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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Historically, only large financial institutions, brokerages, and trading houses could actively trade in the stock market. With instant global news dissemination and low commissions, developments such as discount brokerages and online trading have leveled the playing—or should we say trading—field. It's never been easier for retail investors to trade like pros thanks to trading platforms like Robinhood and zero commissions.

Day trading is a lucrative career (as long as you do it properly). But it can be difficult for newbies, especially if they aren't fully prepared with a strategy. Even the most experienced day traders can lose money.

So, how does day trading work?

Day Trading Basics

Day trading is the practice of buying and selling a security on the same trading day. It occurs in all markets, but is most common in forex and stock markets. Day traders are typically well educated and well funded. For small price movements in highly liquid stocks or currencies, they use leverage and short-term trading strategies.

Day traders are tuned into short-term market events. News trading is a popular strategy. Scheduled announcements like economic data, corporate earnings, or interest rates are influenced by market psychology. Markets react when expectations are not met or exceeded, usually with large moves, which can help day traders.

Intraday trading strategies abound. Among these are:

• Scalping: This strategy seeks to profit from minor price changes throughout the day.
• Range trading: To determine buy and sell levels, range traders use support and resistance levels.
• News-based trading exploits the increased volatility around news events.
• High-frequency trading (HFT): The use of sophisticated algorithms to exploit small or short-term market inefficiencies.

A Disputed Practice

Day trading's profit potential is often debated on Wall Street. Scammers have enticed novices by promising huge returns in a short time. Sadly, the notion that trading is a get-rich-quick scheme persists. Some daytrade without knowledge. But some day traders succeed despite—or perhaps because of—the risks.

Day trading is frowned upon by many professional money managers. They claim that the reward rarely outweighs the risk. Those who day trade, however, claim there are profits to be made. Profitable day trading is possible, but it is risky and requires considerable skill. Moreover, economists and financial professionals agree that active trading strategies tend to underperform passive index strategies over time, especially when fees and taxes are factored in.

Day trading is not for everyone and is risky. It also requires a thorough understanding of how markets work and various short-term profit strategies. Though day traders' success stories often get a lot of media attention, keep in mind that most day traders are not wealthy: Many will fail, while others will barely survive. Also, while skill is important, bad luck can sink even the most experienced day trader.

Characteristics of a Day Trader

Experts in the field are typically well-established professional day traders.
They usually have extensive market knowledge. Here are some prerequisites for successful day trading.

Market knowledge and experience

Those who try to day-trade without understanding market fundamentals frequently lose. Day traders should be able to perform technical analysis and read charts. Charts can be misleading if not fully understood. Do your homework and know the ins and outs of the products you trade.

Enough capital

Day traders only use risk capital they can lose. This not only saves them money but also helps them trade without emotion. To profit from intraday price movements, a lot of capital is often required. Most day traders use high levels of leverage in margin accounts, and volatile market swings can trigger large margin calls on short notice.

Strategy

A trader needs a competitive advantage. Swing trading, arbitrage, and trading news are all common day trading strategies. They tweak these strategies until they consistently profit and limit losses.

Strategy Breakdown:

Type | Risk | Reward

Swing Trading | High | High
Arbitrage | Low | Medium
Trading News | Medium | Medium
Mergers/Acquisitions | Medium | High

Discipline

A profitable strategy is useless without discipline. Many day traders lose money because they don't meet their own criteria. “Plan the trade and trade the plan,” they say. Success requires discipline.

Day traders profit from market volatility. For a day trader, a stock's daily movement is appealing. This could be due to an earnings report, investor sentiment, or even general economic or company news.

Day traders also prefer highly liquid stocks because they can change positions without affecting the stock's price. Traders may buy a stock if the price rises. If the price falls, a trader may decide to sell short to profit.

A day trader wants to trade a stock that moves (a lot).

Day Trading for a Living

Professional day traders can be self-employed or employed by a larger institution.

Most day traders work for large firms like hedge funds and banks' proprietary trading desks. These traders benefit from direct counterparty lines, a trading desk, large capital and leverage, and expensive analytical software (among other advantages). By taking advantage of arbitrage and news events, these traders can profit from less risky day trades before individual traders react.

