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 :)

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Maybe you'll work for a DAO next! Over $1 Billion in NFTs in the Flamingo DAO Another DAO tried to buy the NFL team Denver Broncos. The UkraineDAO raised over $7 Million for Ukraine. The PleasrDAO paid $4m for a Wu-Tang Clan album that belonged to the “pharma bro.”
DAOs move billions and employ thousands. So learn what a DAO is, how it works, and how to create one!

DAO? So, what? Why is it better?

A Decentralized Autonomous Organization (DAO). Some people like to also refer to it as Digital Autonomous Organization, but I prefer the former.
They are virtual organizations. In the real world, you have organizations or companies right? These firms have shareholders and a board. Usually, anyone with authority makes decisions. It could be the CEO, the Board, or the HIPPO. If you own stock in that company, you may also be able to influence decisions. It's now possible to do something similar but much better and more equitable in the cryptocurrency world.

This article informs you:

DAOs- What are the most common DAOs, their advantages and disadvantages over traditional companies? What are they if any?
Is a DAO legally recognized?
How secure is a DAO?
I’m ready whenever you are!

A DAO is a type of company that is operated by smart contracts on the blockchain. Smart contracts are computer code that self-executes our commands. Those contracts can be any. Most second-generation blockchains support smart contracts. Examples are Ethereum, Solana, Polygon, Binance Smart Chain, EOS, etc. I think I've gone off topic. Back on track.   Now let's go!
Unlike traditional corporations, DAOs are governed by smart contracts. Unlike traditional company governance, DAO governance is fully transparent and auditable. That's one of the things that sets it apart. The clarity!
A DAO, like a traditional company, has one major difference. In other words, it is decentralized. DAOs are more ‘democratic' than traditional companies because anyone can vote on decisions. Anyone! In a DAO, we (you and I) make the decisions, not the top-shots. We are the CEO and investors. A DAO gives its community members power. We get to decide.
As long as you are a stakeholder, i.e. own a portion of the DAO tokens, you can participate in the DAO. Tokens are open to all. It's just a matter of exchanging it. Ownership of DAO tokens entitles you to exclusive benefits such as governance, voting, and so on. You can vote for a move, a plan, or the DAO's next investment. You can even pitch for funding. Any ‘big' decision in a DAO requires a vote from all stakeholders. In this case, ‘token-holders'! In other words, they function like stock.

What are the 5 DAO types?

Different DAOs exist. We will categorize decentralized autonomous organizations based on their mode of operation, structure, and even technology. Here are a few. You've probably heard of them:

1. DeFi DAO

These DAOs offer DeFi (decentralized financial) services via smart contract protocols. They use tokens to vote protocol and financial changes. Uniswap, Aave, Maker DAO, and Olympus DAO are some examples. Most DAOs manage billions.

Maker DAO was one of the first protocols ever created. It is a decentralized organization on the Ethereum blockchain that allows cryptocurrency lending and borrowing without a middleman.
Maker DAO issues DAI, a stable coin. DAI is a top-rated USD-pegged stable coin.
Maker DAO has an MKR token. These token holders are in charge of adjusting the Dai stable coin policy. Simply put, MKR tokens represent DAO “shares”.

2. Investment DAO

Investors pool their funds and make investment decisions. Investing in new businesses or art is one example. Investment DAOs help DeFi operations pool capital. The Meta Cartel DAO is a community of people who want to invest in new projects built on the Ethereum blockchain. Instead of investing one by one, they want to pool their resources and share ideas on how to make better financial decisions.

Other investment DAOs include the LAO and Friends with Benefits.

3. DAO Grant/Launchpad

In a grant DAO, community members contribute funds to a grant pool and vote on how to allocate and distribute them. These DAOs fund new DeFi projects. Those in need only need to apply. The Moloch DAO is a great Grant DAO. The tokens are used to allocate capital. Also see Gitcoin and Seedify.

4. DAO Collector

I debated whether to put it under ‘Investment DAO' or leave it alone. It's a subset of investment DAOs. This group buys non-fungible tokens, artwork, and collectibles. The market for NFTs has recently exploded, and it's time to investigate. The Pleasr DAO is a collector DAO. One copy of Wu-Tang Clan's "Once Upon a Time in Shaolin" cost the Pleasr DAO $4 million. Pleasr DAO is known for buying Doge meme NFT. Collector DAOs include the Flamingo, Mutant Cats DAO, and Constitution DAOs. Don't underestimate their websites' "childish" style. They have millions.

5. Social DAO

These are social networking and interaction platforms. For example, Decentraland DAO and Friends With Benefits DAO.

What are the DAO Benefits?

Here are some of the benefits of a decentralized autonomous organization:

• They are trustless. You don’t need to trust a CEO or management team
• It can’t be shut down unless a majority of the token holders agree. The government can't shut - It down because it isn't centralized.
• It's fully democratic
• It is open-source and fully transparent.

