Tools for managing your PhD projects, reading lists, notes, and inspiration.

As a researcher, you have to know everything. But knowledge is useless if it cannot be accessed quickly. An easy-to-use method of archiving information makes taking notes effortless and enjoyable.
As a PhD student in Artificial Intelligence, I use Obsidian (https://obsidian.md) to manage my knowledge.

The article has three parts:

1. What is a note, how to organize notes, tags, folders, and links? This section is tool-agnostic, so you can use most of these ideas with any note-taking app.
2. Instructions for using Obsidian, managing notes, reading lists, and useful plugins. This section demonstrates how I use Obsidian, my preferred knowledge management tool.
3. Workflows: How to use Zotero to take notes from papers, manage multiple projects' notes, create MOCs with Dataview, and more. This section explains how to use Obsidian to solve common scientific problems and manage/maintain your knowledge effectively.

This list is not perfect or complete, but it is my current solution to problems I've encountered during my PhD. Please leave additional comments or contact me if you have any feedback. I'll try to update this article.
Throughout the article, I'll refer to your digital library as your "Obsidian Vault" or "Zettelkasten".
Other useful resources are listed at the end of the article.

1. Philosophy: Taking and organizing notes

Before diving into Obsidian, let's establish a Personal Knowledge Management System and a Zettelkasten. You can skip to Section 2 if you already know these terms.
Niklas Luhmann, a prolific sociologist who wrote 400 papers and 70 books, inspired this section and much of Zettelkasten. Zettelkasten means “slip box” (or library in this article). His Zettlekasten had around 90000 physical notes, which can be found here.
There are now many tools available to help with this process. Obsidian's website has a good introduction section: https://publish.obsidian.md/hub/

Notes

We'll start with "What is a note?" Although it may seem trivial, the answer depends on the topic or your note-taking style. The idea is that a note is as “atomic” (i.e. You should read the note and get the idea right away.
The resolution of your notes depends on their detail. Deep Learning, for example, could be a general description of Neural Networks, with a few notes on the various architectures (eg. Recurrent Neural Networks, Convolutional Neural Networks etc..).
Limiting length and detail is a good rule of thumb. If you need more detail in a specific section of this note, break it up into smaller notes. Deep Learning now has three notes:

• Deep Learning
• Recurrent Neural Networks
  - Convolutional Neural Networks

Repeat this step as needed until you achieve the desired granularity. You might want to put these notes in a “Neural Networks” folder because they are all about the same thing. But there's a better way:

The main issue with folders is that they are not flexible and assume that all notes in the folder belong to a single category. This makes it difficult to make connections between topics.
Deep Learning has been used to predict protein structure (AlphaFold) and classify images (ImageNet). Imagine a folder structure like this:

- /Proteins/ 
     - Protein Folding
- /Deep Learning/
     - /Proteins/ 

Your notes about Protein Folding and Convolutional Neural Networks will be separate, and you won't be able to find them in the same folder.
This can be solved in several ways. The most common one is to use tags rather than folders. A note can be grouped with multiple topics this way. Obsidian tags can also be nested (have subtags).

You can also link two notes together. You can build your “Knowledge Graph” in Obsidian and other note-taking apps like Obsidian.

My Knowledge Graph. Green: Biology, Red: Machine Learning, Yellow: Autoencoders, Blue: Graphs, Brown: Tags.

My Knowledge Graph and the note “Backrpropagation” and its links.

Backpropagation note and all its links

Why use Folders?

Folders help organize your vault as it grows. The main suggestion is to have few folders that "weakly" collect groups of notes or better yet, notes from different sources.
Among my Zettelkasten folders are:

My Zettelkasten's 5 folders

They usually gather data from various sources:

MOC: Map of Contents for the Zettelkasten.
Projects: Contains one note for each side-project of my PhD where I log my progress and ideas. Notes are linked to these.
Bio and ML: These two are the main content of my Zettelkasten and could theoretically be combined.
Papers: All my scientific paper notes go here. A bibliography links the notes. Zotero .bib file
Books: I make a note for each book I read, which I then split into multiple notes.

Keeping images separate from other files can help keep your main folders clean.

I will elaborate on these in the Workflow Section.

My general recommendation is to use tags and links instead of folders.

