Happy new school year to my fellow students! With my first year of grad school under my belt, and my sword and shield out for Round 2, I wanted to share a tool that’s helped me on my journey.

Two years ago, my go-to system for organizing my research and writing “citations in 3 different programs” + “pile everything into a haphazard series of google docs and hope for the best”. I figured this wasn’t great. After doing some reading and trying several alternatives, I discovered Tiddlywiki.

Tiddlywiki is an ancient open-source wiki application in the form of an html file. It has all the tools you need to make a wiki in the form of “tiddlers”, self-contained chunks of info that you can tag and link to each other. When you save the wiki, the program and your text all get wrapped up together into the same .html file – it both stores your info and is the program for running the wiki. It works on any web browser, as well as special programs.

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I stuck with it and here’s why:

  • Wiki format: Wikis seem really compatible with the way my brain works. If I take notes on a book or article, that source gets its own tiddler on the wiki. They can then get interwoven, crosslinked, expanded upon, etc.
  • Elegant: Does most things I want it to. Easy to link to tiddlers and drag them or other files in from other wikis/folders. The structure is transparent and customizable.
  • Robust: Tiddlywikis from a decade ago are still perfectly functional today. The entire program and dataset lives in one small html file that runs on anything with a web browser.
  • Meta-aesthetics: Feeding all my data to Google is a little worrying. Tiddlywiki, meanwhile, is open-source and runs from your computer. The fact that the program is a quine is really neat.
  • Encryption: Tiddlywikis have an encryption function baked in. I don’t know if it’s very good. Consider using Veracrypt for better security. But if you don’t want to do that, here you go. This also means you can upload your wikis and backups to cloud services while keeping them encrypted. (Go to “Tools” in the sidebar, then click on the “set password” button. After you set a password, you can look at the .html file text to be sure that, yes, everything is encrypted into nonsense characters.)
  • Customizable: Easily change the color scheme, any text or formatting, the layout, etc. It’s extremely adaptable. You can also install a variety of plugins, though I haven’t felt the need to myself as of yet.
  • Transportable: My wikis live on a flashdrive and can work on any computer. I took all my research with me to and from work every day this summer for an internship.

Things I like less

  • Saving is not obvious. This simplest version is “edit a copy of a blank tiddlywiki in a web browser, save locally to your computer or a flash drive, repeat every time you edit it”, which is kind of a pain. ** I work on various computers, so my Tiddlywikis are saved on a flash drive. I edit them in web browsers, and save them back to the flash drive when I’m done. I back them up every week. ** On my Ubuntu laptop, I edit them with the program TiddlyDesktop, which makes saving easier.
  • You can use images, but they get saved as raw code into the html file itself (so every image makes the file that much larger), and there aren’t tools for manipulating them. (There is a cute, tiny, and almost useless drawing program baked in.) I tend to save a few images, like graphs or figures from papers, but wouldn’t personally use Tiddlywiki for image-heavy work.
  • Some features (e.g. spellcheck, in-text search with highlighting) depend on the browser or other program you’re using to edit the wikis.
  • Kind of old-looking, not maximally aesthetic.

The number of wikis you have is up to you. I started with one wiki for a specific writing project and one wiki for work, notes and research. My active Tiddlywikis now include:

  • Grad school material
  • Internship research material
  • General writing, notes, and personal research
  • Writing and worldbuilding/characterization/plot details for a novel
  • Recipe storage
  • Quotes and poetry I like

Your mileage may vary.

How do I try it?

First, check out some tiddlywikis that have been converted into websites. Here’s a nice one to explore as an example, a thesis website in Spanish. Here’s one on philosophy. (Note that you can’t actually edit the versions that appear on the website. You can locally save the whole wiki and changes you make to it, though.)

If you like it, here are some resources to get you started. This is the official website, which has lots of helpful documentation. (Note that it’s also a tiddlywiki!)

Here are some youtube videos I also found helpful.

After making a few tiddlywikis, I found that I kept making the same tweaks to them to get them set up in a way useful for me. In that light, I made a new “blank” or “empty” tiddlywiki that had those changes baked in already.

