A Practical Introduction to a Personal Knowledge Base for Scientists (and Other People)

When I first started using Dokuwiki, i just put random notes there, not intending to really use it for much more than a fun hobby project. But it has now grown to a personal knowledge base with random facts, protocols, and information about techniques. I thought it would be useful for myself to write down what I've learned, and thought I could share it with others as well.

The Beginning

I started to self-host a simple wiki, called Dokuwiki, just for fun, as a hobby. Dokuwiki works like Wikipedia, but instead of being an encyclopedia of everything, it is up to you to fill it with information. which you can use to keep information for yourself or a small(-ish) group of people. You can fill Dokuwiki with information about your hobbies, favorite TV show, or anything else you want really. You can share it with the entire internet, or limit visibility to people with an account, or show some parts and hide others.

As you might imagine, Dokuwiki is quite useful to keep track of things you need to remember. That is how I started off: a place to store things you need once per year or less, which you forget every time you need it. Ideas for presents for people I get in random moments of inspiration, clothing sizes of things you basically never buy, ideas for places to go on holiday. All quite useful, but not world changing - more like a digital notebook than anything else.


But I quickly found that Dokuwiki is a great place to store information for scientists. I used to have random word files with protocols laying around, especially for chemical reactions, that are (probably) performed the same every time you do them. But saving them in Dokuwiki is much nicer: it gives you a way of ordering things, you can link relevant literature and related other protocols easily, you can easily share the protocol with colleagues with a link, and Dokuwiki keeps track of your editing history, so if you make a change, at least you know when it happened, and you can match it to what is going on in your (digital?) lab notebook. Quickly, my wiki grew bigger and bigger, as I added more and more protocols.

And then I realized, I could also use Dokuwiki to keep track of tips & tricks for random devices in the lab. Instead of taking notes when you get the introduction for a new device in the lab, and immediately losing the notes and forgetting everything you've learned, I could now write them in my wiki, where they are safely stored. And if I discover useful about a device during experiments, I write that down as well. While we are at it anyway, I also added the full name and other properties and a link to the official manual or documentation. If people have questions about the machine, I could just share this page.

From there on, I fell into the habit of saving everything I knew (and knew I would forget) into Dokuwiki. Interesting conferences? Into the conferences page. Default cap size for glass vials? Sure, why not. And this turned out to be very useful! No longer did I spend an hour finding out what thread size you need to connect Mightex LEDs to Thorlabs 1 inch lens tubes, but I could easily look this up (you need an outer C-mount to outer SM1 connection piece). Dokuwiki became a second brain.

Bringing order

All was good. But I also started running into problems. It became too much. It became harder to find the right information. I needed to give my wiki some ordering. For that, I used a combination of the Johnny Decimal system and Zettelkasten. So how does that work?

Johnny to the rescue

The Johnny Decimal system gives my wiki pages a hierarchy, making them easier to find, and assigns a simple code to everything. It works as a folder structure of the wiki. A code may look like 27.05, 11.02, or 41.02. The first number (so 2 in 27.05) is the “Area”. It is the broad subject, in my case, the 2 indicates “Science”, the 1 indicates “About me” and 4 indicates “Hobbies”. The next number ( so the 7 in 27.05) is the category. In my case, 27 indicates “Devices & techniques”. This category needs to be more specific as an area, but still quite broad (since there can only be 10 categories for each area: 20-29). The number after the dot then specifies the “ID”, so 05 in 27.05, in my case “Microfluidics”. Here, in this page, or possibly sub-pages, I write about the microfluidic devices and setups I have experience with, random information about microfluidics, etc, etc.

This Johnny Decimal system makes it easy to store this kind of structured information: all information has a pretty clear place where it lives, and it is easy to find it back. And if a piece of information could exist in two places in the system you just put it in one place and link to it in the other, or if you did not do that, follow the advice of the creator of the Johnny Decimal system: “Humans are smart. You’ll be okay.” In the spirit of the last quote, I don't keep myself too rigorously to the system; it is a tool, not the goal. If it feels useful to create another subcategory under IDs, go for it. No-one will ever know.