Maps of Content (MOC) 

Making Tables of Contents is a good solution (MOCs).
These are notes that "signposts" your Zettelkasten library, directing you to the right type of notes. It can link to other notes based on common tags. This is usually done with a title, then your notes related to that title. As an example:

An example of a Machine Learning MOC generated with Dataview.

As shown above, my Machine Learning MOC begins with the basics. Then it's on to Variational Auto-Encoders. Not only does this save time, but it also saves scrolling through the tag search section.
So I keep MOCs at the top of my library so I can quickly find information and see my library. These MOCs are generated automatically using an Obsidian Plugin called Dataview (https://github.com/blacksmithgu/obsidian-dataview).
Ideally, MOCs could be expanded to include more information about the notes, their status, and what's left to do. In the absence of this, Dataview does a fantastic job at creating a good structure for your notes.
In the absence of this, Dataview does a fantastic job at creating a good structure for your notes.

2. Tools: Knowing Obsidian

Obsidian is my preferred tool because it is free, all notes are stored in Markdown format, and each panel can be dragged and dropped. You can get it here: https://obsidian.md/

Obsidian interface. 

Obsidian is highly customizable, so here is my preferred interface:

The theme is customized from https://github.com/colineckert/obsidian-things

Alternatively, each panel can be collapsed, moved, or removed as desired. To open a panel later, click on the vertical "..." (bottom left of the note panel).

My interface is organized as follows:

How my Obsidian Interface is organized.

Folders/Search:
This is where I keep all relevant folders. I usually use the MOC note to navigate, but sometimes I use the search button to find a note.

Tags:
I use nested tags and look into each one to find specific notes to link.

cMenu:
Easy-to-use menu plugin cMenu (https://github.com/chetachiezikeuzor/cMenu-Plugin)

Global Graph:
The global graph shows all your notes (linked and unlinked). Linked notes will appear closer together. Zoom in to read each note's title. It's a bit overwhelming at first, but as your library grows, you get used to the positions and start thinking of new connections between notes.

Local Graph:
Your current note will be shown in relation to other linked notes in your library. When needed, you can quickly jump to another link and back to the current note.

Links:
Finally, an outline panel and the plugin Obsidian Power Search (https://github.com/aviral-batra/obsidian-power-search) allow me to search my vault by highlighting text.

Start using the tool and worry about panel positioning later. I encourage you to find the best use-case for your library.

Plugins

An additional benefit of using Obsidian is the large plugin library. I use several (Calendar, Citations, Dataview, Templater, Admonition):
Obsidian Calendar Plugin: https://github.com/liamcain
It organizes your notes on a calendar. This is ideal for meeting notes or keeping a journal.

Calendar addon from hans/obsidian-citation-plugin
Obsidian Citation Plugin: https://github.com/hans/
Allows you to cite papers from a.bib file. You can also customize your notes (eg. Title, Authors, Abstract etc..)

Plugin citation from hans/obsidian-citation-plugin
Obsidian Dataview: https://github.com/blacksmithgu/
A powerful plugin that allows you to query your library as a database and generate content automatically. See the MOC section for an example.
Allows you to create notes with specific templates like dates, tags, and headings.

Templater. Obsidian Admonition: https://github.com/valentine195/obsidian-admonition
Blocks allow you to organize your notes.

Plugin warning. Obsidian Admonition (valentine195)
There are many more, but this list should get you started.

3. Workflows: Cool stuff

Here are a few of my workflows for using obsidian for scientific research. This is a list of resources I've found useful for my use-cases. I'll outline and describe them briefly so you can skim them quickly.
3.1 Using Templates to Structure Notes
3.2 Free Note Syncing (Laptop, Phone, Tablet)
3.3 Zotero/Mendeley/JabRef -> Obsidian — Managing Reading Lists
3.4 Projects and Lab Books
3.5 Private Encrypted Diary

3.1 Using Templates to Structure Notes

Plugins: Templater and Dataview (optional).
To take effective notes, you must first make adding new notes as easy as possible. Templates can save you time and give your notes a consistent structure. As an example:

An example of a note using a template.

