Skip to main content

My custom second brain setup, part 2: How it works

To explain how my custom second brain setup works, I'm going to break down the tools I use for each of the steps in the CODE (Capture, Organize, Distill, Express) workflow.

Brace yourself: the core of my setup is so simple and minimal that you might be disappointed. This simplicity is absolutely intentional and the result of very careful consideration and continuous improvement.

Tools for Capture


I use Readwise Reader to save articles, subscribe to RSS feeds, and add highlights and notes. Readwise (the main app) provides a convenient Markdown export that provides all the highlights and notes since the last export.


I primarily read eBooks using a Kindle. Even though I enjoy reading paper books more, eBooks are so much more efficient for highlighting and capturing notes. I also use Readwise to export my Kindle highlights into Markdown.

When I do want to make notes or highlights in paper books, I'll read at my computer and transcribe any interesting text as I'm reading. This isn't the most ergonomic workflow, as books rarely stay open when I set them down to type, and transcription is tedious and slower than eBook highlights, so I don't really like this workflow. However, it's necessary for books that are only available in print. I may build a compact bookstand that can accommodate books of any size and holds the pages open. Handheld scanners with a pen form factor are a thing, but I don't know how well these work. That could be a viable solution, though.

Videos, podcasts, audiobooks, and other sources

For video and audio content, there's no efficient way (that I'm aware of) to capture snippets of audio as a "highlight" or auto-transcribe a selected portion. It'd be interesting if there are solutions to this, but I don't mind keeping things more manual and low-tech. This little bit of friction is actually a positive, as only the best information feels worth the effort to capture.

I usually watch educational videos on my computer, so I just add notes directly in my second brain as needed.

I'm usually not at my computer when listening to podcasts, so I just pause and make a note to re-listen to the podcast when I'm at my computer. Or better yet, find a transcript that I can save and highlight as if it's an article (going through Readwise Reader and then Readwise for exporting to Markdown). If you have a podcast, please provide transcripts! They're essential for accessibility and benefit anyone who wants to make notes or highlights.

Audiobooks have similar limitations, but I'll usually just get the eBook version if I like the audiobook, and re-read it while making highlights and notes (going through my Kindle and then Readwise for exporting to Markdown).

Voice notes

I use the built-in Recorder app on Android to capture voice notes that auto-generate fairly accurate transcriptions. While this is handy for dictating ideas while I'm driving, for example, it requires some manual migration, and the transcripts aren't as succinct as my written notes or highlights, so they usually require more reworking and trimming to be useful.

Tools for Organize

My second brain: just files and folders

My second brain is just a collection of Markdown files that use Git for version control. These files are structured with folders that follow the PARA (Projects, Areas, Resources, Archive) method:

  1. 00-inbox
    • Default for new notes to be processed later
    • for loose, day-to-day tasks not tied to any project
    • for capturing random thoughts that can be organized and refined later
    • for groceries or anything I need to buy in town
  2. 01-projects
    • Active projects across work and personal life (try to limit to a max of 7)
  3. 02-areas
    • Ongoing areas of interest or processes with a standard to maintain
  4. 03-resources
    • Reference information that's not tied to an ongoing area of effort
  5. 04-archive
    • Information that's no longer relevant or actionable, but can always be promoted again if it's useful

Version control and syncing

With Git for version control, I can easily back up and sync my second brain across many devices. I have full flexibility of using any combination of local storage, automatic file backups, GitHub, GitLab, etc. for safe keeping and redundancy.

I also find the security of version control services like GitHub and GitLab to be much more robust and dependable than self-rolled solutions from productivity apps.

Editing notes on the computer

Because my second brain is just a simple version-controlled folder structure, I can use the same tools I use for coding, which really speeds up my productivity.

For me, that's VSCode with a VIM plugin for efficient editing and searching.

Whenever I'm using my computer, I always have an instance of VSCode with my second brain open and at the ready. No logins needed.

