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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That is, how to snipe all the rares without using ERC721R!

Introduction: Blessed and Lucky 

Mphers was the first mfers derivative, and as a Phunks derivative, I wanted one.

I wanted an alien. And there are only 8 in the 6,969 collection. I got one!

In case it wasn't clear from the tweet, I meant that I was lucky to have figured out how to 100% guarantee I'd get an alien without any extra luck.
Read on to find out how I did it, how you can too, and how developers can avoid it!
How to make rare NFTs without luck.

# How to mint rare NFTs without needing luck

For example, once I knew my alien was #4002, I simply refreshed the mint page until #3992 was minted, and then mint 10 mphers.

How did I know #4002 was extraterrestrial? Let's go back.

First, go to the mpher contract's Etherscan page and look up the tokenURI of a previously issued token, token #1:

As you can see, mphers creates metadata URIs by combining the token id and an IPFS hash.

This method gives you the collection's provenance in every URI, and while that URI can be changed, it affects everyone and is public.

Consider a token URI without a provenance hash, like https://mphers.art/api?tokenId=1.
As a collector, you couldn't be sure the devs weren't changing #1's metadata at will.
The API allows you to specify “if #4002 has not been minted, do not show any information about it”, whereas IPFS does not allow this.

It's possible to look up the metadata of any token, whether or not it's been minted.
Simply replace the trailing “1” with your desired id.

Mpher #4002

These files contain all the information about the mpher with the specified id. For my alien, we simply search all metadata files for the string “alien mpher.”

Take a look at the 6,969 meta-data files I'm using OpenSea's IPFS gateway, but you could use ipfs.io or something else.

Use curl to download ten files at once. Downloading thousands of files quickly can lead to duplicates or errors. But with a little tweaking, you should be able to get everything (and dupes are fine for our purposes).
Now that you have everything in one place, grep for aliens:

The numbers are the file names that contain “alien mpher” and thus the aliens' ids.
The entire process takes under ten minutes. This technique works on many NFTs currently minting.

In practice, manually minting at the right time to get the alien is difficult, especially when tokens mint quickly. Then write a bot to poll totalSupply() every second and submit the mint transaction at the exact right time.

You could even look for the token you need in the mempool before it is minted, and get your mint into the same block!

However, in my experience, the “big” approach wins 95% of the time—but not 100%.
“Am I being set up all along?”

Is a question you might ask yourself if you're new to this.
It's disheartening to think you had no chance of minting anything that someone else wanted.
But, did you have no opportunity? You had an equal chance as everyone else!
Take me, for instance: I figured this out using open-source tools and free public information. Anyone can do this, and not understanding how a contract works before minting will lead to much worse issues.

The mpher mint was fair.

While a fair game, “snipe the alien” may not have been everyone's cup of tea.
People may have had more fun playing the “mint lottery” where tokens were distributed at random and no one could gain an advantage over someone simply clicking the “mint” button.

How might we proceed?
Minting For Fashion Hats Punks, I wanted to create a random minting experience without sacrificing fairness. In my opinion, a predictable mint beats an unfair one. Above all, participants must be equal.

Sadly, the most common method of creating a random experience—the post-mint “reveal”—is deeply unfair. It works as follows:

• During the mint, token metadata is unavailable. Instead, tokenURI() returns a blank JSON file for each id.
• An IPFS hash is updated once all tokens are minted.
• You can't tell how the contract owner chose which token ids got which metadata, so it appears random.

Because they alone decide who gets what, the person setting the metadata clearly has a huge unfair advantage over the people minting. Unlike the mpher mint, you have no chance of winning here.
But what if it's a well-known, trusted, doxxed dev team? Are reveals okay here?
No! No one should be trusted with such power. Even if someone isn't consciously trying to cheat, they have unconscious biases. They might also make a mistake and not realize it until it's too late, for example.

You should also not trust yourself. Imagine doing a reveal, thinking you did it correctly (nothing is 100%! ), and getting the rarest NFT. Isn't that a tad odd Do you think you deserve it? An NFT developer like myself would hate to be in this situation.

Reveals are bad*

UNLESS they are done without trust, meaning everyone can verify their fairness without relying on the developers (which you should never do).
An on-chain reveal powered by randomness that is verifiably outside of anyone's control is the most common way to achieve a trustless reveal (e.g., through Chainlink).