### [[YOUR MOC]]
# Note Title of your note
**Tags**:: 
**Links**::

The top line links to your knowledge base's Map of Content (MOC) (see previous sections). After the title, I add tags (and a link between the note and the tag) and links to related notes.
To quickly identify all notes that need to be expanded, I add the tag “#todo”. In the “TODO:” section, I list the tasks within the note.
The rest are notes on the topic.
Templater can help you create these templates. For new books, I use the following template:

### [[Books MOC]]
# Title
**Author**:: 
**Date::
**Tags:: 
**Links::

A book template example.

Using a simple query, I can hook Dataview to it.

dataview  
table author as Author, date as “Date Finished”, tags as “Tags”, grade as “Grade”  
from “4. Books”  
SORT grade DESCENDING

using Dataview to query templates.

3.2 Free Note Syncing (Laptop, Phone, Tablet)

No plugins used.

One of my favorite features of Obsidian is the library's self-contained and portable format. Your folder contains everything (plugins included).

Ordinary folders and documents are available as well. There is also a “.obsidian” folder. This contains all your plugins and settings, so you can use it on other devices.
So you can use Google Drive, iCloud, or Dropbox for free as long as you sync your folder (note: your folder should be in your Cloud Folder).

For my iOS and macOS work, I prefer iCloud. You can also use the paid service Obsidian Sync.
3.3 Obsidian — Managing Reading Lists and Notes in Zotero/Mendeley/JabRef
Plugins: Quotes (required).

3.3 Zotero/Mendeley/JabRef -> Obsidian — Taking Notes and Managing Reading Lists of Scientific Papers

My preferred reference manager is Zotero, but this workflow should work with any reference manager that produces a .bib file. This file is exported to my cloud folder so I can access it from any platform.

My Zotero library is tagged as follows:

My reference manager's tags

For readings, I usually search for the tags “!!!” and “To-Read” and select a paper. Annotate the paper next (either on PDF using GoodNotes or on physical paper).
Then I make a paper page using a template in the Citations plugin settings:

An example of my citations template.

Create a new note, open the command list with CMD/CTRL + P, and find the Citations “Insert literature note content in the current pane” to see this lovely view.

Citation generated by the article https://doi.org/10.1101/2022.01.24.22269144

You can then convert your notes to digital. I found that transcribing helped me retain information better.

3.4 Projects and Lab Books

Plugins: Tweaker (required).
PhD students offering advice on thesis writing are common (read as regret). I started asking them what they would have done differently or earlier.

Time management requires planning. Keeping track of multiple projects and lab books is difficult during a PhD. How I deal with it:

• One folder for all my projects
• One file for each project
  I use a template to create each project

### [[Projects MOC]]  
# <% tp.file.title %>  
**Tags**::  
**Links**::  
**URL**::  
**Project Description**::## Notes:  
### <% tp.file.last_modified_date(“dddd Do MMMM YYYY”) %>  
#### Done:  
#### TODO:  
#### Notes

You can insert a template into a new note with CMD + P and looking for the Templater option.

I then keep adding new days with another template:

### <% tp.file.last_modified_date("dddd Do MMMM YYYY") %>  
#### Done:  
#### TODO:  
#### Notes:

This way you can keep adding days to your project and update with reasonings and things you still have to do and have done. An example below:

Example of project note with timestamped notes.

3.5 Private Encrypted Diary

This is one of my favorite Obsidian uses.
Mini Diary's interface has long frustrated me. After the author archived the project, I looked for a replacement. I had two demands:

1. It had to be private, and nobody had to be able to read the entries.
2. Cloud syncing was required for editing on multiple devices.

Then I learned about encrypting the Obsidian folder. Then decrypt and open the folder with Obsidian. Sync the folder as usual.
Use CryptoMator (https://cryptomator.org/). Create an encrypted folder in Cryptomator for your Obsidian vault, set a password, and let it do the rest.
If you need a step-by-step video guide, here it is:

Conclusion

So, I hope this was helpful!
In the first section of the article, we discussed notes and note-taking techniques. We discussed when to use tags and links over folders and when to break up larger notes.
Then we learned about Obsidian, its interface, and some useful plugins like Citations for citing papers and Templater for creating note templates.
Finally, we discussed workflows and how to use Zotero to take notes from scientific papers, as well as managing Lab Books and Private Encrypted Diaries.
Thanks for reading and commenting :)

Read original post here

[06/20/2022 update] We have now implemented a powerful text editor, but you can still use markdown.

