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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"Web 3.0" is a trendy buzzword with a vague definition. Everyone agrees it has to do with a blockchain-based internet evolution, but what is it?

Yet, the meaning and prospects for Web3 have become hot topics in crypto communities. Big corporations use the term to gain a foothold in the space while avoiding the negative connotations of “crypto.”

But it can't be evaluated without a definition.

Among those criticizing Web3's vagueness is Cobie:

“Even the crypto community is split on whether Bitcoin is Web3,” he adds.

The phrase was coined by an early crypto thinker, and the community has had years to figure out what it means. Many ideologies and commercial realities have driven reverse engineering.

Web3 is becoming clearer as a concept. It contains ideas. It was probably coined by Ethereum co-founder Gavin Wood in 2014. His definition of Web3 included “trustless transactions” as part of its tech stack. Wood founded the Web3 Foundation and the Polkadot network, a Web3 alternative future.

The 2013 Ethereum white paper had previously allowed devotees to imagine a DAO, for example.

Web3 now has concepts like decentralized autonomous organizations, sovereign digital identity, censorship-free data storage, and data divided by multiple servers. They intertwine discussions about the “Web3” movement and its viability.

These ideas are linked by Cobie's initial Web3 definition. A key component of Web3 should be “ownership of value” for one's own content and data.

Noting that “late-stage capitalism greedcorps that make you buy a fractionalized micropayment NFT on Cardano to operate your electric toothbrush” may build the new web, he notes that “crypto founders are too rich to care anymore.”

Very Important

Many critics of Web3 claim it isn't practical or achievable. Web3 critics like Moxie Marlinspike (creator of sslstrip and Signal/TextSecure) can never see people running their own servers. Early in January, he argued that protocols are more difficult to create than platforms.

While this is true, some projects, like the file storage protocol IPFS, allow users to choose which jurisdictions their data is shared between.

But full decentralization is a difficult problem. Suhaza, replying to Moxie, said:

So, here are the questions: Web3: Is it a go? Is it truly decentralized?

Web3 history is shaped by Web2 failure.

This is the story of how the Internet was turned upside down...

Then came the vision. Everyone can create content for free. Decentralized open-source believers like Tim Berners-Lee popularized it.

Real-world data trade-offs for content creation and pricing.

A giant Wikipedia page married to a giant Craig's List. No ads, no logins, and a private web carve-up. For free usage, you give up your privacy and data to the algorithmic targeted advertising of Web 2.

Our data is centralized and savaged by giant corporations. Data localization rules and geopolitical walls like China's Great Firewall further fragment the internet.

The decentralized Web3 reflects Berners-original Lee's vision: "No permission is required from a central authority to post anything... there is no central controlling node and thus no single point of failure." Now he runs Solid, a Web3 data storage startup.

So Web3 starts with decentralized servers and data privacy.

Web3 begins with decentralized storage.

Data decentralization is a key feature of the Web3 tech stack. Web2 has closed databases. Large corporations like Facebook, Google, and others go to great lengths to collect, control, and monetize data. We want to change it.

Amazon, Google, Microsoft, Alibaba, and Huawei, according to Gartner, currently control 80% of the global cloud infrastructure market. Web3 wants to change that.

Decentralization enlarges power structures by giving participants a stake in the network. Users own data on open encrypted networks in Web3. This area has many projects.

Apps like Filecoin and IPFS have led the way. Data is replicated across multiple nodes in Web3 storage providers like Filecoin.

But the new tech stack and ideology raise many questions.

Giving users control over their data

According to Ryan Kris, COO of Verida, his “Web3 vision” is “empowering people to control their own data.”

Verida targets SDKs that address issues in the Web3 stack: identity, messaging, personal storage, and data interoperability.

A big app suite? “Yes, but it's a frontier technology,” he says. They are currently building a credentialing system for decentralized health in Bermuda.

By empowering individuals, how will Web3 create a fairer internet? Kris, who has worked in telecoms, finance, cyber security, and blockchain consulting for decades, admits it is difficult:

“The viability of Web3 raises some good business questions,” he adds. “How can users regain control over centralized personal data? How are startups motivated to build products and tools that support this transition? How are existing Web2 companies encouraged to pivot to a Web3 business model to compete with market leaders?

Kris adds that new technologies have regulatory and practical issues:

Each project has varying degrees of decentralization. The diehards say DApps that use centralized storage are no longer “Web3” companies. But fully decentralized technology is hard to build.

Web2.5?

Some argue that we're actually building Web2.5 businesses, which are crypto-native but not fully decentralized. This is vital. For example, the NFT may be on a blockchain, but it is linked to centralized data repositories like OpenSea. A server failure could result in data loss.

However, according to Apollo Capital crypto analyst David Angliss, OpenSea is “not exactly community-led”. Also in 2021, much to the chagrin of crypto enthusiasts, OpenSea tried and failed to list on the Nasdaq.

This is where Web2.5 is defined.

“Web3 isn't a crypto segment. “Anything that uses a blockchain for censorship resistance is Web3,” Angliss tells us.

“Web3 gives users control over their data and identity. This is not possible in Web2.”

“Web2 is like feudalism, with walled-off ecosystems ruled by a few. For example, an honest user owned the Instagram account “Meta,” which Facebook rebranded and then had to make up a reason to suspend. Not anymore with Web3. If I buy ‘Ethereum.ens,' Ethereum cannot take it away from me.”

Angliss uses OpenSea as a Web2.5 business example. Too decentralized, i.e. censorship resistant, can be unprofitable for a large company like OpenSea. For example, OpenSea “enables NFT trading”. But it also stopped the sale of stolen Bored Apes.”

