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

Creating 10,000 auto-generated artworks, deploying a smart contract to the Ethereum / Polygon blockchain, setting up some tools, etc.

There is so much to do from launching to running an NFT project. Creating parts for artworks, generating 10,000 unique artworks and metadata, creating a smart contract and deploying it to a blockchain network, creating a website, creating a Twitter account, setting up a Discord server, setting up an OpenSea collection. In addition, you need to have MetaMask installed in your browser and have some ETH / MATIC. Did you get tired of doing all this? Don’t worry, once you know what you need to do, all you have to do is do it one by one.

To be honest, it’s best to run an NFT project in a team of three or more, including artists, developers, and marketers. However, depending on your motivation, you can do it by yourself. Some people might come later to offer help with your project. The most important thing is to take a step as soon as possible.

Creating Parts for Artworks

There are lots of free/paid software for drawing, but after all, I think Adobe Illustrator or Photoshop is the best. The images of Skulls In Love are a composite of 48x48 pixel parts created using Photoshop.

How Many Parts Should You Create?

Are you wondering how many parts you should create to avoid duplication as much as possible when generating your artworks? My friend Stephane, a developer, has created a great tool to help with that.

Generating 10,000 Unique Artworks and Metadata

I highly recommend using the HashLips Art Engine to generate your artworks and metadata. Perhaps there is no better artworks generation tool at the moment.

GitHub: https://github.com/HashLips/hashlips_art_engine
YouTube:

Storing Artworks and Metadata

Ideally, the generated artworks and metadata should be stored on-chain, but if you want to store them off-chain, you should use IPFS. Do not store in centralized storage. This is because data will be lost if the server goes down or if the company goes down. On the other hand, IPFS is a more secure way to find data because it utilizes a distributed, decentralized system.

Storing to IPFS is easy with Pinata, NFT.Storage, and so on. The Skulls In Love uses Pinata. It’s very easy to use, just upload the folder containing your artworks.

Creating and Deploying a Smart Contract

You don’t have to create a smart contract from scratch. There are many great NFT projects, many of which publish their contract source code on Etherscan / PolygonScan. You can choose the contract you like and reuse it. Of course, that requires some knowledge of Solidity, but it depends on your efforts. If you don’t know which contract to choose, use the HashLips smart contract. It’s very simple, but it has almost all the functions you need.

GitHub: https://github.com/HashLips/hashlips_nft_contract

Creating a Website

The website here is not just a static site to showcase your project, it’s a so-called dApp that allows you to access your smart contract and mint NFTs. In fact, this level of dApp is not too difficult for anyone who has ever created a website. Because the ethers.js / web3.js libraries make it easy to interact with your smart contract. There’s also no problem connecting wallets, as MetaMask has great documentation.

The Skulls In Love uses a simple, fast, and modern dApp that I built from scratch using Next.js. It is published on GitHub, so feel free to use it.

Why do people mint NFTs on a website?

Ethereum’s gas fees are high, so if you mint all your NFTs, there will be a huge initial cost. So it makes sense to get the buyers to help with the gas fees for minting.
What about Polygon? Polygon’s gas fees are super cheap, so even if you mint 10,000 NFTs, it’s not a big deal. But we don’t do that. Since NFT projects are a kind of game, it involves the fun of not knowing what will come out after minting.

Creating a Twitter Account

I highly recommend creating a Twitter account. Twitter is an indispensable tool for announcing giveaways and reaching more people. It’s better to announce your project and your artworks little by little, 1–2 weeks before launching your project.

Creating and Setting Up a Discord Server

I highly recommend creating a Discord server as well as a Twitter account. The Discord server is a community and its home. Fans of your NFT project will want to join your community and interact with many other members. So, carefully create each channel on your Discord server to make it a cozy place for your community members.

If you are unfamiliar with Discord, you may be particularly confused by the following:
What bots should I use?
How should I set roles and permissions?
But don’t worry. There are lots of great YouTube videos and blog posts about these.
It’s also a good idea to join the Discord servers of some NFT projects and see how they’re made. Our Discord server is so simple that even beginners will find it easy to understand. Please join us and see it!

UPDATED: As your Discord server grows, you cannot manage it on your own. In this case, you will be hiring several moderators, but choose carefully before hiring. And don’t give them important role permissions right after hiring. Initially, the same permissions as other members are sufficient. After a while, you can add permissions as needed, such as kicking/banning, using the “@every” tag, and adding roles. Again, don’t immediately give significant permissions to your Mod role. Your server can be messed up by fake moderators.

