How to Use Obsidian to Boost Research Productivity
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:
- 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.
- Instructions for using Obsidian, managing notes, reading lists, and useful plugins. This section demonstrates how I use Obsidian, my preferred knowledge management tool.
- 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
Carl Sagan: “To make an apple pie from scratch, you must first create the universe.”
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:
#Tags and [[Links]] over /Folders/
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.
“Deep stuff Leo,” one person said. So my main issue is basic organization, losing track of my tasks and the reasons for them.
As a result, I'd go on other experiments that didn't make sense, and have to reverse engineer my logic for thesis writing. - PhD student now wise Postdoc
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:
- It had to be private, and nobody had to be able to read the entries.
- 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
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Adopt Elon Musk's learning strategy to succeed.
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No doubt here.
His name connotes success and intelligence.
He knows rocket science, engineering, AI, and solar power.
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You can apply these rules and become anyone you want.
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He starts with the tree's trunk, making sure he learns the basics before going on to branches and leaves.
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Elon Musk transformed industries this way. As his expertise grew, he connected branches and leaves from different trees.
Musk read two books a day as a child. He didn't specialize like most people. He gained from his multidisciplinary education. It helped him stand out and develop billion-dollar firms.
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Did I say entertain yourself?
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Read full article here
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10 Years of Trying to Manage Time and Improve My Productivity.
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James Clear's article mentions Eisenhower Box.
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Essential vs non-essential
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The S&P 500 was down 24% from its January highs at its low point this year. Bear market.
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Stock crash recovery
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During a bear market, you don't know if it will end quickly or feel like death by a thousand cuts.
Recessions vs. bear markets
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I agree. Four-decade high inflation. Since 1945, inflation has exceeded 5% nine times. Each inflationary spike caused a recession. Only slowing economic demand seems to stop price spikes.
This could happen again. Stocks seem to be pricing in a recession.
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Economic cycles are hard to predict. Even Wall Street makes mistakes.
Bears vs. bulls
Bear markets for U.S. stocks always end. Every stock market crash in U.S. history has been followed by new all-time highs.
How should investors view the recession? Investing risk is subjective.
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Without a degree and experience, you can get a high-paying tech job.
Most organizations follow this hiring rule: you chat with HR, interview with your future boss and other senior managers, and they make the final hiring choice.
If you've ever applied for a job, you know how arduous it can be. A newly snapped photo and a glossy resume template can wear you out. Applying to Google can change this experience.
According to an Universum report, Google is one of the world's most coveted employers. It's not simply the search giant's name and reputation that attract candidates, but its role requirements or lack thereof.
Candidates no longer need a beautiful resume, cover letter, Ivy League laurels, or years of direct experience. The company requires no degree or experience.
Elon Musk started it. He employed the two-hands test to uncover talented non-graduates. The billionaire eliminated the requirement for experience.
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Google's hiring is interesting. After its certification course, applicants can work in project management. Instead of academic degrees and experience, the company analyzes coursework.
Google finds the best project managers and technical staff in exchange. Google uses three strategies to find top talent.
Chase down the innovators
Google eliminates restrictions like education, experience, and others to find the polar bear amid the snowfall. Google's free project management education makes project manager responsibilities accessible to everyone.
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Firsthand knowledge follows the same rule. A lack of past information might be an employer's benefit. This is true for creative teams or businesses that prefer to innovate.
Or when corporations conduct differently from the competition. No-experience candidates can offer fresh perspectives. Fast Company reports that people with no sales experience beat those with 10 to 15 years of experience.
Give the aptitude test first priority.
Google wants the best candidates. Google wouldn't be able to receive more applications if it couldn't screen them for fit. Its well-organized online training program can be utilized as a portfolio.
Google learns a lot about an applicant through completed assignments. It reveals their ability, leadership style, communication capability, etc. The course mimics the job to assess candidates' suitability.
Basic screening questions might provide information to compare candidates. Any size small business can use screening questions and test projects to evaluate prospective employees.
Effective training for employees
Businesses must train employees regardless of their hiring purpose. Formal education and prior experience don't guarantee success. Maintaining your employees' professional knowledge gaps is key to their productivity and happiness. Top-notch training can do that. Learning and development are key to employee engagement, says Bob Nelson, author of 1,001 Ways to Engage Employees.
Google's online certification program isn't available everywhere. Improving the recruiting process means emphasizing aptitude over experience and a degree. Instead of employing new personnel and having them work the way their former firm trained them, train them how you want them to function.
If you want to know more about Google’s recruiting process, we recommend you watch the movie “Internship.”
Micah Daigle
3 years ago
Facebook is going away. Here are two explanations for why it hasn't been replaced yet.
And tips for anyone trying.
We see the same story every few years.
BREAKING NEWS: [Platform X] launched a social network. With Facebook's reputation down, the new startup bets millions will switch.
