a system that discouraged actually looking at what's already out there in case you infringed it knowingly, you might as well just let people file for anything but keep it secret for N years.

That's not the impression I got from lawyers in the past, but I think I just have a lot of fear in the area.

Getting real legal advice for this is something I should probably do.

If he weren't stealing IP, why would he be taking notes about company IP in a private notebook? Someone asking that question and not liking your answer is the risk.

I take notes about company IP in a notebook _all the time_. Part of my job is to document the things I learn about or create in my notebook, precisely so that we can establish a work timeline on a piece of technology if necessary.

I keep dedicated work notebooks, and while most of the time it's a way for me to Write Things during meetings to make sure I prioritize tasks and whatnot, I have quite frequently used them to document new things I'm learning about. Almost anything non-trivial is worth writing about, sketching about, and diagramming the major pieces and relationships. Whether it's a piece of infrastructure that our team might use for packaging and deployment, a workflow for a tool we are building (or needing to cooperate), or even just something cool that a co-worker is presenting about, it ends up in my notebook.

A notebook created on company time obviously belongs to the company, disputing that would certainly be a reason for suspicion, but why would anyone dispute it?

I have been keeping a digital notebook: each day I make a new file `~/logbook/YYYY-MM-DD.txt`, and there I write my thoughts, small code fragments, results of running said fragments, etc. As well as quick summaries of meetings and todo items.

I've done something similar, but I keep going back to paper because it's a lot easier to vary formatting, reorder and restructure things etc. I still want to find a digital structure that is sufficiently flexible, but so far I haven't come up with anything that feels good enough.

In fact, it drove me to write my own editor recently (because, frankly, it felt more straight forward to write my own editor than to learn elisp well enough to do what I wanted with Emacs)

I've tried both, because as an IT guy it made sense to use, you know, computerized tools. But as a DBA, I live and die by checklists and multi-column quick reference tables. I find these are much easier to create, maintain, and update on paper than they are in Notepad++, for example. I also trained myself to use the mouse with my left hand so I can write with the other, and so it's a lot less disruptive to my workflow and train of thought than having to jump back and forth between multiple app windows. My current favorite is the Leichtturm (sp?) 1917 with the dot grid.

It's one of the toughest usability problems in computing, I think. Replacing paper is remarkably hard. I had hopes for tablets, but input lag is too disruptive still, and they still suffer from the problem that I can't flick through pages or spread them out on a desk. I'll probably keep trying to find a solution for the rest of my life, and keep failing...

I work in an industry not far from publishing and I'm fairly regularly asked about "the future of the book". The thought experiment I run people through is to look at the book like you might a piece of technology. It's UI, cost, features, durability, battery life, etc. Paper holds up pretty well as a technology.

The UI really has a lot going for it, though part of that is that we've spent our whole lives learning it. Plus many of the shortcomings of paper have been at least partially overcome by clever workarounds (like indexes).

The input lag on the latest iPad Pro is remarkably small to the point where I don't notice it anymore. The bigger problem for me is feel, a stylus on glass just doesn't feel like writing on paper. But other than that, as you said, the bigger problem is still software.

I really need something that syncs across all devices, can take handwritten or keyboard input, is searchable, and organizable via some kind of embedded links to other content in the "notebook". Usually you can get like half of those things in one piece of software.

I was really hoping the Microsoft "Courier" tablet concept would become a reality, but nothing yet...

Agreed. I really, really wanted to find a slick way of doing lab notebook / bullet journaling electronically, I tried Notepad++ Workspaces and OneNote. But neither of them really worked for late-night ops work, troubleshooting notes, etc., and I kept migrating back to paper. Plus, there's just something wonderfully satisfying about checking off a list with a pen.

How long did it take you to learn to use your mouse with your left hand? That sounds handy.

I currently get around window confusion by programming the F keys to certain windows. E.g. if I hit ctrl-shift-f1, my currently focused window will be bound to f1. If I hit f1, that window will be brought to the top. I did this with xbindkeys and xdotool.

So when I first start a session, I bind everything. F1 my IDE, F2 my command line, F3 my notes, F4 my browser.