Markdown:

Headers

SYNTAX:

# This is a heading 1
## This is a heading 2
### This is a heading 3 
#### This is a heading 4

RESULT:

This is a heading 1

This is a heading 2

This is a heading 3

This is a heading 4

Emphasis

SYNTAX:

**This text will be bold**
~~Strikethrough~~
*You **can** combine them*

RESULT:

This text will be italic
This text will be bold
You can combine them

Images

SYNTAX:

![Engelbart](https://history-computer.com/ModernComputer/Basis/images/Engelbart.jpg)

RESULT:

Videos

SYNTAX:

https://www.youtube.com/watch?v=7KXGZAEWzn0

RESULT:

Links

SYNTAX:

[Int3grity website](https://www.int3grity.com)

RESULT:

Int3grity website

Tweets

SYNTAX:

https://twitter.com/samhickmann/status/1503800505864130561

RESULT:

Blockquotes

SYNTAX:

> Human beings face ever more complex and urgent problems, and their effectiveness in dealing with these problems is a matter that is critical to the stability and continued progress of society. \- Doug Engelbart, 1961

RESULT:

Inline code

SYNTAX:

Text inside `backticks` on a line will be formatted like code.

RESULT:

Text inside backticks on a line will be formatted like code.

Code blocks

SYNTAX:

'''js
function fancyAlert(arg) {
if(arg) {
$.facebox({div:'#foo'})
}
}
'''

RESULT:

function fancyAlert(arg) {
  if(arg) {
    $.facebox({div:'#foo'})
  }
}

Maths

We support LaTex to typeset math. We recommend reading the full documentation on the official website

SYNTAX:

$$[x^n+y^n=z^n]$$

RESULT:

[x^n+y^n=z^n]

Tables

SYNTAX:

| header a | header b |
| ---- | ---- |
| row 1 col 1 | row 1 col 2 |

RESULT:

header a	header b	header c
row 1 col 1	row 1 col 2	row 1 col 3

Photo by Juanjo Jaramillo on Unsplash

Calling APIs is the most common thing to do in any modern web application. When it comes to talking with an API then most of the time we need to do a lot of repetitive things like getting data from an API call, handling the success or error case, and so on.

When calling tens of hundreds of API calls we always have to do those tedious tasks. We can handle those things efficiently by putting a higher level of abstraction over those barebone API calls, whereas in some small applications, sometimes we don’t even care.

The problem comes when we start adding new features on top of the existing features without handling the API calls in an efficient and reusable manner. In that case for all of those API calls related repetitions, we end up with a lot of repetitive code across the whole application.

In React, we have different approaches for calling an API. Nowadays mostly we use React hooks. With React hooks, it’s possible to handle API calls in a very clean and consistent way throughout the application in spite of whatever the application size is. So let’s see how we can make a clean and reusable API calling layer using React hooks for a simple web application.

I’m using a code sandbox for this blog which you can get here.

import "./styles.css";
import React, { useEffect, useState } from "react";
import axios from "axios";

export default function App() {
  const [posts, setPosts] = useState(null);
  const [error, setError] = useState("");
  const [loading, setLoading] = useState(false);

  useEffect(() => {
    handlePosts();
  }, []);

  const handlePosts = async () => {
    setLoading(true);
    try {
      const result = await axios.get(
        "https://jsonplaceholder.typicode.com/posts"
      );
      setPosts(result.data);
    } catch (err) {
      setError(err.message || "Unexpected Error!");
    } finally {
      setLoading(false);
    }
  };

  return (
    <div className="App">
      <div>
        <h1>Posts</h1>
        {loading && <p>Posts are loading!</p>}
        {error && <p>{error}</p>}
        <ul>
          {posts?.map((post) => (
            <li key={post.id}>{post.title}</li>
          ))}
        </ul>
      </div>
    </div>
  );
}

I know the example above isn’t the best code but at least it’s working and it’s valid code. I will try to improve that later. For now, we can just focus on the bare minimum things for calling an API.

Here, you can try to get posts data from JsonPlaceholer. Those are the most common steps we follow for calling an API like requesting data, handling loading, success, and error cases.

