Building a Second Brain


Building a Second Brain is about creating a reliable system – outside your physical skin-and-bone bodily boundaries – for storing, organising, digesting, and eventually transforming information into Good Creative Output.

Much like any well-integrated tool, I am currently using Emacs Org Mode as Second Brain core tool. This system also includes many other peripheral components that make up the complete Second Brain system.

I will follow the below overview diagram introducte each components one by one.


  1. Emacs/Getting Started with Doom Emacs

Org-mode modules


  • Task management (pomodoro method; time-blocking)
  • Time management (appointments; time-blocking)

TODO’s and tags

  • These are identifiers in an org-file as tasks or reminders.
  • The types of TODO’s can either be set globally in your init file, or they can be file/buffer specific.
  • They are created as a subtree (think ‘heading’), or in-line (‘org-inlinetask).
  • You can assign deadlines, scheduled date and time, active timestamps, and inactive timestamps


These are customizable org-headings that you can create on-the-go. They can be regular TODO’s or just notes.


Populates all your TODO’s and appointments into a singular view. Default is week-view. Using org-super-agenda, I set up my agenda as a daily view with appointments, deadlines, and a habit tracker.


Another way of accessing your TODO’s that are outside of your agenda. I am using it to keep my project-specific TODO’s in the main project org file.



A note-taking package that replicates Roam Research which is based on the Zettelkasten method. I use it to build my literature review and I use org-roam-server to visualize my notes into a network. It builds on the strength of org-mode’s hyperlinking properties.


Utilizes a combination of org-ref, helm-bibtex, and bibtex-completion to streamline note-taking workflow with references within the org-roam ecosystem.


I use it to annotate PDFs and take notes within the same buffer.

  • Works extremely well with PDF-tools.
  • org-noter-create-skeleton


An effective way of “copy/pasting” text from one org file (let’s say an org-roam note or a section of your thesis/dissertation) into your main org file. It will export all the transcluded text. Sort of equivalent to “#+INCLUDE:”

Reference Management

Research/Getting Started with Zotero