It took about two weeks of daily use. I switched my mouse at work to be left handed and committed myself to not switching back if I got frustrated. Before I knew it, it felt as natural as my other hand, and I can go back and forth with ease. I'd actually say that off-hand mousing is now my preferred state. It helped that at the time I was doing a lot of work in Adobe Illustrator so I was really getting a lot of fine-control practice. You might try playing a game like Minesweeper for a similar effect.

I would love to keep paper notes but I find the opposite for myself. It's very easy to reorder or restructure a digital document and very difficult for me to re-organize my random ramblings on paper.

Maybe you could share your methods paper methods in a blog post or something; I'd be interested in reading it.

Have you tried OrgMode? I find it sufficient for most needs.

Especially with Org-Babel you can develop and document scripts at the same time. Give it a shot if you haven't before.

I've tried it. I find it alternatively constrains my formatting too much and uses too much syntax that I don't like. It certainly looks very flexible, and I'll probably steal ideas from it all over the place, but it's just not for me.

I think that's actually one of the biggest challenges in this space. E.g. there are a zillion different Todo apps or notetaking apps largely because there is an infinite set of possible ways of working with them and people develop very specific styles.

I think this is one of the reasons for the success of things like Trello: Trello is very generic and impose very few limits on what you can do with it. But even Trello won't conquer even the Todo/lists type niche entirely because it's not generic enough.

Same for things like OrgMode. It may get me 90% of the way there, but paper gets me 95% of the way there, because I'm effectively implementing my own workflow in my mind exactly how I happen to decide I want it right now.

And "right now" is a big part, because one of the things I've found both with plain text and with paper is that workflow at least for me does not remain static very long. My preferred format changes frequently depending on type of project or even specific tasks or just over time. Any "perfect" application to handle this would need to be able to accommodate that without making me conform to the tool.

Instead when I try tools for this, I often end up finding one I like, spending time on it, only to then start feeling constrained by it not because I've learned new limitations I wasn't aware of, but because the way I use the tool is slowly drifting towards a new workflow.

This might be a personal flaw, but from seeing people take notes, I think you'll often find that part of the flexibility of paper is exactly that your workflow can drift over time without making you hit a wall.

I think it would be really cool to write a text editor. But elisp is also really easy to learn. A couple of weeks and you can be writing extensions.

I have an irrational dislike of Lisps... I do know the basics, but I've never been able to get into it even after 23 years of Emacs..

Meanwhile, it took me less than a day to have the basics in place (not entirely from scratch; I borrowed a very basic starting point [1]) in Ruby, and I've spent less than a week getting it to a point where I probably using it about 3/4 of the time (falling back to Emacs on occasion) (my own editor isn't pushed anywhere, but it will appear here [2]).

Of course it's not as feature-full and polished as Emacs, but it has most of the features I need, including sufficiently tolerable auto-indent and syntax highlighting (courtesy of "rouge", a Ruby highlighting library that can output ANSI codes), and with a bunch of custom transformation rules to e.g. add lots of extra stuff to my Markdown files to make my notes look nicer.

One thing I find is that with respect to things like this it's very much a 20% of the time to get 80% there thing, but if you write software mostly for your own use, getting 80% there is often sufficient. E.g. I haven't added a "safe" extension mechanism - my editor will crash if I decide to customize something, because the "extensions" are modifying the core of the editor rather than get treated as an embedded language.

That'd not really be acceptable as a general purpose editor. But as my editor for my personal use, it's quite ok (and loss of any substantial amount of data is easy enough to protect against). It's shortcuts like that which makes it viable. E.g. I also know that trying to open a gigantic file with it would be silly, but I very rarely do that, and can resort to a "grown up" editor when I need to.

[1] https://github.com/agorf/femto

[2] https://github.com/vidarh/re

Ditto for this (800+ entries so far). If you've got a script set up to make/open them, I've found it's also useful to have it append the current time automatically each time you jot down a note, so you have rough time stamps.

I wrote a simple program that does this same thing:


Over time I have settled into the following "personal best practices" of sorts to track my research:

1. I add papers that I read to Mendeley. This makes them accessible across devices. Also makes them searchable. Before: Used to keep them in a Dropbox folder, with a specific naming scheme that has the title and the author names (some if not all) in the title.