Here it is: the Eukaryote Writes Blog empty tiddlywiki. You may find it better than the default empty wiki. It comes with a couple new color schemes, a table of contents, and some layout tweaks, among other small changes.

Other research tools

All hail the exobrain!

I keep track of research citations formally with Zotero, or the tool my work prefers. For informal reading, I’ll also just note the authors and title and/or URL of the source (in my tiddlywiki!) so I can find it later.

For keeping track of time spent working, I’ve gotten some utility out of KanbanFlow. I like the Pomodoro Technique, and KanbanFlow has both pomodoro timers and a nice task-sorting and task-prioritization system built in. I currently don’t worry about tracking time, and use Google Calendar, a bullet journal, and a bastardized Kanban Board variant to keep my brain in order.

Previously, I used the website MarinaraTimer to time pomodoros. I love it for exactly two reasons: the ability to pause pomodoros, and the sound effect “Ominous Woosh”.

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8 comments, sorted by Click to highlight new comments since: Today at 1:40 AM

I enthusiastically endorse the use of wiki software (and wikis) for almost any conceivable purpose. However, I have to say that, having investigated a variety of wiki platforms, TiddlyWiki in particular did not strike me as very promising.

My recommendation would be PmWiki, which (in addition to many other salutary qualities) is quite possibly the single most customizable platform of this type I’ve ever seen. There’s a truly staggering number of add-ons (called “recipes”) available (take a look at just the ones I’ve made and contribute to, for example).

Examples of sites and pages built with PmWiki are:

EDIT: What may be of particular interest to folks here is that PmWiki has support available for:

In addition to embedding images in the HTML file (which, as you discuss, is not a great choice) TiddlyWiki allows linking external images. In particular, you can use relative paths to link to image files on the same drive as the TiddlyWiki. I use this functionality a lot. It has the disadvantage that your Wiki is no longer a standalone HTML file, but it's still a standalone folder, which is often good enough.

Please share your example of using Tiddlywiki for quotes.

Sure. It's not much right now.

I put each quote and source combo on their own tiddler, then tag it with a bunch of stuff that might help me find it later. I'll probably refine the system as I start referring back to it more.

I used TiddlyWiki a lot for my PhD work and it was excellent, but haven't touched it since for some reason. Maybe I'll pick it back up.

One thing I remember doing was modifying the JS so that it linkifies any mention of a Tiddler, rather than only doing it when you put the name in the 'make this a link' syntax. I found it handy to have it so that any time I mentioned an author, framework, algorithm, dataset etc it would effortlessly be a link to my other notes about that topic. I'll see if I can find the files.

Thanks for the description! I found this software years ago, but somehow I didn't notice that you can save the data.

For people who like the idea of a wiki, but have some objection against Tiddlywiki, I would recommend trying WikidPad (desktop app, can save in one file, automatically generates page tree, supports lookup by keywords) or MediaWiki (online app, all functionality of Wikipedia including writing your own macros).


I've found the way my knowledge management workflow works is that I have particular future situations I anticipate being in, and I want to keep a list of things I'd like to be reminded of in that particular situation. (This is very broad and could include stuff like: I decide I want to write post X, or start company Y, or I'm struggling with problem Z, etc.) Usually this doesn't require a lot of nonlinear structure, I'm basically just looking at a bunch of lists. The most important feature is a hotkey for jumping to the list in question. Here is an old post with more details (which also has comments from others on personal knowledge management):


The thing I'm least satisfied with is when bits of text belong in multiple lists, but the intersection of the two list domains doesn't feel broad enough to justify the overhead of a dedicated list. It sounds like the tiddler concept handles this situation pretty well. I wonder if autocompleting tags could be an effective substitute for my jump-to-note hotkey...

TiddlyWiki is a great tool, incredibly flexible.  I've seen it camouflaged as basically any other app out there (Roam clones,  kanban boards, etc.). 

The best (and meatiest) example I've ever seen of a (public) personal knowledge base is Soren Bjornstad's, https://zettelkasten.sorenbjornstad.com/  .  He's the author of the -- in itself very impressive --  self-TW-hosted book https://groktiddlywiki.com/read/  He is also, in a way, a philosopher of the whole thing,