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

The metaverse is the most commonly used term in current technology discussions. While the entire tech ecosystem awaits the metaverse's full arrival, defining it is difficult. Imagine the internet in the '80s! The metaverse is a three-dimensional virtual world where users can interact with digital solutions and each other as digital avatars.
The metaverse is a three-dimensional virtual world where users can interact with digital solutions and each other as digital avatars.

Among the metaverse hype, the Decentraland vs Sandbox debate has gained traction. Both are decentralized metaverse platforms with no central authority. So, what's the difference and which is better? Let us examine the distinctions between Decentraland and Sandbox.

2 Popular Metaverse Platforms Explained

The first step in comparing sandbox and Decentraland is to outline the definitions. Anyone keeping up with the metaverse news has heard of the two current leaders. Both have many similarities, but also many differences. Let us start with defining both platforms to see if there is a winner.

Decentraland

Decentraland, a fully immersive and engaging 3D metaverse, launched in 2017. It allows players to buy land while exploring the vast virtual universe. Decentraland offers a wide range of activities for its visitors, including games, casinos, galleries, and concerts. It is currently the longest-running metaverse project.

Decentraland began with a $24 million ICO and went public in 2020. The platform's virtual real estate parcels allow users to create a variety of experiences. MANA and LAND are two distinct tokens associated with Decentraland. MANA is the platform's native ERC-20 token, and users can burn MANA to get LAND, which is ERC-721 compliant. The MANA coin can be used to buy avatars, wearables, products, and names on Decentraland.

Sandbox

Sandbox, the next major player, began as a blockchain-based virtual world in 2011 and migrated to a 3D gaming platform in 2017. The virtual world allows users to create, play, own, and monetize their virtual experiences. Sandbox aims to empower artists, creators, and players in the blockchain community to customize the platform. Sandbox gives the ideal means for unleashing creativity in the development of the modern gaming ecosystem.

The project combines NFTs and DAOs to empower a growing community of gamers. A new play-to-earn model helps users grow as gamers and creators. The platform offers a utility token, SAND, which is required for all transactions.

What are the key points from both metaverse definitions to compare Decentraland vs sandbox?

It is ideal for individuals, businesses, and creators seeking new artistic, entertainment, and business opportunities. It is one of the rapidly growing Decentralized Autonomous Organization projects. Holders of MANA tokens also control the Decentraland domain.

Sandbox, on the other hand, is a blockchain-based virtual world that runs on the native token SAND. On the platform, users can create, sell, and buy digital assets and experiences, enabling blockchain-based gaming. Sandbox focuses on user-generated content and building an ecosystem of developers.

Sandbox vs. Decentraland

If you try to find what is better Sandbox or Decentraland, then you might struggle with only the basic definitions. Both are metaverse platforms offering immersive 3D experiences. Users can freely create, buy, sell, and trade digital assets. However, both have significant differences, especially in MANA vs SAND.

For starters, MANA has a market cap of $5,736,097,349 versus $4,528,715,461, giving Decentraland an advantage.
The MANA vs SAND pricing comparison is also noteworthy. A SAND is currently worth $3664, while a MANA is worth $2452.

The value of the native tokens and the market capitalization of the two metaverse platforms are not enough to make a choice. Let us compare Sandbox vs Decentraland based on the following factors.

Workstyle

The way Decentraland and Sandbox work is one of the main comparisons. From a distance, they both appear to work the same way. But there's a lot more to learn about both platforms' workings. Decentraland has 90,601 digital parcels of land.

Individual parcels of virtual real estate or estates with multiple parcels of land are assembled. It also has districts with similar themes and plazas, which are non-tradeable parcels owned by the community. It has three token types: MANA, LAND, and WEAR.

Sandbox has 166,464 plots of virtual land that can be grouped into estates. Estates are owned by one person, while districts are owned by two or more people. The Sandbox metaverse has four token types: SAND, GAMES, LAND, and ASSETS.

Age

The maturity of metaverse projects is also a factor in the debate. Decentraland is clearly the winner in terms of maturity. It was the first solution to create a 3D blockchain metaverse. Decentraland made the first working proof of concept public. However, Sandbox has only made an Alpha version available to the public.

Backing

The MANA vs SAND comparison would also include support for both platforms. Digital Currency Group, FBG Capital, and CoinFund are all supporters of Decentraland. It has also partnered with Polygon, the South Korean government, Cyberpunk, and Samsung.

SoftBank, a Japanese multinational conglomerate focused on investment management, is another major backer. Sandbox has the backing of one of the world's largest investment firms, as well as Slack and Uber.

Compatibility

Wallet compatibility is an important factor in comparing the two metaverse platforms. Decentraland currently has a competitive advantage. How? Both projects' marketplaces accept ERC-20 wallets. However, Decentraland has recently improved by bridging with Walletconnect. So it can let Polygon users join Decentraland.

Scalability

Because Sandbox and Decentraland use the Ethereum blockchain, scalability is an issue. Both platforms' scalability is constrained by volatile tokens and high gas fees. So, scalability issues can hinder large-scale adoption of both metaverse platforms.

Buying Land

Decentraland vs Sandbox comparisons often include virtual real estate. However, the ability to buy virtual land on both platforms defines the user experience and differentiates them. In this case, Sandbox offers better options for users to buy virtual land by combining OpenSea and Sandbox. In fact, Decentraland users can only buy from the MANA marketplace.

Innovation

The rate of development distinguishes Sandbox and Decentraland. Both platforms have been developing rapidly new features. However, Sandbox wins by adopting Polygon NFT layer 2 solutions, which consume almost 100 times less energy than Ethereum.

Collaborations

The platforms' collaborations are the key to determining "which is better Sandbox or Decentraland." Adoption of metaverse platforms like the two in question can be boosted by association with reputable brands. Among the partners are Atari, Cyberpunk, and Polygon. Rather, Sandbox has partnered with well-known brands like OpenSea, CryptoKitties, The Walking Dead, Snoop Dogg, and others.

Platform Adaptivity

Another key feature that distinguishes Sandbox and Decentraland is the ease of use. Sandbox clearly wins in terms of platform access. It allows easy access via social media, email, or a Metamask wallet. However, Decentraland requires a wallet connection.

Prospects

The future development plans also play a big role in defining Sandbox vs Decentraland. Sandbox's future development plans include bringing the platform to mobile devices. This includes consoles like PlayStation and Xbox. By the end of 2023, the platform expects to have around 5000 games.

Decentraland, on the other hand, has no set plan. In fact, the team defines the decisions that appear to have value. They plan to add celebrities, creators, and brands soon, along with NFT ads and drops.

Final Words

The comparison of Decentraland vs Sandbox provides a balanced view of both platforms. You can see how difficult it is to determine which decentralized metaverse is better now. Sandbox is still in Alpha, whereas Decentraland has a working proof of concept.

Sandbox, on the other hand, has better graphics and is backed by some big names. But both have a long way to go in the larger decentralized metaverse.