Despite the excitement surrounding each new platform (Diaspora, Ello, Path, MeWe, Minds, Vero, etc.), no major exodus occurred.
Snapchat and TikTok attracted teens with fresh experiences (ephemeral messaging and rapid-fire videos). These features aren't Facebook, even if Facebook replicated them.
Facebook's core is simple: you publish items (typically text/images) and your friends (generally people you know IRL) can discuss them.
It's cool. Sometimes I don't want to, but sh*t. I like it.
Because, well, I like many folks I've met. I enjoy keeping in touch with them and their banter.
I dislike Facebook's corporation. I've been cautiously optimistic whenever a Facebook-killer surfaced.
None succeeded.
Why? Two causes, I think:
People couldn't switch quickly enough, which is reason #1
Your buddies make a social network social.
Facebook started in self-contained communities (college campuses) then grew outward. But a new platform can't.
If we're expected to leave Facebook, we want to know that most of our friends will too.
Most Facebook-killers had bottlenecks. You have to waitlist or jump through hoops (e.g. setting up a server).
Same outcome. Upload. Chirp.
After a week or two of silence, individuals returned to Facebook.
Reason #2: The fundamental experience was different.
Even when many of our friends joined in the first few weeks, it wasn't the same.
There were missing features or a different UX.
Want to reply with a meme? No photos in comments yet. (Trying!)
Want to tag a friend? Nope, sorry. 2019!
Want your friends to see your post? You must post to all your friends' servers. Good luck!
It's difficult to introduce a platform with 100% of the same features as one that's been there for 20 years, yet customers want a core experience.
If you can't, they'll depart.
The causes that led to the causes
Having worked on software teams for 14+ years, I'm not surprised by these challenges. They are a natural development of a few tech sector meta-problems:
Lean startup methodology
Silicon Valley worships lean startup. It's a way of developing software that involves testing a stripped-down version with a limited number of people before selecting what to build.
Billion people use Facebook's functions. They aren't tested. It must work right away*
*This may seem weird to software people, but it's how non-software works! You can't sell a car without wheels.
2. Creativity
Startup entrepreneurs build new things, not copies. I understand. Reinventing the wheel is boring.
We know what works. Different experiences raise adoption friction. Once millions have transferred, more features (and a friendlier UX) can be implemented.
3. Cost scaling
True. Building a product that can sustain hundreds of millions of users in weeks is expensive and complex.
Your lifeboats must have the same capacity as the ship you're evacuating. It's required.
4. Pure ideologies
People who work on Facebook-alternatives are (understandably) critical of Facebook.
They build an open-source, fully-distributed, data-portable, interface-customizable, offline-capable, censorship-proof platform.
Prioritizing these aims can prevent replicating the straightforward experience users expect. Github, not Facebook, is for techies only.
What about the business plan, though?
Facebook-killer attempts have followed three models.
Utilize VC funding to increase your user base, then monetize them later. (If you do this, you won't kill Facebook; instead, Facebook will become you.)
Users must pay to utilize it. (This causes a huge bottleneck and slows the required quick expansion, preventing it from seeming like a true social network.)
Make it a volunteer-run, open-source endeavor that is free. (This typically denotes that something is cumbersome, difficult to operate, and is only for techies.)
Wikipedia is a fourth way.
Wikipedia is one of the most popular websites and a charity. No ads. Donations support them.
A Facebook-killer managed by a good team may gather millions (from affluent contributors and the crowd) for their initial phase of development. Then it might sustain on regular donations, ethical transactions (e.g. fees on commerce, business sites, etc.), and government grants/subsidies (since it would essentially be a public utility).
When you're not aiming to make investors rich, it's remarkable how little money you need.
If you want to build a Facebook competitor, follow these tips:
Drop the lean startup philosophy. Wait until you have a finished product before launching. Build it, thoroughly test it for bugs, and then release it.
Delay innovating. Wait till millions of people have switched before introducing your great new features. Make it nearly identical for now.
Spend money climbing. Make sure that guests can arrive as soon as they are invited. Never keep them waiting. Make things easy for them.
Make it accessible to all. Even if doing so renders it less philosophically pure, it shouldn't require technical expertise to utilize.
Constitute a nonprofit. Additionally, develop community ownership structures. Profit maximization is not the only strategy for preserving valued assets.
Last thoughts
Nobody has killed Facebook, but Facebook is killing itself.
The startup is burying the newsfeed to become a TikTok clone. Meta itself seems to be ditching the platform for the metaverse.
I wish I was happy, but I'm not. I miss (understandably) removed friends' postings and remarks. It could be a ghost town in a few years. My dance moves aren't TikTok-worthy.
Who will lead? It's time to develop a social network for the people.
Greetings if you're working on it. I'm not a company founder, but I like to help hard-working folks.