Now this Johnny Decimal system works well for well-structured information (like how a specific device works, what buttons to press). But it does not really work well for more random tidbits of information you may pick up from papers or experiments that you want to remember: what glue does and does not work on PDMS, or the acting mechanism of enzyme-micropumps. For this, Zettelkasten are more appropriate. In this system there is explicitly no hierarchical categorization system.

If there is a fact or piece of knowledge you want to remember, you write it down on a page. Keep it short and to the point, and write in your own words. Add a source if you have one. Now, we add tags; if the page you wrote is just a list of glues that do and do not work on PDMS surfaces, then good tags would probably be “glue”, “PDMS”, and “microfluidics”. You could also link another, related notes.

Now, this PDMS-glue example feels a bit mundane - it will not help you write papers. But if you have a more deep thought, you can also write it in a note, an tag it properly. These tags can help couple facts together that you maybe had not considered before. It may help your creative process, leading to new original ideas!

But it is also quite a good system to store mundane experimental thoughts, don't let people tell you otherwise!

The Zettelkasten-content on the internet seems to be dominated by people who love spending time writing long assays on how they manage their personal knowledge base1), so be aware of that when you go deeper down this road.

Details about my system

Getting Dokuwiki

To get your own Dokuwiki, you have two choices. Either you host it yourself, which is relatively easy, if you are into that kind of thing, or you pay someone to do it for you. For instance, see here for some people offering to host dokuwiki, starts around 4 euros/month at the time of writing.

Also, and I must really stress this, other wiki-like software will probably work as well. Dokuwiki works very well, is simple, and has many extensions available. And (good for self-hosters), if you screw up; worst case you just have a bunch of text files which you can always access, and easily export using i.e. Pandoc. But, if you are interested, on this page I give some alternatives to Dokuwiki.

My Johnny Decimal categories

So, if you want to do this seriously, you will need to come up with Johnny Decimal areas and categories. If you just start, they will probably arise more-or-less organically2), but if you want to see how I do it, I give a rough outline of my Areas, Categories and IDs below. I censured it a bit, but they are mostly real categories. Note that a lot of this is not actual scientific - I use the Johnny Decimal system to keep track of many things in my life.

Johnny Decimal Example
  • [10] Personal
    • [11] About me
      • [11.01] To do list
      • [11.02] Clothing
      • [11.03] Things I should tell people to buy me as gifts
      • [11.04] Family tree
    • [12] Things I carry/use everyday
      • [12.01] Laptop
      • [12.02] Phone
      • [12.03] Email
      • [12.04] Bike
      • [12.05] Recipes/cooking
      • [12.06] Watch
    • [13] Health
      • [13.01] Docters visit 12-08-20XX
    • [14] Education
      • [14.01] BSc & MSc
      • [14.02] So-and-so summerschool
      • [14.03] Efficient writing (PhD course)
      • [14.04] Teaching skills (PhD course)
      • [14.05] German course Summer 2023
    • [15] Media
      • [15.01] Films
      • [15.02] TV Series
      • [15.03] Podcasts
      • [15.04] eBooks
      • [15.05] Audio-books
    • [16] Events
      • [17.01] PhD defense
      • [17.02] Some other thing I organized
    • [18] Associations and volunteering work
      • [18.01] MSV Alchimica
      • [18.02] RIC
      • [18.03] Mainzer Ruderverein
    • [19] Travel and Hollidays
      • [19.01] Austria 2020
      • [19.02] Alta Via 1 2021
      • [19.03] Etc
      • [19.99] Vague Plans and Ideas
  • [20] Science
    • [21] Data
    • [22] Knowledge
      • [22.01] Journals
      • [22.02] Groups/Labs/People
      • [22.03] Visualisation
      • [22.04] Writing
      • [22.05] Data extraction
      • [22.06] Standards
    • [23] Protocols
      • [23.01] Glass cleaning and fictionalization
        • I actually keep sub-IDs here with specific protocols
        • [23.01]A: Hydrophobic Vapour Coating of Capillaries
        • [23.02]B: Safe-ish alternative to piranha treatment
      • [23.02] Click reactions
        • You get the idea.
      • [23.03] Microfluidics
      • [23.04] Colloidal synthesis
      • [23.05] 3D printing
      • [23.06] Whatever
      • [23.99] Things that do not work
    • [24] Conferences, talks, posters
      • [24.01] Some conference, June 2022
      • [24.02] Some other COnference, August 2023
      • [24.98] Posters - general
      • [24.99] Possible conferences
    • [25] Projects
      • [25.01] Colloidal Cyclopentane
      • [25.02] Tetravalent patchy particles in 2D
      • [25.03] Equilibrium Patchy Gels
      • [25.99] Possible interesting projects
    • [26] Grants & Proposals
      • [26.01] Possible Grants
      • [26.02] 2023 - Humboldt
    • [27] Devices & techniques
      • [27.01] Microscopy
        • I make sub-IDs here for specific devices. It is usefull if they have unique codes, so I can refer to them in my lab notebook
        • [27.01]A That one microscope in that one room
        • [27.01]B That other microscope
        • [27.01]C That super-fancy superresolution microscope
      • [27.02] DLS
      • [27.03] 3D printing
      • [27.04] DMD
      • [27.05] Microfluidics
      • [27.07] Optics (spectroscopy, etc)
      • [27.08] Centrifuge
      • [27.09] Cameras
      • [27.10] Simulations and stuff
  • [30] Finances
    • [31] Taxes etc.
      • [31.01] Rundfunkbeitrag
      • [31.02] Taxes 2021
      • [31.03] etc
    • [32] Bank stuff
      • [33.01] Blah
    • [33] Insurences
      • [33.01] Health insurence
      • [33.02] Household insurance
    • [34] Pension, Social security
      • [34.01] German Sozialversiecherung
  • [40] Hobby
    • [41] Hiking
      • [41.01] Equipment
      • [41.02] Possible hikes
    • [42] Selfhosting
      • [42.01] Device 1
      • [42.02] Service 2
      • [42.03] Checklist for new devices
      • [42.98] Overview netwerk
      • [42.99] Vague future plans
    • [43] Reading
      • [43.01] Book reviews
    • [44] Rowing
      • [44.01] Diplomas
  • [50] Government
    • [51] Government general
      • [51.01] Voting 2023