What about DAO drawbacks?

We've been saying DAOs are the bomb? But are they really the shit? What could go wrong with DAO?
DAOs may contain bugs. If they are hacked, the results can be catastrophic.
No trade secrets exist. Because the smart contract is transparent and coded on the blockchain, it can be copied. It may be used by another organization without credit. Maybe DAOs should use Secret, Oasis, or Horizen blockchain networks.

Are DAOs legally recognized??

In most counties, DAO regulation is inexistent. It's unclear. Most DAOs don’t have a legal personality. The Howey Test and the Securities Act of 1933 determine whether DAO tokens are securities. Although most countries follow the US, this is only considered for the US. Wyoming became the first state to recognize DAOs as legal entities in July 2021 after passing a DAO bill. DAOs registered in Wyoming are thus legally recognized as business entities in the US and thus receive the same legal protections as a Limited Liability Company.

In terms of cyber-security, how secure is a DAO?

Blockchains are secure. However, smart contracts may have security flaws or bugs. This can be avoided by third-party smart contract reviews, testing, and auditing

Finally, Decentralized Autonomous Organizations are timeless. Let us examine the current situation: Ukraine's invasion. A DAO was formed to help Ukrainian troops fighting the Russians. It was named Ukraine DAO. Pleasr DAO, NFT studio Trippy Labs, and Russian art collective Pussy Riot organized this fundraiser. Coindesk reports that over $3 million has been raised in Ethereum-based tokens. AidForUkraine, a DAO aimed at supporting Ukraine's defense efforts, has launched. Accepting Solana token donations. They are fully transparent, uncensorable, and can’t be shut down or sanctioned.
DAOs are undeniably the future of blockchain. Everyone is paying attention. Personally, I believe traditional companies will soon have to choose between adapting or being left behind.

Although Mexico and Ukraine are thousands of miles apart, this legislation would link their responses.

Context

Ukraine was a Soviet republic until 1991. A significant proportion of the population, particularly in the east, is ethnically Russian. In February, the Russian military invaded Ukraine, intent on overthrowing its democratically elected government.

This could be the biggest European land invasion since WWII. In response, President Joe Biden sent 3,000 troops to NATO countries bordering Ukraine to help with Ukrainian refugees, with more troops possible if the situation worsened.

In July 2021, the US Border Patrol reported its highest monthly encounter total since March 2000. Some Republicans compare Biden's response to the Mexican border situation to his response to the Ukrainian border situation, though the correlation is unclear.

What the bills do

Two new Republican bills seek to link the US response to Ukraine to the situation in Mexico.

The Secure America's Borders First Act would prohibit federal funding for Ukraine until the US-Mexico border is “operationally controlled,” including a wall as promised by former President Donald Trump. (The bill even mandates a 30-foot-high wall.)

The USB (Ukraine and Southern Border) Act, introduced on February 8 by Rep. Matt Rosendale (R-MT0), would allow the US to support Ukraine, but only if the number of Armed Forces deployed there is less than the number deployed to the Mexican border. Madison Cawthorne introduced H.R. 6665 on February 9th (R-NC11).

What backers say

Supporters argue that even if the US should militarily assist Ukraine, our own domestic border situation should take precedence.

After failing to secure our own border and protect our own territorial integrity, ‘America Last' politicians on both sides of the aisle now tell us that we must do so for Ukraine. “Before rushing America into another foreign conflict over an Eastern European nation's border thousands of miles from our shores, they should first secure our southern border.”

“If Joe Biden truly cared about Americans, he would prioritize national security over international affairs,” Rep. Cawthorn said in a separate press release. The least we can do to secure our own country is send the same number of troops to the US-Mexico border to assist our border patrol agents working diligently to secure America.

What opponents say

The president has defended his Ukraine and Mexico policies, stating that both seek peace and diplomacy.

Our nations [the US and Mexico] have a long and complicated history, and we haven't always been perfect neighbors, but we have seen the power and purpose of cooperation,” Biden said in 2021. “We're safer when we work together, whether it's to manage our shared border or stop the pandemic. [In both the Obama and Biden administration], we made a commitment that we look at Mexico as an equal, not as somebody who is south of our border.”

No mistake: If Russia goes ahead with its plans, it will be responsible for a catastrophic and unnecessary war of choice. To protect our collective security, the United States and our allies are ready to defend every inch of NATO territory. We won't send troops into Ukraine, but we will continue to support the Ukrainian people... But, I repeat, Russia can choose diplomacy. It is not too late to de-escalate and return to the negotiating table.”

Odds of passage

The Secure America's Borders First Act has nine Republican sponsors. Either the House Armed Services or Foreign Affairs Committees may vote on it.

Rep. Paul Gosar, a Republican, co-sponsored the USB Act (R-AZ4). The House Armed Services Committee may vote on it.

With Republicans in control, passage is unlikely.