Setting Up Your OpenSea Collection

Before you start selling your NFTs, you need to reserve some for airdrops, giveaways, staff, and more. It’s up to you whether it’s 100, 500, or how many.

After minting some of your NFTs, your account and collection should have been created in OpenSea. Go to OpenSea, connect to your wallet, and set up your collection. Just set your logo, banner image, description, links, royalties, and more. It’s not that difficult.

Promoting Your Project

After all, promotion is the most important thing. In fact, almost every successful NFT project spends a lot of time and effort on it.

In addition to Twitter and Discord, it’s even better to use Instagram, Reddit, and Medium. Also, register your project in NFTCalendar and DISBOARD

About Promoters

You’ll probably get lots of contacts from promoters on your Discord, Twitter, Instagram, and more. But most of them are scams, so don’t pay right away. If you have a promoter that looks attractive to you, be sure to check the promoter’s social media accounts or website to see who he/she is. They basically charge in dollars. The amount they charge isn’t cheap, but promoters with lots of followers may have some temporary effect on your project. Some promoters accept 50% prepaid and 50% postpaid. If you can afford it, it might be worth a try. I never ask them, though.

When Should the Promotion Activities Start?

You may be worried that if you promote your project before it starts, someone will copy your project (artworks). It is true that some projects have actually suffered such damage. I don’t have a clear answer to this question right now, but:

• Do not publish all the information about your project too early
• The information should be released little by little
• Creating artworks that no one can easily copy
  I think these are important.
  If anyone has a good idea, please share it!

About Giveaways

When hosting giveaways, you’ll probably use multiple social media platforms. You may want to grow your Discord server faster. But if joining the Discord server is included in the giveaway requirements, some people hate it. I recommend holding giveaways for each platform. On Twitter and Reddit, you should just add the words “Discord members-only giveaway is being held now! Please join us if you like!”.

If you want to easily pick a giveaway winner in your browser, I recommend Twitter Picker.

Precautions for Distributing Free NFTs

If you want to increase your Twitter followers and Discord members, you can actually get a lot of people by holding events such as giveaways and invite contests. However, distributing many free NFTs at once can be dangerous. Some people who want free NFTs, as soon as they get a free one, sell it at a very low price on marketplaces such as OpenSea. They don’t care about your project and are only thinking about replacing their own “free” NFTs with Ethereum. The lower the floor price of your NFTs, the lower the value of your NFTs (project). Try to think of ways to get people to “buy” your NFTs as much as possible.

Ethereum vs. Polygon

Even though Ethereum has high gas fees, NFT projects on the Ethereum network are still mainstream and popular. On the other hand, Polygon has very low gas fees and fast transaction processing, but NFT projects on the Polygon network are not very popular.

Why? There are several reasons, but the biggest one is that it’s a lot of work to get MATIC (on Polygon blockchain, use MATIC instead of ETH) ready to use. Simply put, you need to bridge your tokens to the Polygon chain. So people need to do this first before minting your NFTs on your website. It may not be a big deal for those who are familiar with crypto and blockchain, but it may be complicated for those who are not. I hope that the tedious work will be simplified in the near future.

If you are confident that your NFTs will be purchased even if they are expensive, or if the total supply of your NFTs is low, you may choose Ethereum. If you just want to save money, you should choose Polygon. Keep in mind that gas fees are incurred not only when minting, but also when performing some of your smart contract functions and when transferring your NFTs.
If I were to launch a new NFT project, I would probably choose Ethereum or Solana.

Conclusion

Some people may want to start an NFT project to make money, but don’t forget to enjoy your own project. Several months ago, I was playing with creating generative art by imitating the CryptoPunks. I found out that auto-generated artworks would be more interesting than I had imagined, and since then I’ve been completely absorbed in generative art.

This is one of the Skulls In Love artworks:

This character wears a cowboy hat, black slim sunglasses, and a kimono. If anyone looks like this, I can’t help laughing!

The Skulls In Love NFTs can be minted for a small amount of MATIC on the official website. Please give it a try to see what kind of unique characters will appear 💀💖

Thank you for reading to the end. I hope this article will be helpful to those who want to launch an NFT project in the future ✨