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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Instagram (IG) is officially joining NFT. With the debut of new in-app NFT functionalities, influential producers can interact with blockchain tech on the social media platform.

Meta unveiled intentions for an Instagram NFT marketplace in March, but these latest capabilities focus more on content sharing than commerce. And why shouldn’t they? IG's entry into the NFT market is overdue, given that Twitter and Discord are NFT hotspots.

The NFT marketplace/Web3 social media race has continued to expand, with the expected Coinbase NFT Beta now live and blazing a trail through the NFT ecosystem.

IG's focus is on visual art. It's unlike any NFT marketplace or platform. IG NFTs and artists: what's the deal? Let’s take a look.

What are Instagram’s NFT features anyways?

As said, not everyone has Instagram's new features. 16 artists, NFT makers, and collectors can now post NFTs on IG by integrating third-party digital wallets (like Rainbow or MetaMask) in-app. IG doesn't charge to publish or share digital collectibles.

NFTs displayed on the app have a "shimmer" aesthetic effect. NFT posts also have a "digital collectable" badge that lists metadata such as the creator and/or owner, the platform it was created on, a brief description, and a blockchain identification.

Meta's social media NFTs have launched on Instagram, but the company is also preparing to roll out digital collectibles on Facebook, with more on the way for IG. Currently, only Ethereum and Polygon are supported, but Flow and Solana will be added soon.

How will artists use these new features?

Artists are publishing NFTs they developed or own on IG by linking third-party digital wallets. These features have no NFT trading aspects built-in, but are aimed to let authors share NFTs with IG audiences.

Creators, like IG-native aerial/street photographer Natalie Amrossi (@misshattan), are discovering novel uses for IG NFTs.

Amrossi chose to not only upload his own NFTs but also encourage other artists in the field. "That's the beauty of connecting your wallet and sharing NFTs. It's not just what you make, but also what you accumulate."

Amrossi has been producing and posting Instagram art for years. With IG's NFT features, she can understand Instagram's importance in supporting artists.

Web2 offered Amrossi the tools to become an artist and make a life. "Before 'influencer' existed, I was just making art. Instagram helped me reach so many individuals and brands, giving me a living.

Even artists without millions of viewers are encouraged to share NFTs on IG. Wilson, a relatively new name in the NFT space, seems to have already gone above and beyond the scope of these new IG features. By releasing "Losing My Mind" via IG NFT posts, she has evaded the lack of IG NFT commerce by using her network to market her multi-piece collection.

"'Losing My Mind' is a long-running photo series. Wilson was preparing to release it as NFTs before IG approached him, so it was a perfect match.

Wilson says the series is about Black feminine figures and media depiction. Respectable effort, given POC artists have been underrepresented in NFT so far.

“Over the past year, I've had mental health concerns that made my emotions so severe it was impossible to function in daily life, therefore that prompted this photo series. Every Wednesday and Friday for three weeks, I'll release a new Meta photo for sale.

Wilson hopes these new IG capabilities will help develop a connection between the NFT community and other internet subcultures that thrive on Instagram.

“NFTs can look scary as an outsider, but seeing them on your daily IG feed makes it less foreign,” adds Wilson. I think Instagram might become a hub for NFT aficionados, making them more accessible to artists and collectors.

What does it all mean for the NFT space?

Meta's NFT and metaverse activities will continue to impact Instagram's NFT ecosystem. Many think it will be for the better, as IG NFT frauds are another problem hurting the NFT industry.

IG's new NFT features seem similar to Twitter's PFP NFT verifications, but Instagram's tools should help cut down on scams as users can now verify the creation and ownership of whole NFT collections included in IG posts.

Given the number of visual artists and NFT creators on IG, it might become another hub for NFT fans, as Wilson noted. If this happens, it raises questions about Instagram success. Will artists be incentivized to distribute NFTs? Or will those with a large fanbase dominate?

Elise Swopes (@swopes) believes these new features should benefit smaller artists. Swopes was one of the first profiles placed to Instagram's original suggested user list in 2012.

Swopes says she wants IG to be a magnet for discovery and understands the value of NFT artists and producers.

"I'd love to see IG become a focus of discovery for everyone, not just the Beeples and Apes and PFPs. That's terrific for them, but [IG NFT features] are more about using new technology to promote emerging artists, Swopes added.

“Especially music artists. It's everywhere. Dancers, writers, painters, sculptors, musicians. My element isn't just for digital artists; it can be anything. I'm delighted to witness people's creativity."