Web3 (or Web2.5, depending on the context) has been described as a new way to privatize internet.

“Being in the crypto ecosystem doesn't make it Web3,” Angliss says. The biggest risk is centralized closed ecosystems rather than a growing Web3.

LooksRare and OpenDAO are two community-led platforms that are more decentralized than OpenSea. LooksRare has even been “vampire attacking” OpenSea, indicating a Web3 competitor to the Web2.5 NFT king could find favor.

The addition of a token gives these new NFT platforms more options for building customer loyalty. For example, OpenSea charges a fee that goes nowhere. Stakeholders of LOOKS tokens earn 100% of the trading fees charged by LooksRare on every basic sale.

Maybe Web3's time has come.

So whose data is it?

Continuing criticisms of Web3 platforms' decentralization may indicate we're too early. Users want to own and store their in-game assets and NFTs on decentralized platforms like the Metaverse and play-to-earn games. Start-ups like Arweave, Sia, and Aleph.im  propose an alternative.

To be truly decentralized, Web3 requires new off-chain models that sidestep cloud computing and Web2.5.

“Arweave and Sia emerged as formidable competitors this year,” says the Messari Report. They seek to reduce the risk of an NFT being lost due to a data breach on a centralized server.

Aleph.im, another Web3 cloud competitor, seeks to replace cloud computing with a service network. It is a decentralized computing network that supports multiple blockchains by retrieving and encrypting data.

“The Aleph.im network provides a truly decentralized alternative where it is most needed: storage and computing,” says Johnathan Schemoul, founder of Aleph.im. For reasons of consensus and security, blockchains are not designed for large storage or high-performance computing.

As a result, large data sets are frequently stored off-chain, increasing the risk for centralized databases like OpenSea

Aleph.im enables users to own digital assets using both blockchains and off-chain decentralized cloud technologies.

Aleph.im raised $10 million in mid-January 2022, and Ubisoft uses its network for NFT storage. This is the first time a big-budget gaming studio has given users this much control.

It also suggests Web3 could work as a B2B model, even if consumers aren't concerned about “decentralization.” Starting with gaming is common.

Can Tokenomics help Web3 adoption?

Web3 consumer adoption is another story. The average user may not be interested in all this decentralization talk. Still, how much do people value privacy over convenience? Can tokenomics solve the privacy vs. convenience dilemma?

Holon Global Investments' Jonathan Hooker tells us that human internet behavior will change. “Do you own Bitcoin?” he asks in his Web3 explanation. How does it feel to own and control your own sovereign wealth? Then:

“The business model must find what that person values,” he says. Putting their own health records on centralized systems they don't control?

“How vital are those medical records to that person at a critical time anywhere in the world? Filecoin and IPFS can help.”

Web3 adoption depends on NFT storage competition. A free off-chain storage of NFT metadata and assets was launched by Filecoin in April 2021.

Denationalization and blockchain technology have significant implications for data ownership and compensation for lending, staking, and using data. 

Tokenomics can change human behavior, but many people simply sign into Web2 apps using a Facebook API without hesitation. Our data is already owned by Google, Baidu, Tencent, and Facebook (and its parent company Meta). Is it too late to recover?

Maybe. “Data is like fruit, it starts out fresh but ages,” he says. "Big Tech's data on us will expire."

Web3 founder Kris agrees with Hooker that “value for data is the issue, not privacy.” People accept losing their data privacy, so tokenize it. People readily give up data, so why not pay for it?

"Personalized data offering is valuable in personalization. “I will sell my social media data but not my health data.”

Purists and mass consumer adoption struggle with key management.

Others question data tokenomics' optimism. While acknowledging its potential, Box founder Aaron Levie questioned the viability of Web3 models in a Tweet thread:

“Why? Because data almost always works in an app. A product and APIs that moved quickly to build value and trust over time.”

Levie contends that tokenomics may complicate matters. In addition to community governance and tokenomics, Web3 ideals likely add a new negotiation vector.

“These are hard problems about human coordination, not software or blockchains,”. Using a Facebook API is simple. The business model and user interface are crucial.

For example, the crypto faithful have a common misconception about logging into Web3. It goes like this: Web 1 had usernames and passwords. Web 2 uses Google, Facebook, or Twitter APIs, while Web 3 uses your wallet. Pay with Ethereum on MetaMask, for example.

But Levie is correct. Blockchain key management is stressed in this meme. Even seasoned crypto enthusiasts have heart attacks, let alone newbies.

Web3 requires a better user experience, according to Kris, the company's founder. “How does a user recover keys?”

And at this point, no solution is likely to be completely decentralized. So Web3 key management can be improved. ”The moment someone loses control of their keys, Web3 ceases to exist.”

That leaves a major issue for Web3 purists. Put this one in the too-hard basket.

Is 2022 the Year of Web3?

Web3 must first solve a number of issues before it can be mainstreamed. It must be better and cheaper than Web2.5, or have other significant advantages.

Web3 aims for scalability without sacrificing decentralization protocols. But decentralization is difficult and centralized services are more convenient.

Ethereum co-founder Vitalik Buterin himself stated recently"

This is why (centralized) Binance to Binance transactions trump Ethereum payments in some places because they don't have to be verified 12 times."

“I do think a lot of people care about decentralization, but they're not going to take decentralization if decentralization costs $8 per transaction,” he continued.

“Blockchains need to be affordable for people to use them in mainstream applications... Not for 2014 whales, but for today's users."

For now, scalability, tokenomics, mainstream adoption, and decentralization believers seem to be holding Web3 hostage.

Much like crypto's past.

But stay tuned.