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

What can't Google do?
Seriously, nothing! Google rocks.
Google is a major player in online tools and services. We use it for everything, from research to entertainment.
Did I say entertain yourself?
Yes, with so many features and options, it can be difficult to fully utilize Google.

#1. Drive Google Mad

You can make Google's homepage dance if you want to be silly.
Just type “Google Gravity” into Google.com. Then select I'm lucky.
See the page unstick before your eyes!

#2 Play With Google Image

Google isn't just for work.
Then have fun with it!
You can play games right in your search results. When you need a break, google “Solitaire” or “Tic Tac Toe”. 

#3. Do a Barrel Roll

Need a little more excitement in your life? Want to see Google dance?
Type “Do a barrel roll” into the Google search bar.
Then relax and watch your screen do a 360. 

#4  No Internet?  No issue!

This is a fun trick to use when you have no internet.
If your browser shows a “No Internet” page, simply press Space.
Boom!
We have dinosaurs! Now use arrow keys to save your pixelated T-Rex from extinction.

#5 Google Can Help

Play this Google coin flip game to see if you're lucky.
Enter “Flip a coin” into the search engine.
You'll see a coin flipping animation. If you get heads or tails, click it. 

#6. Think with Google

My favorite Google find so far is the “Think with Google” website.
Think with Google is a website that offers marketing insights, research, and case studies.
I highly recommend it to entrepreneurs, small business owners, and anyone interested in online marketing. 

#7. Google Can Read Images!

This is a cool Google trick that few know about.
You can search for images by keyword or upload your own by clicking the camera icon on Google Images.
Google will then show you all of its similar images.

#8. Modify the Google Logo!

Clicking on the “I'm Feeling Lucky” button on Google.com takes you to a random Google Doodle.
Each year, Google creates a Doodle to commemorate holidays, anniversaries, and other occasions.

#9. What is my IP?

Simply type “What is my IP” into Google to find out.
Your IP address will appear on the results page.

#10. Send a Self-Destructing Email With Gmail, 

Create a new message in Gmail. Find an icon that resembles a lock and a clock near the SEND button. That's where the Confidential Mode is.
By clicking it, you can set an expiration date for your email. Expiring emails are automatically deleted from both your and the recipient's inbox.

#11. Blink, Google Blink!

This is a unique Google trick.
Type “blink HTML” into Google. The words “blink HTML” will appear and then disappear.
The text is displayed for a split second before being deleted.
To make this work, Google reads the HTML code and executes the “blink” command. 

#12. The Answer To Everything

This is for all Douglas Adams fans.
The answer to life, the universe, and everything is 42, according to Google.
An allusion to Douglas Adams' Hitchhiker's Guide to the Galaxy, in which Ford Prefect seeks to understand life, the universe, and everything.

#13. Google in 1998

It's a blast!
Type “Google in 1998” into Google. "I'm feeling lucky"
You'll be taken to an old-school Google homepage.
It's a nostalgic trip for long-time Google users. 

#14. Scholarships and Internships

Google can help you find college funding!
Type “scholarships” or “internships” into Google.
The number of results will surprise you. 

#15. OK, Google. Dice!

To roll a die, simply type “Roll a die” into Google.
On the results page is a virtual dice that you can click to roll. 

#16. Google has secret codes!

Hit the nine squares on the right side of your Google homepage to go to My Account. Then Personal Info.
You can add your favorite language to the “General preferences for the web” tab. 

#17. Google Terminal 

You can feel like a true hacker.
Just type “Google Terminal” into Google.com. "I'm feeling lucky"
Voila~!
You'll be taken to an old-school computer terminal-style page.
You can then type commands to see what happens.

Have you tried any of these activities? Tell me in the comments.

Read full article here

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.