2. Notes go into a LaTex document. Either I maintain the document in its own Git repo or have it on ShareLaTex. Before: Used to maintain a MarkDown document, but I realized that to submit technical reports (PDF documents with tables, formulae, graphs and citations) I can now simply copy-paste from my LaTex "notebook".

3. Codes go into a Git repo.

4. For the stuff I am currently reading, I usually print out some of it and carry them around in a folder. Which also has some blank sheets and a pen. But long term conclusions make it back to my LaTeX notes. This folder is like my a materialized working memory.

FYI: if it matters, area of research: ML

As someone who works in both wet-lab work and bioinformatics, there is a horrible disconnect between my lab notebook for wet-lab work and my computational work (which mainly consists of jupyter notebooks or dated python scripts).

I've still not seen a product or workflow that can combine the two. Electronic notebooks for bench work really don't work.

I might suggest using git to track your code, then you can write down the first six letters of hashes in the lab notebook for the commits that correspond.

What's wrong with electronic lab notebooks for bench work, and what would you hope to see in a 'notebook' that combines wet work with computational work?

Quite often I want to sketch things, or stick in a paper printout from old-school lab-equipment. Both if these are a pain on a computer.

With a lab book you can take it round with you from lab area to lab area or quickly jot something down. I suppose you could give each researcher a designated "lab-only" laptop, though waiting for software to load up etc just to write down a few numbers is a lot of hassle.

I use a cheap chromebook as a dedicated lab laptop. I set up a digital lab notebook with vimwiki, taskwiki and git, and sync to a git server (and other computers I use). I only have to open it up and vim is ready to jot down things.

> In short, this is where you record everything that happens during the experiment. This means any deviation from the protocol, whether it was planned, an accident, an error or a mistake needs to be written down.


I cannot tell you how many times I have run into a problem and found it because of a small mistake. On the other hand, I've gained ideas from mistakes. When doing any type of experiment you will ALWAYS make mistakes. These variables end up becoming extremely important and are often not written down because experimenters are embarrassed.

Brevity is nice in lab books, but if you are going to error, error on the side of verbose.

I really wish that it was standard procedure to treat a lab notebook like a journal, in contrast to the status quo and this paper.

Scientific papers today try to separate the knowledge discovered from the authors own steps. It would be so useful to learn about the false starts and misunderstandings they had; that knowledge is just as important as the discovery itself in my opinion.

I absolutely agree with you.

Over time, I have developed the habit of writing thoughts and detailed discussions of why certain things were done in my lab notebooks (I was taught not to do that as an undergraduate). It's very frustrating to have to follow someone else's work, particularly unpublished work, without knowing what had gone into designing experiments.

Context: I'm an academic in applied math. Like most of you, I juggle multiple things -- courses, projects, students, committees. I spend most of my tube time in Emacs (yes, I know this half sentence tells you how old I am), and for each "project" (a research project, a course I'm teaching, a student I'm working with, etc) I keep an org file with a log of day-to-day or week-to-week progress. Every so often I go back and write an entry about my plans for the next month or so. This has worked reasonably well for me.

A very nice thing about org-mode is that most of the rest of the time I'm either writing code or papers, and all of that is in Emacs too. So if a thought pops up about a project while I'm in the middle of something else, it's really easy to jot it down in the right place and go back to it later.

I'm a 28-year old engineering undergraduate and I spend most of my time in e-macs as of about a year ago. It took a little time to get used to, but it's been worth it.

I've recently fallen in love with org-mode and I want to ask you about using it as an engineering journal: how can I make it legally authenticatable? If I keep my journals in org-mode, is a private github repository sufficient for security and authentication?

You can always create a new set of commits (git will let you change the dates to what ever you want) and force push to master. Will look completely legit, unless somebody else has a prior checkout, or a hash.

That is how you make it work: at the end of each workday, email somebody neutral the hash of head.

