Skip to main content

My custom second brain setup, part 1: Why go custom?

Building a second brain last year had the biggest impact on my productivity, learning, and organization in my entire career. It led to many of the successes I covered in my 2022 year in review and provided incredible value in my work, self development, and creative output.

What is a second brain?

A second brain is a productivity system that gives focus, structure, and actionability to all the information we encounter in our lives.

It acts as a central store for all areas of your professional and personal life. By getting all information out of your head, you can keep your "working memory" clean, which is calming and leads to clearer thinking.

A second brain follows the CODE (Capture, Organize, Distill, Express) workflow:

  1. Capture
    • Highlight or take notes on the most relevant, interesting, and impactful information from source materials (articles, books, videos, podcasts, etc.)
    • Write down any ideas or tasks as you think of them to get them out of your head
  2. Organize
    • Structure this information based on actionability
  3. Distill
    • Use progressive summarization to refine highlights and notes down to the essential details and most novel ideas
  4. Express
    • Recombine existing ideas and generate new ones to create meaningful work

My second brain setup needs to account for this full process with as little complexity and overhead as possible.

Most people build their second brain using a productivity/knowledge management app like Evernote, Notion, Obsidian, or Roam, sometimes with multiple layers of other services and integrations that support a complex CODE workflow.

With so many great options, some of which are completely free, why build a custom setup?

Past pains and lock-in

I've been burnt by lost data. A few years ago, a collection I maintained with over 15 years of my past writing vanished suddenly from my Google Drive. This happened without a trace, not even appearing in my file history or trash, and could not be recovered. That was a deeply painful experience that discouraged me from writing much at all for nearly 2 years.

I've also lost a lot of time migrating between tools repeatedly due to pricing and plans changing suddenly, companies going out of business or being acquired, and other stressful experiences.

I first drafted my second brain in 2021 using Notion and quickly felt locked in. I was also frustrated by how long the app took to load, poor offline support, and block limits as the pricing structure changed. When I migrated off Notion to my custom setup, the process was tedious. Even going from Notion's flavor of Markdown to standard Markdown required a fair bit of manual conversion and per-file review.

These apps work for many people and not everyone needs to build a custom second brain. Lock-in happens to varying degrees with any paid service. For some people, those tradeoffs are totally worth it. Sometimes a level of lock-in provides even provides convenience within an ecosystem, but it's not a good fit for me.


My second brain needed to have the following qualities:

  • Quick and easy to access
  • Simple
  • Efficient
  • Lightweight
  • Secure
  • Easy to maintain
  • Independent of specific companies or services
  • Flexible
  • Fully works offline
  • Convenient editing and syncing across my devices

Existing options

I'm not interested in Evernote, and moved away from Notion.

Obsidian and Roam are other interesting options that have free plans. They offer intricate relational graphs, backlinks, and other power features are probably great for abstract thinkers, but the interfaces and interactions are definitely more complex as well. They both have mobile apps, which is a plus, but I'm hesitant about long-term lock-in.

If I had to pick an existing tool, I'd probably go with Dendron. It's an impressive open-source project that adds knowledge management features directly into VSCode. Some features even match Obsidian and Roam, such as the relational graphs that connect topics across notes. These features are more complex than what I need, but seem pretty optional. The main downside of Dendron is the lock-in with VSCode and lack of mobile editing. I use VSCode, but have considered using VIM directly in the terminal. So VSCode may not always be my editor, and I need a way to edit my second brain from my phone.

After evaluating all the existing options, I was craving more flexibility, efficiency, and simplicity than what was available.

Time to go custom

Often people build custom tools to have features that don't exist, or to support nuanced, intricate workflows. In my case, I actually wanted the opposite: strip out as much complexity, overhead, and outsourcing as possible so I can enjoy a simple, focused, portable second brain setup.

In the next post in this series, I'll detail the tools I use for each of the Capture, Organize, Distill, and Express steps of the CODE workflow. In following posts, I'll then cover my minimal productivity process using my custom second brain setup, and wrap things up by covering the limitations of my setup that are actually some of its main strengths.

Next: part 2: How it works.