Swopes, Wilson, and Amrossi all believe IG's new features can help smaller artists. It remains to be seen how these new features will effect the NFT ecosystem once unlocked for the rest of the IG NFT community, but we will likely see more social media NFT integrations in the months and years ahead.

As a tech-savvy person (and software engineer) or just a casual technology user, I'm sure you've had this same question countless times: How do I make money online? and how do I make money with my PC/Mac?
You're in luck! Today, I will list the top 5 easiest ways to make money online. Maybe a top ten in the future? Top 5 tips for 2022.

1. Using the gig economy

There are many websites on the internet that allow you to earn extra money using skills and equipment that you already own.
I'm referring to the gig economy. It's a great way to earn a steady passive income from the comfort of your own home. For some sites, premium subscriptions are available to increase sales and access features like bidding on more proposals.
Some of these are:

• Freelancer
• Upwork
• Fiverr (⭐ my personal favorite)
• TaskRabbit

2. Mineprize

MINEPRIZE is a great way to make money online. What's more, You need not do anything! You earn money by lending your idle CPU power to MINEPRIZE.
To register with MINEPRIZE, all you need is an email address and a password. Let MINEPRIZE use your resources, and watch the money roll in! You can earn up to $100 per month by letting your computer calculate. That's insane.

3. Writing

“O Romeo, Romeo, why art thou Romeo?” Okay, I admit that not all writing is Shakespearean. To be a copywriter, you'll need to be fluent in English. Thankfully, we don't have to use typewriters anymore.

Writing is a skill that can earn you a lot of money (claps for the rhyme).
Here are a few ways you can make money typing on your fancy keyboard:
Self-publish a book
Write scripts for video creators
Write for social media
Book-checking
Content marketing help
What a list within a list!

4. Coding

Yes, kids. You've probably coded before if you understand 
You've probably coded before if you understand 

Computational thinking (or coding) is one of the most lucrative ways to earn extra money, or even as a main source of income.
Of course, there are hardcode coders (like me) who write everything line by line, binary di — okay, that last part is a bit exaggerated.
But you can also make money by writing websites or apps or creating low code or no code platforms.
But you can also make money by writing websites or apps or creating low code or no code platforms.
Some low-code platforms
Sheet : spreadsheets to apps :
Loading... We'll install your new app... No-Code Your team can create apps and automate tasks. Agile…
www.appsheet.com

Low-code platform | Business app creator - Zoho Creator
Work is going digital, and businesses of all sizes must adapt quickly. Zoho Creator is a...
www.zoho.com

Sell your data with TrueSource. NO CODE NEEDED
Upload data, configure your product, and earn in minutes.
www.truesource.io

Cool, huh?

5. Created Content

If we use the internet correctly, we can gain unfathomable wealth and extra money. But this one is a bit more difficult. Unlike some of the other items on this list, it takes a lot of time up front.
I'm referring to sites like YouTube and Medium. It's a great way to earn money both passively and actively. With the likes of Jake- and Logan Paul, PewDiePie (a.k.a. Felix Kjellberg) and others, it's never too late to become a millionaire on YouTube. YouTubers are always rising to the top with great content.

6. NFTs and Cryptocurrency

It is now possible to amass large sums of money by buying and selling digital assets on NFTs and cryptocurrency exchanges. Binance's Initial Game Offer rewards early investors who produce the best results.
One awesome game sold a piece of its plot for US$7.2 million! It's Axie Infinity. It's free and available on Google Play and Apple Store.

7. Affiliate Marketing

Affiliate marketing is a form of advertising where businesses pay others (like bloggers) to promote their goods and services. Here's an example. I write a blog (like this one) and post an affiliate link to an item I recommend buying — say, a camera — and if you buy the camera, I get a commission!
These programs pay well:

• Elementor
• AWeber
• Sendinblue
• ConvertKit\sLeadpages
• GetResponse
• SEMRush\sFiverr
• Pabbly

8. Start a blog

Now, if you're a writer or just really passionate about something or a niche, blogging could potentially monetize that passion!
Create a blog about anything you can think of. It's okay to start right here on Medium, as I did.

9. Dropshipping

And I mean that in the best possible way — drop shopping is ridiculously easy to set up, but difficult to maintain for some.
Luckily, Shopify has made setting up an online store a breeze. Drop-shipping from Alibaba and DHGate is quite common. You've got a winner if you can find a local distributor willing to let you drop ship their product!

10. Set up an Online Course

If you have a skill and can articulate it, online education is for you.
Skillshare, Pluralsight, and Coursera have all made inroads in recent years, upskilling people with courses that YOU can create and earn from.

That's it for today! Please share if you liked this post. If not, well —