Ah, interesting question. This I do not know. Unlike my colleagues in biology, we are not actually required to keep lab notebooks or something equivalent. Perhaps someone more knowledgeble than I can answer...

I went to school for both chemistry and electrical engineering. I've since acquired the habit of using a lab notebook with everything I do. It's an amazingly useful utility both for recall but also record keeping.

Make it a habit yourself and you won't be disappointed.

I'm a programmer and I was inspired to start keeping a log from a talk I heard about using the scientific method for troubleshooting. My log is more of everything the article says not to do; a journal, notes from meetings, list of what I've done. I find it keeps me more productive and focused, and I've seen immediate benefits in terms of remembering details on how to do something. I use QOwnNotes, make an entry every day, and tag it liberally.

Does anyone keep a coding journal?

I recently bought a dedicated Moleskine to record algorithms and design patterns I use at work and university. It's been really fun to record multiple solutions and then be able to review my writing several days or weeks later to note an optimal solution.

Looking for formatting tips similar to Bullet[0] journaling, but for more STEM-related notekeeping.

[0] http://bulletjournal.com/

I love pen and paper (and a big fan of Bullet Journal), but for keeping a coding journal, I keep mine digitally since it is easier to add entry, edit and search. Most code snippets are easier to copy and paste rather than writing on paper and then typing it back later. I can type much faster than write with hands. There's plenty of good apps/editors for note taking: Vim (what I'm using), Evernote, OneNote, Emacs with Org Mode, Notational Velocity, etc. Jupyter is also another alternative for coding journal.

I use QOwnNotes to log my conversations, snippets, howtos, and daily work journal. I've seen immediate benefits, like productivity, focus, and knowledge.

I've written my own[0] (shameless plug) just to have the features I want because I couldn't find something that felt right (snappy, fast, not a web app, not too bloated since I want text only, etc.) and it also was a big improvement over m previous 'Notepad++ with tons of txt files' approach.

[0] - https://github.com/FRex/botes

Perhaps just write your own to fit your specific needs if a general one is too clunky or misses features? I did so because I couldn't find what I want but my program is unstyled plaintext only: https://github.com/FRex/botes

I just use private gist.github.com completely searchable and if I feel like over documenting something I can.

I can highly recommend keeping a lab notebook and the article has an excellent summary. In my case I prefer the bound and stitched notebooks.

Since I keep several projects going at once in the notebook I've developed a system to make that possible in a notebook where the pages are numbered and not removable.

The start of the project gets a note in the table of contents of the first page # for that project.

When I switch to a new project I draw a horizontal line across the page and attach a 'post-it' flag to that page. These are like those 'sign here' flags they are easily removable. And I've got a multi-color pack of flags adhered to the inside cover of the notebook.

When I go back to a previous project, I draw a horizontal line in the notebook and using the flags find where I had stopped on the project earlier in the notebook. I then draw an oval and write "To: ###" where the ### is the page number of where I pick up that project again. I remove the post it flag and on the page where I've restarted I draw an oval with "From: ###".

If I switch projects again later I again put a post-it flag and the horizontal line.

This wasn't my idea, as far as I can tell newspapers and magazine have used this to link parts of a story through the publication since forever.

When I'm disciplined about it (sometimes I have to go back and fix up my linked lists :-) I can review any project fairly quickly from the start, and when I'm further into the notebook, follow links backwards to quickly remind myself of what the last thing I had done was.

I really helps me keep multiple things moving forward in my day to day.

To my fellow pen & paper nerds in this thread:

For serious, sturdy bound notebooks check out snco.com (Scientific Notebook Company).

When I worked in academic medicine that's where the department sourced all their notebooks. If a notebook can be called "overbuilt," these are.

No affiliation other than 'satisfied customer.'

NB for the Rest of the World: they do make an A4 version, which is what I ordered. /* I'm the rare ISO216 compliant Yankee. :-D */

Wow, those are way cheaper than I expected. Thanks for the link.

That sounds pretty decent for you, but it sounds a little terrible for the guy who has to come in a decade later and figure out what you were doing. I'm a much bigger fan of having one notebook for each thing, just so everything is all in the same place.

