Lab notebooks and Zettelkasten

KChousos

Hello everyone,

I'm in the process of starting my master's thesis. I'm entertaining the following idea for a candidate workflow:

1. Having the digital slipbox for ideas/knowledge work for my research
2. Having a physical lab/research notebook as more of a log of my daily efforts and my more unrefined thoughts, kind of like a "research scratchpad".¹

Although I would like to adopt such a workflow, if for nothing else than a brief escape from staring at screens all day, I have a few concerns. First, I suspect that it might lead to decision fatigue about what goes where. Second, I get FOMO regarding the features that an electronic counterpart—such as a big OrgMode file—would offer, e.g. automatic time-tracking. But alas, this seems kind of secondary and most likely I would not make much use of it.

Does this distinction make sense for anyone? Do you think that having a research notebook is redundant? Any thoughts welcome. Cheers.

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1. Whether tasks/subprojects management will go there or on my main bullet journal is something for later ↩︎

KChousos

Follow-up: Probably important to state is the fact that my research will be on post-quantum cryptography, so highly theoretical and math-focused. As such, it's not like I'll be keeping measurements, tracking experiments etc. like for example a chemistry student would.

tomp

@KChousos said:
Follow-up: Probably important to state is the fact that my research will be on post-quantum cryptography, so highly theoretical and math-focused. As such, it's not like I'll be keeping measurements, tracking experiments etc. like for example a chemistry student would.

If there are going to be many equations, setting them up and modifying them in LaTex would be painful. You may want to capture just the final products in the digital system.

Also, do you need to have unmodifiable timestamped lab notebook pages? That would argue for at least part paper in a sewn lab book.

zettelsan

I think the hybrid approach would work. If you are in the Emacs ecosystem already, I'd highly recommend workflows using Org with some LaTeX integration. (Just because it works well.)

You digitize knowledge that are sufficiently distilled, so that writing papers/thesis will be simpler, less time-consuming. When you set things up properly, bibliography/reference and citations are easier to manage digitally as well.

Yet, working out math in detail and such, you may still want to do by hand. You learn and retain better that way. Use them to create distilled notes. You could also digitize hand-written notes later by scanning, etc., if you want to save them and physical space.

Aside: Back in the days as a grad student, there was this classmate who took all his notes in LaTeX using his Linux laptop, including drawing with touch pad... (The rest of students were busy taking notes on paper.) That sounds crazy, but when you are sufficiently fluent in typing and LaTeX, doing so doesn't really slow you down much.

ctietze

I sort of practice a similar separation but wholly digitally. I don't have anything to do outside of computers that is not 'hobby' time. (I could see myself using a physical logbook for house renovation or gardening, though)

Unrefined lab notes don't go in the Zettelkasten usually. I treat them as data points, external, until something to extract from them emerges. -- I'm programming, so these are log files, documentation links, and such, and when I find out something new, I pull from these to create notes in my Zettelkasten to teach my future self about whatever happened.

harr

@KChousos said:
Does this distinction make sense for anyone?

Yes, it does. Notebooks are a centuries old tool for taking notes. They should work well for such a log, because:

• they encourage you to write linearly. You start on the first page and write from there. If you want to go back in time you simply leaf back in your notebook.
• they can't be changed. You can't go back and insert a page or rearrange pages or erase text (provided you use a non-erasable pen). If you want a log that documents the sequence in which you had your thoughts and developed your ideas, a paper notebook helps
• island of order. Even if you have a chaotic whiteboard, desk, personal library or computer files, where everything changes all the time, your log stays simple. You just write one page after the other
• no batteries needed. Sounds silly, but can make a difference.
• no overorganizing with unnecessary detail.

If you buy a notebook with page numbers, you can easily reference individual pages and/or add an index.

The big question is, if you enjoy writing in such a notebook. Some people do, some people don't.

KChousos

@tomp said:
If there are going to be many equations, setting them up and modifying them in LaTex would be painful. You may want to capture just the final products in the digital system.

I agree that working through math by typesetting them is a terrible idea. But in my mind initial calculations and other scribbles would exist in random paper sheets on my desk, before distilling them in the research notebook, otherwise there would be too much noise.

Also, do you need to have unmodifiable timestamped lab notebook pages? That would argue for at least part paper in a sewn lab book.

Not really. All this is from a personal preference

@zettelsan said:
I think the hybrid approach would work. If you are in the Emacs ecosystem already, I'd highly recommend workflows using Org with some LaTeX integration. (Just because it works well.)

You digitize knowledge that are sufficiently distilled, so that writing papers/thesis will be simpler, less time-consuming. When you set things up properly, bibliography/reference and citations are easier to manage digitally as well.

Already doing that. My slipbox is implemented using the localauthor/zk Emacs package in Org files with LaTeX snippets and Org citations from a mega biblatex file. That's where my GTD-esque task management system resides currently, but I've found that I seldom make use of the different tags, categories, agenda features etc. of Org-Mode (except from scheduled and deadline dates), hence my current conundrum towards a simpler and more analog workflow.

Aside: Back in the days as a grad student, there was this classmate who took all his notes in LaTeX using his Linux laptop, including drawing with touch pad... (The rest of students were busy taking notes on paper.) That sounds crazy, but when you are sufficiently fluent in typing and LaTeX, doing so doesn't really slow you down much.

Tried something similar for a semester or two. Even though I could keep up, the context switch made me miss stuff and sometimes I was focusing more on typesetting than listening to the lecturer.

@harr said:
Yes, it does. Notebooks are a centuries old tool for taking notes. They should work well for such a log, because:

• they encourage you to write linearly. You start on the first page and write from there. If you want to go back in time you simply leaf back in your notebook.
• they can't be changed. You can't go back and insert a page or rearrange pages or erase text (provided you use a non-erasable pen). If you want a log that documents the sequence in which you had your thoughts and developed your ideas, a paper notebook helps

Yes, that's kind of what I have in mind. Basically I would like to have a dedicated research log/journal/scrapbook.

• island of order. Even if you have a chaotic whiteboard, desk, personal library or computer files, where everything changes all the time, your log stays simple. You just write one page after the other

Exactly.

If you buy a notebook with page numbers, you can easily reference individual pages and/or add an index.

Yes, I already make use of numeric IDs for journal pages and for slipbox notes based on both the advice on this site and the Bullet Journal method. This would be just another aspect of that.

The big question is, if you enjoy writing in such a notebook. Some people do, some people don't.

I do and I hope that the medium will make procrastination harder than when I'm able to tweak my Emacs config

My thoughts regarding the synergy between the research notebook and my slipbox originate from an article by Bob Doto [1] where he proposes treating journals (more like diaries in this case) like any other external reference. Thus, my notebook can be an append-only log of my efforts while the important knowledge collected or created in it can be stored in a more refined form inside my slipbox, making the thesis writing process easier down the line.

References

[1] B. Doto, “Using Diaries and Journals as Source Material for Zettelkasten Notes,” Bob Doto. Accessed: Jul. 02, 2026. [Online]. Available: https://writing.bobdoto.computer/using-diaries-and-journals-as-source-material-for-zettelkasten-notes/