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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WWDC 2022 began early Tuesday morning. WWDC brought a ton of new features (which went for just shy of two hours).

With so many announcements, we thought we'd compile them. And now...

WWDC?

WWDC is Apple's developer conference. This includes iOS, macOS, watchOS, and iPadOS (all of its iPads). It's where Apple announces new features for developers to use. It's also where Apple previews new software.

Virtual WWDC runs June 6-10.  You can rewatch the stream on Apple's website.

WWDC 2022 news:

Completely everything. Really. iOS 16 first.

iOS 16.

iOS 16 is a major iPhone update. iOS 16 adds the ability to customize the Lock Screen's color/theme. And widgets. It also organizes notifications and pairs Lock Screen with Focus themes. Edit or recall recently sent messages, recover recently deleted messages, and mark conversations as unread. Apple gives us yet another reason to stay in its walled garden with iMessage.

New iOS includes family sharing. Parents can set up a child's account with parental controls to restrict apps, movies, books, and music. iOS 16 lets large families and friend pods share iCloud photos. Up to six people can contribute photos to a separate iCloud library.

Live Text is getting creepier. Users can interact with text in any video frame. Touch and hold an image's subject to remove it from its background and place it in apps like messages. Dictation offers a new on-device voice-and-touch experience. Siri can run app shortcuts without setup in iOS 16. Apple also unveiled a new iOS 16 feature to help people break up with abusive partners who track their locations or read their messages. Safety Check.

Apple Pay Later allows iPhone users to buy products and pay for them later. iOS 16 pushes Mail. Users can schedule emails and cancel delivery before it reaches a recipient's inbox (be quick!). Mail now detects if you forgot an attachment, as Gmail has for years. iOS 16's Maps app gets "Multi-Stop Routing," .

Apple News also gets an iOS 16 update. Apple News adds My Sports. With iOS 16, the Apple Watch's Fitness app is also coming to iOS and the iPhone, using motion-sensing tech to track metrics and performance (as long as an athlete is wearing or carrying the device on their person). 

iOS 16 includes accessibility updates like Door Detection.

watchOS9

Many of Apple's software updates are designed to take advantage of the larger screens in recent models, but they also improve health and fitness tracking.

The most obvious reason to upgrade watchOS every year is to get new watch faces from Apple. WatchOS 9 will add four new faces.

Runners' workout metrics improve.
Apple quickly realized that fitness tracking would be the Apple Watch's main feature, even though it's been the killer app for wearables since their debut. For watchOS 9, the Apple Watch will use its accelerometer and gyroscope to track a runner's form, stride length, and ground contact time. It also introduces the ability to specify heart rate zones, distance, and time intervals, with vibrating haptic feedback and voice alerts.

The Apple Watch's Fitness app is coming to iOS and the iPhone, using the smartphone's motion-sensing tech to track metrics and performance (as long as an athlete is wearing or carrying the device on their person).

We'll get sleep tracking, medication reminders, and drug interaction alerts. Your watch can create calendar events. A new Week view shows what meetings or responsibilities stand between you and the weekend.

iPadOS16

WWDC 2022 introduced iPad updates. iPadOS 16 is similar to iOS for the iPhone, but has features for larger screens and tablet accessories. The software update gives it many iPhone-like features.

iPadOS 16's Home app, like iOS 16, will have a new design language. iPad users who want to blame it on the rain finally have a Weather app. iPadOS 16 will have iCloud's Shared Photo Library, Live Text and Visual Look Up upgrades, and FaceTime Handoff, so you can switch between devices during a call.

Apple highlighted iPadOS 16's multitasking at WWDC 2022. iPad's Stage Manager sounds like a community theater app. It's a powerful multitasking tool for tablets and brings them closer to emulating laptops. Apple's iPadOS 16 supports multi-user collaboration. You can share content from Files, Keynote, Numbers, Pages, Notes, Reminders, Safari, and other third-party apps in Apple Messages.

M2-chip

WWDC 2022 revealed Apple's M2 chip. Apple has started the next generation of Apple Silicon for the Mac with M2. Apple says this device improves M1's performance.

M2's second-generation 5nm chip has 25% more transistors than M1's. 100GB/s memory bandwidth (50 per cent more than M1). M2 has 24GB of unified memory, up from 16GB but less than some ultraportable PCs' 32GB. The M2 chip has 10% better multi-core CPU performance than the M2, and it's nearly twice as fast as the latest 10-core PC laptop chip at the same power level (CPU performance is 18 per cent greater than M1).

New MacBooks

Apple introduced the M2-powered MacBook Air. Apple's entry-level laptop has a larger display, a new processor, new colors, and a notch.

M2 also powers the 13-inch MacBook Pro. The 13-inch MacBook Pro has 24GB of unified memory and 50% more memory bandwidth. New MacBook Pro batteries last 20 hours. As I type on the 2021 MacBook Pro, I can only imagine how much power the M2 will add.

macOS 13.0 (or, macOS Ventura)

macOS Ventura will take full advantage of M2 with new features like Stage Manager and Continuity Camera and Handoff for FaceTime. Safari, Mail, Messages, Spotlight, and more get updates in macOS Ventura.

Apple hasn't run out of California landmarks to name its OS after yet. macOS 13 will be called Ventura when it's released in a few months, but it's more than a name change and new wallpapers. 

Stage Manager organizes windows

Stage Manager is a new macOS tool that organizes open windows and applications so they're still visible while focusing on a specific task. The main app sits in the middle of the desktop, while other apps and documents are organized and piled up to the side.

Improved Searching

Spotlight is one of macOS's least appreciated features, but with Ventura, it's becoming even more useful. Live Text lets you extract text from Spotlight results without leaving the window, including images from the photo library and the web.

Mail lets you schedule or unsend emails.

We've all sent an email we regret, whether it contained regrettable words or was sent at the wrong time. In macOS Ventura, Mail users can cancel or reschedule a message after sending it. Mail will now intelligently determine if a person was forgotten from a CC list or if a promised attachment wasn't included. Procrastinators can set a reminder to read a message later.

Safari adds tab sharing and password passkeys

Apple is updating Safari to make it more user-friendly... mostly. Users can share a group of tabs with friends or family, a useful feature when researching a topic with too many tabs. Passkeys will replace passwords in Safari's next version. Instead of entering random gibberish when creating a new account, macOS users can use TouchID to create an on-device passkey. Using an iPhone's camera and a QR system, Passkey syncs and works across all Apple devices and Windows computers.

Continuity adds Facetime device switching and iPhone webcam.

With macOS Ventura, iPhone users can transfer a FaceTime call from their phone to their desktop or laptop using Handoff, or vice versa if they started a call at their desk and need to continue it elsewhere. Apple finally admits its laptop and monitor webcams aren't the best. Continuity makes the iPhone a webcam. Apple demonstrated a feature where the wide-angle lens could provide a live stream of the desk below, while the standard zoom lens could focus on the speaker's face. New iPhone laptop mounts are coming.

System Preferences

System Preferences is Now System Settings and Looks Like iOS
Ventura's System Preferences has been renamed System Settings and is much more similar in appearance to iOS and iPadOS. As the iPhone and iPad are gateway devices into Apple's hardware ecosystem, new Mac users should find it easier to adjust.

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