At the Markdown file level, I use standard Markdown syntax, with the occasional table. The only custom thing I do is simple frontmatter in each file with created and modified dates:

created: YYYY-MM-DD
modified: YYYY-MM-DD

This is easy to add with a Markdown snippet I created in VSCode that I invoke with /top and autocomplete:

In markdown.code-snippets:

"Markdown frontmatter": {
	"prefix": "/top",
	"body": [
		"created: $1",
		"modified: $1",
		"# $0"
	"description": "Default frontmatter"

Editing notes on mobile

I edit notes on mobile using the Git Journal app.

I configured Git Journal to name all new files to by default. Traversing folders in Git Journal isn't the easiest, so by default it stores all new notes in the 00-inbox folder, which I can organize later when I'm working on a computer.

Git Journal automatically adds and updates the created and modified timestamps in frontmatter for each file, which matches my manual process.

Git Journal works well overall. Managing folders and files is a little clunky, so I organize them later when I'm at my computer. It does have a custom toolbar with some WYSIWYG options, but I'd really like to have dedicated indent/outdent buttons.

Tools for Distill

Progressive summarization is an efficient way to distill highlights and notes down to the most interesting and impactful information. It's an iterative process that involves 3 passes of using text formatting to highlight certain text with increasing levels of emphasis.

In an app like Evernote or Notion, this may involve the following passes:

  1. First pass: bold the most important text
  2. Second pass: underline the most important bolded text
  3. Third pass: highlight (add a background color to) the most important underlined and bolded text

The result of this third pass is often less than 10% of the original highlights and notes. Since highlights are often 10% or less of the original source information, the output of progressive summarization is the most essential 1% of ideas that offer the majority of value.

Since all my notes are authored in Markdown, I can use its simple syntax for progressive summarization:

  1. First pass: italicize with * (*idea to highlight*)
  2. Second pass: bold with ** (**idea to highlight**)
  3. Third pass: bold and italicize with *** (***idea to highlight***)

This syntax is easy to type, and just so happens to visually indicate the level of importance with 1, 2, or 3 asterisks (*), even when viewing Markdown as plain text.

Tools for Express

The main channels I use to express new ideas and content are my personal blog and my YouTube channel, with some very light posting to social media.

My personal site uses 11ty with Markdown for posts, so I draft all posts in my second brain and copy them into my site's codebase when I'm ready to publish. All I need to do for publishing is add some frontmatter for meta information (title and description), sprinkle in some WebC components if needed, and a published date. Then, I simply commit it up to trigger a new build. It's critical that this process requires only a couple minutes of work to go from finished draft to published post.

For other channels, my second brain has substantially accelerated my learning and creative output with so much valuable information and thoughts to build upon. I can quickly search my notes for ideas across a topic, rework them as an outline for a video or as a quick social post, and then create the final content.

Alongside authoring written content in Markdown, I've experimented with dictating blog post drafts using Recorder for Android or, but this has been less efficient for me. Exporting text from these tools and manually formatting into more structured Markdown content is tedious. And, although I largely have aligned my speaking voice and writing voice over the last few years, my off-the-cuff dictating isn't as well structured and sequenced as my writing, so it requires a lot more editing to get from initial draft to finished post.

I can probably improve on this with more detailed outlines before dictating content, but I'm more likely just to just write directly. I might refocus my dictating experiments into recording podcast episodes or YouTube videos in the future instead.

All together

Here are all the tools that compose my second brain setup:

  • Kindle (eBook highlights and notes)
  • Readwise Reader (article highlights and notes)
  • Readwise (export highlights and notes to Markdown)
  • VSCode (creating and editing notes)
  • Recorder (Android app for voice recording)
  • Git Journal (creating and editing notes on mobile)
  • Git (version control)
  • Git repository hosting and automatic file backup services (use multiple for redundancy, privacy, and security)

At its core, my second brain really is just a collection of Markdown files in folders, with my text editor (VSCode) as the primary tool. A key attribute of this setup is I can use any text editor to edit and maintain my second brain, and I can store it anywhere. I can structure everything to suit my needs, and any conventions are purely of my own choosing. For me, this simplicity offers pretty much everything I could want.

In the remaining posts in this series, I'll cover my minimal productivity process using my custom second brain setup, and then wrap things up by covering the limitations of my setup that are actually some of its main strengths.

Next: part 3: Minimalist productivity.