* [60] Work

  • [61] Jobhunting
    • [61.01] CV, coverletter, etc.
    • [61.02] Postdoc 2022
  • [62] Contracts, etc.
    • [62.01] PhD UvA
    • [62.02] Postdoc Mainz
  • [70] Interests
  • [71] Culture & Sports
  • [72] Adorable vagueness
    • [74.01] Niche websites
    • [74.02] Weird articles
  • [80] Living
  • [81] Moving
    • [81.01] Moving Haarlem - Mainz
  • [82] Furniture, furnishing, decoration
    • [82.01] That nice new cupboard
    • [82.02] Stuff that goes on a wall
  • [83] Contracts etc.
    • [83.01] House Mainz
    • [83.02] House I had before
  • [84] Gas, water, electricity, etc.

Implement in Dokuwiki

The implementation of the Johnny Decimal system in Dokuwiki is not complicated. Every Area is a folder (or “namespace” in the wiki-jargon). Every Category is a sub-folder to an Area folder. And every ID is a subfolder of a category. Inside of category, you make one main page, with links to other pages in the same ID (using for instance the NSpages plugin), see an example below.

A specific example: say you need the note about how CNC milling works:

Area [20], for Science > Category [27], for Devices & Techniques > ID [27.03]. for 3D printing and additive manufacturing.

So the final location is probably something like 20/27/27.03/cnc, and looks something like the image below.

Zettelkasten in Dokuwiki

So how do you use Zettelkasten in Dokuwiki? You make a folder (or namespace in wiki-talk) specifically for your Zettelkasten system. And there, you just start creating pages for your notes. Do not create a deeper hierarchy, but do link other notes where appropriate. You can tag stuff in Dokuwiki using the tag plugin. You can see what other pages notes linked the current note using the backlinks plugin. Just start adding notes, and things will probably fall into place. And don't forget that Dokuwiki has a search function that generally works well.


And that is it. I hope this helped you, or inspired you! And if not, that is also fine; it was actually quite useful for myself to write this all down.

This introduction to Zettelkasten is longer than basically the entire detailed explanation of the Johnny decimal system, and a fair bit of it consists of praises to its founding father, Luhmann
Let's quote the spiritual father of the Johnny Decimal system again: “Humans are smart. You’ll be okay.”


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