I tried multiple notebooks first, but I find I am not careful enough to avoid writing in the 'wrong' notebook. Not killer of course, just frustrating. And since most of what I've done is software I had an unpleasant experience at Intel of going into a meeting about a project which digressed into a meeting about another project and then had the 'wrong' notebook with me for data and details.

Do you do anything in particular to keep your notebooks separate?

I use 5mm A4 squared paper in cheap A4 card folders (pad goes in front of pages torn out which are numbered), I use different colored folders and I have a rule that pad goes in a folder before I get a different pad out, I think in 3 years I've written in the wrong pad one or twice.

The advantage of this approach is that I can jot random crap in a pad and then if it's really not relevant just rip it out and bin it, I only number the top page of the pad that way if I do need to bin it I can just write the same number on the next page.

Having all the pages (neatly) torn out also means I can shove them through the scanner tray on the copiers at work which is nice and of course spread them around my desk, put third party pages in (and number them) etc.

I usually keep the folders for a few months then if I haven't referred to them (I write the last date I did on the back of the folder) I just scan them into decent quality TIFF's and recycle them.

Why not have a notebook per project which is how we used to do it at my first company

I think that depends greatly how much back and forth you do and how intertwined things are. E.g. a lot of my projects have common threads that leads to switching back and forth, and if I were to keep separate notebooks I might easily end up with dozens if I wanted to keep strictly contiquous notes for each project.

Ah true most of our projects where separate

This post is from the NIH intramural (Bethesda/DC campus) training site.

The NIH has research in genomics, neuroscience, machine learning, cell biology, and there's lots of cross talk between these fields.

There are PhD students at NIH (via partnerships with other universities, one example: http://neuroscience.brown.edu/gpp/), postbacs who stay for a few years to do research after undergrad, and postdocs.

As you can see from resources like this on lab notebooks, the central NIH training office takes mentorship and learning seriously. As do the scientists. If you want to know more about NIH intramural research you can message me.

(Our group uses Evernote extensively for lab notebooks; the image markup brings a ton of value. We follow a lot of the recommendations here.)

I have gone back & forth with Notebook and Digital.

The current system that seems to work for me, is to have a ring binder similar to this : https://www.staples.com/1-2-Staples-Standard-5-1-2-x-8-1-2-M...

Then buy paper fillers : https://www.amazon.com/Avery-Filler-Inches-Sheets-14230/dp/B...

Some rules I follow:

* Every time I start a new project or topic, I start on a new page.

* Have tabs/stickers along the side of the paper that starts a new project

* If you are continuing to write on a paper/project that has stuff on it already, continue on a new page. Since its a binder, you can always move sheets around.

Once I am done with a project, I move it to digital form by arranging it like a mind-map onto a digital notebook. This serves two purposes. 1. reinforces the main concepts in my head. 2. Digital makes it easy to search.

Having tried a lot of them, the only one that I like that has all the features I am looking for is MILKR (https://milkr.io) - no affiliation.

The best advice I've read on keeping a lab notebook is to not worry about neatness.

Being a perfectionist, I used to delay writing things down, because I felt I needed to take time to "do it right". Or, I'd write things on scraps of paper with the intention of copying it later.

Giving myself permission to make a mess was liberating, and ultimately increased my productivity and the amount I was recording.

I also recommend taking photos of entries at the end of each day, to keep a digital backup.

The book “Wreak this Journal” is designed to help people get over the reverence they have for blank journals, and it’s fun for kids.


This. I've had a few false starts at daily journaling and it mostly came down to being a perfectionist. In the past I'd only write down a handful of todos / notes because I didn't want to "mess it up".

I decided to spend 1 month (started at beginning of nov) and only use my bound notebook for everything including diagramming / working things out that I'd normally do on a whiteboard or scrap paper.

I do REALLY like that I have a permanent record of some ideas that I'd normally just lose to the ether.

At the end of the day who gives a fuck if its perfect, I'm only writing it for myself anyway.