If we try to call another API from the same component then how that would gonna look? Let’s see.

500: Internal Server Error

Now it’s going insane! For calling two simple APIs we’ve done a lot of duplication. On a top-level view, the component is doing nothing but just making two GET requests and handling the success and error cases. For each request, it’s maintaining three states which will periodically increase later if we’ve more calls.

Let’s refactor to make the code more reusable with fewer repetitions.

Step 1: Create a Hook for the Redundant API Request Codes

Most of the repetitions we have done so far are about requesting data, handing the async things, handling errors, success, and loading states. How about encapsulating those things inside a hook?

The only unique things we are doing inside handleComments and handlePosts are calling different endpoints. The rest of the things are pretty much the same. So we can create a hook that will handle the redundant works for us and from outside we’ll let it know which API to call.

500: Internal Server Error

Here, this request function is identical to what we were doing on the handlePosts and handleComments. The only difference is, it’s calling an async function apiFunc which we will provide as a parameter with this hook. This apiFunc is the only independent thing among any of the API calls we need.

With hooks in action, let’s change our old codes in App component, like this:

500: Internal Server Error

How about the current code? Isn’t it beautiful without any repetitions and duplicate API call handling things?

Let’s continue our journey from the current code. We can make App component more elegant. Now it knows a lot of details about the underlying library for the API call. It shouldn’t know that. So, here’s the next step…

Step 2: One Component Should Take Just One Responsibility

Our App component knows too much about the API calling mechanism. Its responsibility should just request the data. How the data will be requested under the hood, it shouldn’t care about that.

We will extract the API client-related codes from the App component. Also, we will group all the API request-related codes based on the API resource. Now, this is our API client:

import axios from "axios";

const apiClient = axios.create({
  // Later read this URL from an environment variable
  baseURL: "https://jsonplaceholder.typicode.com"
});

export default apiClient;

All API calls for comments resource will be in the following file:

import client from "./client";

const getComments = () => client.get("/comments");

export default {
  getComments
};

All API calls for posts resource are placed in the following file:

import client from "./client";

const getPosts = () => client.get("/posts");

export default {
  getPosts
};

Finally, the App component looks like the following:

import "./styles.css";
import React, { useEffect } from "react";
import commentsApi from "./api/comments";
import postsApi from "./api/posts";
import useApi from "./hooks/useApi";

export default function App() {
  const getPostsApi = useApi(postsApi.getPosts);
  const getCommentsApi = useApi(commentsApi.getComments);

  useEffect(() => {
    getPostsApi.request();
    getCommentsApi.request();
  }, []);

  return (
    <div className="App">
      {/* Post List */}
      <div>
        <h1>Posts</h1>
        {getPostsApi.loading && <p>Posts are loading!</p>}
        {getPostsApi.error && <p>{getPostsApi.error}</p>}
        <ul>
          {getPostsApi.data?.map((post) => (
            <li key={post.id}>{post.title}</li>
          ))}
        </ul>
      </div>
      {/* Comment List */}
      <div>
        <h1>Comments</h1>
        {getCommentsApi.loading && <p>Comments are loading!</p>}
        {getCommentsApi.error && <p>{getCommentsApi.error}</p>}
        <ul>
          {getCommentsApi.data?.map((comment) => (
            <li key={comment.id}>{comment.name}</li>
          ))}
        </ul>
      </div>
    </div>
  );
}

Now it doesn’t know anything about how the APIs get called. Tomorrow if we want to change the API calling library from axios to fetch or anything else, our App component code will not get affected. We can just change the codes form client.js This is the beauty of abstraction.

Apart from the abstraction of API calls, Appcomponent isn’t right the place to show the list of the posts and comments. It’s a high-level component. It shouldn’t handle such low-level data interpolation things.

So we should move this data display-related things to another low-level component. Here I placed those directly in the App component just for the demonstration purpose and not to distract with component composition-related things.

Final Thoughts

The React library gives the flexibility for using any kind of third-party library based on the application’s needs. As it doesn’t have any predefined architecture so different teams/developers adopted different approaches to developing applications with React. There’s nothing good or bad. We choose the development practice based on our needs/choices. One thing that is there beyond any choices is writing clean and maintainable codes.