Seedling Planted February 14, 2026 6 min read

Building Mycelium: A Digital Garden Theme for People Who Actually Write

Why I built a digital garden theme around how I actually think and write

#obsidian #astro #digital-garden #open-source #tools

How I think

My thinking isn’t linear. It’s sporadic chunks of information. I’ll have 50 different thoughts and maybe two or three paragraphs on each. Each one is its own coherent little entity. I perceive them, write them down, reflect on them, and then I see afterwards that they actually do connect and they do make sense.

Rest in peace Twitter, back when Twitter was Twitter. I could take down ten tweets and that would put my thoughts together into what would be a comprehensive blog. That’s how I try to think. Not in straight lines but in these sporadic chunks that I have to capture, sit with, and then see the structure in.

In college they teach you to write five-paragraph essays. When you submit a paper to a conference, you go through the papers that were previously submitted to that conference and look for a similar format, and you share your work with people who are your peers in that format. My writing doesn’t work like that. Whether I’m writing the essays on yad.codes, or doing comedy writing, or working on technical posts, there’s no difference in the process. It’s a mix of ideas. It’s more than a mixed bag though. They’re coherent, they’re all like little entities on their own, and the structure comes after.

Most tools don’t work this way. A blog sorts by date. A word processor gives you a blank page and expects a beginning, middle, and end. A CMS wants categories and a publish button. Every time I try to start a blog, the static site generator drags me down. I spend more time configuring the site than writing for it. The theme doesn’t do what I want, the markdown processing is wrong, the build breaks, and by the time I get it working I’ve lost whatever I wanted to write about.

Gardens, not streams

Mike Caufield gave a talk in 2015 called The Garden and the Stream that named what I was looking for. The stream is chronological: Twitter, blogs sorted by date, news feeds. The garden is topological: linked by context, not by when you wrote it. A garden accumulates knowledge. A stream buries it.

When you think in chunks and the connections emerge after, you need a garden, not a stream. The idea goes back to Mark Bernstein’s Hypertext Gardens in 1998. Maggie Appleton wrote a thorough history. It connects to commonplace books, Zettelkasten, personal wikis. Ward Cunningham built the first wiki in 1995 so knowledge could be linked, editable, and collaborative. Aaron Swartz co-authored RSS 1.0 at 14, helped build Creative Commons, wrote “Who Writes Wikipedia?”, built Open Library. His whole body of work pointed in one direction: knowledge should be portable, collaborative, and public.

A digital garden is a small, personal version of the same idea.

Gwern

Gwern Branwen’s site is the best example I’ve found of what this can look like. Long-form essays with sidenotes so you can add nuance without losing your argument. Metadata on confidence and importance so the reader knows upfront how sure you are. Content that grows over time instead of being published once and forgotten. Everything interlinked. His site treats writing as ongoing research. You can see someone’s actual thinking on display, changing over time, with the uncertainty visible. That’s what I wanted for my technical writing.

Obsidian

Obsidian is the ideal simple reader and note taker. Each note is a file. Each file is a chunk. Wikilinks connect them. The vault is just a folder on your computer. Local markdown files mean if Obsidian disappears tomorrow, you still have your notes. You can open them in any text editor. You can sync them with whatever you want (Git, iCloud, Syncthing, Dropbox). The plugin ecosystem is community-driven. The markdown is standard enough that other tools can read it.

Building your own toolkit

I’m an independent researcher. There are more of us now than there used to be. We have more tools than ever, but having access to tools isn’t the same as having a workflow. Nobody else can put that together for you. You have to figure out how the pieces fit for the way you actually think and work.

A digital garden is part of that. It’s where your research lives in public, connected and growing. It has to be simple enough that you actually use it.

What I built

So I built Mycelium. An Astro 5 theme. One workflow: write in Obsidian, publish with Astro. The src/content/ folder is your Obsidian vault. You write there, the site builds from the same files. No export step, no conversion, no “publish” button that goes through someone else’s server.

Sidenotes in the margin, because thoughts have layers and footnotes break the reading. Confidence and importance ratings in the post header, because not everything I write is equally certain and pretending otherwise is dishonest. Growth indicators that show whether a post is a seedling, budding, or evergreen based on how connected it is, because writing isn’t finished, it’s growing. Link previews on hover. Drop caps.

Wikilinks with Obsidian’s native syntax. Automatic backlinks, because if one chunk links to another, the connection should be visible from both sides. D3.js graph visualization showing how everything connects, because the whole point is that the chunks connect and you should be able to see it. Callout blocks that render the same in Obsidian and on the site.

Beyond that: color themes, a command palette, KaTeX for math, collapsible sections, and the usual static site stuff (RSS, sitemap, OG images). It deploys anywhere static. The full feature list is on the GitHub repo.

Open source

Mycelium is MIT licensed and on GitHub. Version 1.0.0 shipped February 8, 2026. The theme updates separately from your content, and there’s an interactive setup script with sample content that ships as drafts.

The live site is running it.

References

Digital gardens

Open knowledge

Tools