Tubby Cats did an excellent job on this reveal, and I highly recommend their contract and launch reflections. Their reveal was also cool because it was progressive—you didn't have to wait until the end of the mint to find out.

In his post-launch reflections, @DefiLlama stated that he made the contract as trustless as possible, removing as much trust as possible from the team.

And @DefiLlama is a superstar developer. Imagine how much stress maximizing trustlessness will cause you!

That leaves me with a bad solution that works in 99 percent of cases and is much easier to implement: random token assignments.

Introducing ERC721R: A fully compliant IERC721 implementation that picks token ids at random.

ERC721R implements the opposite of a reveal: we mint token ids randomly and assign metadata deterministically.
This allows us to reveal all metadata prior to minting while reducing snipe chances.
Then import the contract and use this code:

What is ERC721R and how does it work

First, a disclaimer: ERC721R isn't truly random. In this sense, it creates the same “game” as the mpher situation, where minters compete to exploit the mint. However, ERC721R is a much more difficult game.
To game ERC721R, you need to be able to predict a hash value using these inputs:

This is impossible for a normal person because it requires knowledge of the block timestamp of your mint, which you do not have.

To do this, a miner must set the timestamp to a value in the future, and whatever they do is dependent on the previous block's hash, which expires in about ten seconds when the next block is mined.

This pseudo-randomness is “good enough,” but if big money is involved, it will be gamed. Of course, the system it replaces—predictable minting—can be manipulated.
The token id is chosen in a clever implementation of the Fisher–Yates shuffle algorithm that I copied from CryptoPhunksV2.

Consider first the naive solution: (a 10,000 item collection is assumed):

1. Make an array with 0–9999.
2. To create a token, pick a random item from the array and use that as the token's id.
3. Remove that value from the array and shorten it by one so that every index corresponds to an available token id.

This works, but it uses too much gas because changing an array's length and storing a large array of non-zero values is expensive.

How do we avoid them both? What if we started with a cheap 10,000-zero array? Let's assign an id to each index in that array.

Assume we pick index #6500 at random—#6500 is our token id, and we replace the 0 with a 1.

But what if we chose #6500 again? A 1 would indicate #6500 was taken, but then what? We can't just "roll again" because gas will be unpredictable and high, especially later mints.

This allows us to pick a token id 100% of the time without having to keep a separate list. Here's how it works:

1. Make a 10,000 0 array.
2. Create a 10,000 uint numAvailableTokens.
3. Pick a number between 0 and numAvailableTokens. -1
4. Think of #6500—look at index #6500. If it's 0, the next token id is #6500. If not, the value at index #6500 is your next token id (weird!)
5. Examine the array's last value, numAvailableTokens — 1. If it's 0, move the value at #6500 to the end of the array (#9999 if it's the first token). If the array's last value is not zero, update index #6500 to store it.
6. numAvailableTokens is decreased by 1.
7. Repeat 3–6 for the next token id.

So there you go! The array stays the same size, but we can choose an available id reliably. The Solidity code is as follows:

GitHub url

Unfortunately, this algorithm uses more gas than the leading sequential mint solution, ERC721A.

This is most noticeable when minting multiple tokens in one transaction—a 10 token mint on ERC721R costs 5x more than on ERC721A. That said, ERC721A has been optimized much further than ERC721R so there is probably room for improvement.

Conclusion

Listed below are your options:

• ERC721A: Minters pay lower gas but must spend time and energy devising and executing a competitive minting strategy or be comfortable with worse minting results.
• ERC721R: Higher gas, but the easy minting strategy of just clicking the button is optimal in all but the most extreme cases. If miners game ERC721R it’s the worst of both worlds: higher gas and a ton of work to compete.
• ERC721A + standard reveal: Low gas, but not verifiably fair. Please do not do this!
• ERC721A + trustless reveal: The best solution if done correctly, highly-challenging for dev, potential for difficult-to-correct errors.

Did I miss something? Comment or tweet me @dumbnamenumbers.
Check out the code on GitHub to learn more! Pull requests are welcome—I'm sure I've missed many gas-saving opportunities.

Thanks!

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