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https://github.com/robertmartin8/MolecularNotes

My Obsidian Second Brain setup
https://github.com/robertmartin8/MolecularNotes

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My Obsidian Second Brain setup

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README 

        
![logo](http://reasonabledeviations.com/assets/images/secondbrain1/logo_big.png)



This repository contains my Obsidian implementation of **Molecular Notes** – a Second Brain system that I use to organise my thinking. You can read about the philosophy of Molecular Notes [here](https://reasonabledeviations.com/2022/04/18/molecular-notes-part-1/) and more about the Obsidian implementation [here](https://reasonabledeviations.com/2022/06/12/molecular-notes-part-2/)).



**Note:** I am not accepting PRs as this repo represents my personal workflow. *However*, if you have a use case that the current iteration of MolecularNotes doesn't address, it would be awesome if you could [create an issue](https://github.com/robertmartin8/MolecularNotes/issues) and share the modification you made so that others can get some inspiration!



## Basic setup instructions



1. Install [Obsidian](https://obsidian.md/) and create an Obsidian Vault (a folder to store all your notes). Mine is named `ObsidianVault` and I put it in my home folder.

2. Clone this repository into your vault (on GitHub click the green `Code` button, then `Download ZIP`, and copy-paste the contents into your vault using Finder or File explorer)

3. Delete the README.md file.

4. In Obsidian, go to Settings -> Files & Links -> Default location for new attachments -> _attachments  (make this folder if it doesn't exist).

5. Set up templates:

	1. Settings -> Core plugins -> Templates (switch on). 

	2. Settings -> Templates -> Template folder location -> _templates.

	3. (Optional) set hotkey in Settings -> Hotkeys -> Templates: Insert Template -> ⌘T

6. Check you have the below plugins enabled: Settings -> Core Plugins

7. (Optional) Change the colour theme to something you like! You can find this in Settings -> Appearance -> Themes



### Plugins



These are the core plugins I am using (most are enabled by default):



- File explorer: duh

- Search: duh 

- Quick switcher: a very useful way of quickly jumping to a new note: you just press ⌘O then start typing the note name to jump to it.

- Graph view: duh

- Backlinks / Outgoing links: duh

- Tag pane: a helpful way of looking at your tags

- Page preview: nice syntax

- Templates: a must

- Note composer: I have this but I've only used it rarely

- Command palette: a must

- Starred: a new-ish plugin that helps you save common searches

- Markdown format importer: useful in my workflows to paste Notion content into Obsidian

- Word count: up to you

- Workspaces: handy! I've saved a note view and a graph view.

- Sync: optional but I like it



Community plugins:



- Mind Map: occasionally useful to visualise notes as a mindmap

- Obsidian git: I like having an extra backup to a private github

- Tag wrangler: very useful extension for renaming tags



## Advanced setup



Make sure you have python 3 installed on your system. The helper script can be run from your Obsidian Vault:



```

cd ObsidianVault && python _scripts/obsidian_util.py

```



In my `~/.zshrc` I then created an alias for this, such that when I type `obsidian` into terminal my script runs. 



```

alias obsidian="cd $HOME/ObsidianVault && python _scripts/obsidian_util.py"

```



### Polymer dashboard



The Polymer dashboard (a spaced repetition tool) requires `streamlit` to be installed (`pip install streamlit`). It can be run using:



```

cd ObsidianVault && streamlit run _scripts/polymer.py

```



If you are having trouble with Polymer, please follow the below steps:



1. Shut down the dashboard (e.g ctrl-C wherever you ran `streamlit run _scripts/polymer.py`)

2. Delete the `_scripts/db.json` file. **Note:** this will delete your current flashcard progress

3. Re-run the dashboard



### GPT embeddings



See [this blog post](https://reasonabledeviations.com/2023/02/05/gpt-for-second-brain/) for more information.



`_scripts/gpt_search.py` implements a smart search. To get it working:



1. Install the dependencies: `pip install openai tiktoken tenacity click tabulate`.

2. Put in your OpenAI key at the top of the file.

3. Open terminal and create an alias. My tool is called `nmr` but you can call it something else. 



```

alias nmr="cd $HOME/ObsidianVault && python _scripts/gpt_search.py"

```



## Organising my Second Brain



The ideas behind this are discussed in the blog posts, but here is a reference.



### Folders



- Underscore folders represent Obsidian internals

- `Topics` stores Topic types for faster browsing

- `Sources` contains my notes on any information media: books, articles, videos etc

- `Molecules` contains my personal observations/ideas/thoughts

- `Authors` are Source note authors.

- Atoms go in the top level



### Tags



I use tags to represent "is-a" relations (i.e types)



- Core types:

	- atom: the base note type for an individual piece of knowledge derived from a source

	- molecule: my own observation – a permanent note

	- topic: used to signify that a note is a category placeholder

	- author: the creator of a piece of content

	- todo: something I need to fill in

	- project: a long-term project

- Source types:

	- book

	- article: e.g blog post, web article

	- post: social media / forum

	- academic: textbook, journal article

	- video

	- podcast

	- primer (e.g sellside)

	- presentation

	- course 

- Atom types:

	- tool: something that I can use to solve a problem

	- cognitive-bias

	- framework: a way of thinking about the world

	- school-of-thought: a historical school of thought

	- theorem: a mathematical law

	- person: someone of note

	- event: a historical event

	- amusing: a popular saying, aphorism, "law"

	- heuristic: a "common wisdom" way of doing something

	- trading-strat: a trading strategy

	- instrument: a financial instrument