Giving myself that permission has been difficult but a fruitful endeavor so far.. I'm hoping to adopt some of the other cool spread ideas I've found on r/bulletjournal

As someone who doesn't come from the educational world, this idea confuses me:

  Most importantly, your lab notebook is not yours.
Many of the ideas presented on slide 4 seem a bit antithetical to a bit of the reason why someone would keep a good notebook. If I wasn't going to keep it, why would I bother? Or is this based off the idea that the institution is paying for it, therefore they own your research/knowledge?

Yes. It's theoretically a legal document of all of the work done in a lab.

Note: as the slides mention you can (and probably should) keep copies of your notebooks.

A loose analogy is that a lab notebook in this context is more like a courtroom transcript than a personal journal. It's a primary record of experimental data and procedures. Also there can be multiple people running a single experiment and recording data in a common lab notebook.

Because they are part of what you're being paid to do in that case.

Being paid to do something does not automatically make all that is involved in the doing of that thing property of they payee.

If I am being paid to produce some deliverable product or deliverable service, then the infrastructure used to create that may very much not be a deliverable or property of the customer.

My point isn't "you are wrong", but rather, there is not necessarily an automatic assignment of such intermediate products. And depending on the type of work (and/or customers / employers you're working for), the answer may vary. Law, custom, employment contracts, and/or engagement contracts will almost certainly play a role here.

If that governing rule is "you shall maintain a project journal and that journal is considered work product and property of the employer", then yes, that is part of what you're being paid to do. Though this may still give you rights to the contents of that journal.

In his case the point is that the engineering notebooks are parts of the deliverables you're paid to produce: They're documentation that staff are very explicitly trained to and expected to produce in a format that is conducive to e.g. handovers as part of their normal duties, and the expectations of this are very clearly set out.

If you wish to also produce a personal engineering notebook for your own personal purposes, then that is a separate issue. The very fact that this document sets this out as a task that involves producing a notebook that is not yours makes it a work product. If you put things in there you don't think your employer should have rights to, then that is your fault for putting it in there instead of in your personal notes.

The salient datum is not "being paid" but the contractual obligation.

Fault and negotiating advantage are a deeper issue. I'll note these though I'm not interested in going into it further presently.

"being paid" is here used to point out that they are part of the duties of the job covered by the contract. If they aren't part of your contracted work, you're not being paid for it.

There's nothing to go further into - these are very straight-forward issues when they are presented to you as a part of your duties. They are less so if you on personal initiative decide to keep additional notes for your own use, but the context here is a presentation to employees presenting instructions for how to carry out this work duty, so that hardly applies in this case.

Been using this for decades; my first boss, a PhD physicist, out of college got me started on using this. It's still being sold today: https://www.amazon.com/National-Computation-Notebook-Inches-...

Nobody has mentioned Wacom Bamboo series digitizers, which is what I am using. It allows me to sync notes I'm writing on plain paper with my phone/tablet. It even tries to OCR my handwriting (which doesn't work flawlessly, but since I have a habit of writing subject titles in all caps, I can at least search by those).

I have never tried it, but I am interested in the Grinnell field notebook methodology:


It would require carbon paper and a 2nd notebook at least to cover 'backups' and in that sense, I highly prefer electronic note taking.

Haven't look at them in half a decade but smart pens always seemed like a solid idea to meet this need. Livescribe was the primary one I looked at years ago but I know there were multiple competitors and technologies available. The end goal being that when you write on paper the strokes are saved digitally. Now tablets are probably nearly completely taking digital handwriting over but I've never felt as comfortable writing on glass screens as on paper.

There's RocketBook. I use it pretty regularly, but you aren't left with a hard copy if that's your preference — unless you print the results.

You could of course also just use a doc scanner on your phone and keep your hardcopy notebook instead.


I picked it up during the Kickstarter campaign. If it has one advantage, it will auto-send your notes to one/more preset destinations out of seven, like email it to you or someone else, send to Evernote, OneNote, etc. It's worked alright for me so far.

I never much liked the writing on glass feeling, either. Growing up I was a bibliophile and always preferred working with paper. I'm trying this out as a happy middle.

If you only need archival, it might be easier to get an autofeeding scanner like a ScanSnap and scan all of the pages when you're done with a notebook. I used mine to scan a lot of old notebooks before throwing them away.

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