My ideal personal knowledge system would entail a rofi-like search from the desktop that ties into my knowledge repos, such as Zotero, this linkblog, my blog, Wallabag, Calibre server, and more. Even better if the search was powered by a self-hosted LLM. A tall order, to be sure ;-)

Here I'm collecting notes on projects or posts that are along the lines of this vision.

TiddlyWiki (Ness Labs)

TiddlyWiki is (much more than) an open source alternative to Roam Research. You can self-host it. Your entire Wiki (including all notes) is just one HTML file (if you want, it could also be separate markdown files), so sharing should be easy.

You need to choose a method for saving your changes. Many options to choose from, including Node.js, TiddlyDesktop, Beaker browser, WebDAV, TiddlyFox (not so much), or Git.

Via Tom Critchlow
Another good post by Le Cunff: open source and self-hosted alternatives to Roam

There's a TiddlyWiki subreddit and a TiddlyWiki Google group.
A reddit post listing open source alternatives to Roam Research.
A long discussion on HN on pros and cons of Roam based on Roam: Why I Love It and How I Use It by Nat Eliason.
And a post by Jack Baty comparing TiddlyWiki and Roam.
Another blog post, Tiddlywiki for organizing notes and research.

An introduction to TiddlyWiki by Scott Nesbitt.

TiddlyBlink is an adaptation of TiddlyWiki, inspired by Roam's bi-directional links.
For the knowledge graph view, there's TiddlyMap.

• TiddlyMapProject video showing how to setup TiddlyMap on TiddlyWiki
  https://news.ycombinator.com/item?id=22104366
  I tried it out in Beaker browser. Worked well (TiddlyWiki, Markdown plugin). But I could not install TiddlyBlink, for some reason. Perhaps try a different browser?

There's also TiddlyRoam, which combines TiddlyMap and TiddlyBlink. The announcement reddit post, and source on github.

Roam (and by extension, TiddlyRoam) is a form of Zettelkasten.

You can apply different Tiddly themes (here's one).

Using TiddlyRoam with TiddlyDesktop, I still cannot figure out how to install plugins. If I use the built-in plugin library, and install e.g., Markdown parser, I get prompted to save and reload, do so, and then... nothing. Plugin is not installed, and the Wiki content starts over from scratch, whether I create a new HTML file or replace the existing one. What's up with that? A few edits later, the plugin now works as expected. Maybe it just took some time to apply, or maybe I restarted TiddlyDesktop (not sure).

The TiddlyMap page has an example of mapping a literature collection (using icons set with group styles).

Foam

Foam is another FOSS alternative to Roam.
It's built into VSCode/VSCodium, which is a big selling point for me.

Logseq

Logseq. FOSS.

• https://github.com/logseq/logseq

Emacs org-mode

There's also org-roam (built on Emacs org-mode)

• Video on org-roam setup from Matt Williams
• Visualise Org-Roam Networks With igraph and R, by Peter Prevos, 2021-08-14

Popup IndieWebCamp Session 2020 (video recording of Zoom session), on wikis, blogs and such. Via kickscondor.com.

Obsidian

Obsidian is not libre (not open source) software, but provided for free for personal use. For that reason, although popular, I cannot recommend it.
Also see this blog post on how to create nice tables in Obsidian with plugins.

• https://github.com/anoopkcn/obsidian-reference-map
• https://thesiswhisperer.com/2023/02/01/building-a-second-brain-for-writing-with-obsidian/

ZotHero

Something like ZotHero but for rofi/Linux would be really cool. Too bad ZotHero is only for Alfred (MacOS).

• https://github.com/deanishe/zothero

Assorted links

• Knowledge repository, post in the Level1techs forum
• Second Brain Software: From Files to ZettelKasten, Level1Techs, video 22 min, 2022-02-24
• Dreaming of a free mind with tiddlywiki+ freemind mindmaps
• FreeMind to TiddlyWiki integration
  
• https://github.com/michaeljmcd/mm2tiddlywikitext
• https://github.com/byzheng/rtiddlywiki
• https://github.com/raphaelsty/knowledge (web app that creates your own knowledge graph based on your Github stars, Twitter likes, HN upvotes and Zotero database).