Individual traders often manage other people’s money or simply trade with their own. They rarely have access to a trading desk, but they frequently have strong ties to a brokerage (due to high commissions) and other resources. However, their limited scope prevents them from directly competing with institutional day traders. Not to mention more risks. Individuals typically day trade highly liquid stocks using technical analysis and swing trades, with some leverage. 

Day trading necessitates access to some of the most complex financial products and services. Day traders usually need:

Access to a trading desk

Traders who work for large institutions or manage large sums of money usually use this. The trading or dealing desk provides these traders with immediate order execution, which is critical during volatile market conditions. For example, when an acquisition is announced, day traders interested in merger arbitrage can place orders before the rest of the market.

News sources

The majority of day trading opportunities come from news, so being the first to know when something significant happens is critical. It has access to multiple leading newswires, constant news coverage, and software that continuously analyzes news sources for important stories.

Analytical tools

Most day traders rely on expensive trading software. Technical traders and swing traders rely on software more than news. This software's features include:

• Automatic pattern recognition: It can identify technical indicators like flags and channels, or more complex indicators like Elliott Wave patterns.

• Genetic and neural applications: These programs use neural networks and genetic algorithms to improve trading systems and make more accurate price predictions.

• Broker integration: Some of these apps even connect directly to the brokerage, allowing for instant and even automatic trade execution. This reduces trading emotion and improves execution times.

• Backtesting: This allows traders to look at past performance of a strategy to predict future performance. Remember that past results do not always predict future results.

Together, these tools give traders a competitive advantage. It's easy to see why inexperienced traders lose money without them. A day trader's earnings potential is also affected by the market in which they trade, their capital, and their time commitment.

Day Trading Risks

Day trading can be intimidating for the average investor due to the numerous risks involved. The SEC highlights the following risks of day trading:

Because day traders typically lose money in their first months of trading and many never make profits, they should only risk money they can afford to lose.
Trading is a full-time job that is stressful and costly: Observing dozens of ticker quotes and price fluctuations to spot market trends requires intense concentration. Day traders also spend a lot on commissions, training, and computers.
Day traders heavily rely on borrowing: Day-trading strategies rely on borrowed funds to make profits, which is why many day traders lose everything and end up in debt.
Avoid easy profit promises: Avoid “hot tips” and “expert advice” from day trading newsletters and websites, and be wary of day trading educational seminars and classes. 

Should You Day Trade?
As stated previously, day trading as a career can be difficult and demanding.

• First, you must be familiar with the trading world and know your risk tolerance, capital, and goals.
• Day trading also takes a lot of time. You'll need to put in a lot of time if you want to perfect your strategies and make money. Part-time or whenever isn't going to cut it. You must be fully committed.
• If you decide trading is for you, remember to start small. Concentrate on a few stocks rather than jumping into the market blindly. Enlarging your trading strategy can result in big losses.
• Finally, keep your cool and avoid trading emotionally. The more you can do that, the better. Keeping a level head allows you to stay focused and on track.
  If you follow these simple rules, you may be on your way to a successful day trading career.

Is Day Trading Illegal?

Day trading is not illegal or unethical, but it is risky. Because most day-trading strategies use margin accounts, day traders risk losing more than they invest and becoming heavily in debt.

How Can Arbitrage Be Used in Day Trading?

Arbitrage is the simultaneous purchase and sale of a security in multiple markets to profit from small price differences. Because arbitrage ensures that any deviation in an asset's price from its fair value is quickly corrected, arbitrage opportunities are rare.

Why Don’t Day Traders Hold Positions Overnight?

Day traders rarely hold overnight positions for several reasons: Overnight trades require more capital because most brokers require higher margin; stocks can gap up or down on overnight news, causing big trading losses; and holding a losing position overnight in the hope of recovering some or all of the losses may be against the trader's core day-trading philosophy.

What Are Day Trader Margin Requirements?

Regulation D requires that a pattern day trader client of a broker-dealer maintain at all times $25,000 in equity in their account.

How Much Buying Power Does Day Trading Have?

Buying power is the total amount of funds an investor has available to trade securities. FINRA rules allow a pattern day trader to trade up to four times their maintenance margin excess as of the previous day's close.

The Verdict

Although controversial, day trading can be a profitable strategy. Day traders, both institutional and retail, keep the markets efficient and liquid. Though day trading is still popular among novice traders, it should be left to those with the necessary skills and resources.