Dilip's Log

OBTF as Second Brain with Org mode

Sat, 06 Sep 2025 00:00:00 +0000

One Big Text File is simply writing down mostly everything in single file to organize or manage data. This single file acts as the source of knowledge and holds all notes.

Second brain has been a buzz word, thanks to the sourcing of Zettelkasten method, every productivity freak is on the stance to organize their life and get things done.

But I soon came to the conclusion by reading many blogs and reddit discussions that, searching is far superior than organizing. On internet all we do is search for information, and not organize or build system just to get info. This is how note taking should work as well. Just for efficient retrieval and storage.

Thanks to my introduction to emacs and getting deep into rabbit hole, Org mode has been the great tool to handle plain text file as an Organization platform. Just like emacs (OS), Org mode can also be extended to endless limit (I dare say it). If emacs is OS, Org mode is for me Init system (systemd).

You can read more about my note taking journey in this post.

This context is also written in favor to post it on r/obtf

Org mode is the best tool for managing OBTF

Many popular workflow would go by simple format as bullet points with Time date and info, and regexp based searching via CLI (rg, vim, grep, sed…. bash scripts)

Org mode has many bells and whistles (features) that aid in this method. Tags, integration with commands and rich source of documentation (one of the best things of Emacs or org mode). Thanks to emacs and protesilaos stavrou I learnt how important are documentation and writing sensible notes. It means alot for future self to recognize and re-instantiate the thoughts and state.

Org mode has an datetree method which has file heading hierarchy in the Year > Month > Day and 4th nested heading follows any notes.

 * 2022
 ** 2022-10 October
 *** 2022-10-07 Friday
 *** 2022-10-08 Saturday
 **** <Any notes I'm capturing> :tag1:tag2:

This gives out the leverage of journaling, but also a lazy man's organization. I use tagging extensively to most of the (4th) heading based on context so as to narrow down to filter.

 # learning notes --- l@
 #+tags: l@coding l@emacs l@bioinfo l@nix l@bash l@julia l@rstats l@python l@devnote l@latex l@til

 # generic notes to remember or readme --- n@
 #+tags: n@linux n@shell n@cli n@book n@idea

 # projects --- p@
 #+tags: p@webcli p@cyanate p@scitomep

These tag help to categorize the heading in some (lazy) way

Org mode has org-sparse-tree bound to C-c / which helps to narrow down based on tag or property. Also another emacs package consult helps to take it up further via consult-line and consult-org-heading along with org-ql package. Org mode also has #+select_tags to export headings to file.

 #+select_tags: r@book

With that we can C-c C-e (org-export-dispatch) and press "O O" (make sure org is in org-export-backends) to get temporary Org buffer only with those heading. This logically acts as an individual file with that tag/category, thus being atomic in my sense. Org-sparse-tree might also be same.

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Key takeaways

whatever the system or the tool is, the main takeaways every resource provides is to review the notes and write it for future self. Every capture is to review back and make the fleeting note into and rich information. This OBTF with org mode satisfies that needs given that user reviews the notes and visits back to digest it again.

My MSc journey with Emacs Orgmode

Fri, 06 Jun 2025 00:00:00 +0000

I wrote and used emacs orgmode for all of my post-grad Masters classes, presentations, projects and thesis.

Before post-grad itself I was introduced to Emacs world and enjoyed getting good with it. As I used it, I realized emacs is not just an text editor, its an Personal Development Environment itself and user has power to craft it as they need. This was a worthwhile investment.

My initial plan when I started Masters (Bioinformatics) was to fully stay organized and be productive. I was a freak at this, I was reading up many blogs and digesting discussion on being productive. I even read books such as,

Getting things Done
How to Smart notes by Sonke Ahrens Introduces on Zettelkasten note-taking system. Although hyped up, I believe system does not function as brain.
Deep Work by Cal Newport Insights on focused working and being distraction-less.
Second Brain by Tiago Forte Again, whole thing about Zettelkasten. Popularized the term "Second brain" itself.
Atomic Habits by James Clear Mentions on starting habits in small steps.
A system for Writing by Bob Doto Latest book, emphasis on above all books and zettelkasten.

I could have been an normie student like others and be at ease, but why did I choose to burden with Emacs and Orgmode..?

I valued investment and growth. I could see the development and learning of skills compared to working with traditional GUI applications.

Note taking

Note-taking is understandable, its just format of text to store and read. And org-mode was superior and helped me alot. I later on embraced single big org file, and started using tags heavily with context based tagging.

t -> task; t@shop t@meeting t@work
p -> project; p@plan p@lncrna p@thesis
l -> learn; l@nix l@python

So on which really helps with narrowing using consult package and org-ql for querying. I eventually formed my own second brain with org mode like an zettelkasten system. This became my personal knowledge management (PKM) as well which empowered me to stay organized.

Reports/Doc

Org mode can produce pdf via latex or ODT/docx format. That eventually guided me for submission of assignments and documents for sharing. Although it was an hassle to get formatting correct as they instructed, where as others just did them in breeze via M$ word and AI crap generated.

Although there was not much work with reports, I had good workflow of storing notes and working with integration and stayed organized.

Presentations

I thought to give presentations in Emacs editor itself, but that did not make the cut for required normie friendly slides. The magically I came across revealJS and observed many people in tech presentations and talks used them. There was active development of org-reveal package as well, in new form from OER gitlab repo.

This workflow was definitely more painful, to get as they expect. The default works, but tweaking were more. But revealjs and org package provided many options and it sufficed for completing the setup along with power of HTML and CSS.

I had local.scss file for color and designing slides, and org generated html files.

Thesis

The final saga of the journey, since thesis takes time to write, I thought to not bother with complicating this task. My initial thought was to either use Latex, if it was too much headache then simply follow given docx format file and write. Thankfully there was another player getting really popular, a new typesetting "Typst". It did the magic and wonders.

The syntax and process was very robust and simple. The documentation was standard and was simple enough to grasp and tweak everything. And here was well someone had made basic org export support for typst format. Although IMHO typst syntax is so easy to understand and I loved to write and learn the syntax. Workflow was bliss with it, I wonder why I did not discover it earlier. Maybe I'm not a mathematician to have it for demand, but it was a good skill to have it in my hands.

Conclusion

The main draw from this experience was that investing in tools that allow extending and allow programming to customize and tweak as I require was a major win and good rewards. These were added up skills that makes working with related tasks a breeze ahead.