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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A full 6-part email sales cycle
The essential elements you must incorporate
placeholders and text-filled images
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Problem
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Dr Mehmet Yildiz
2 years ago
How I train my brain daily for clarity and productivity.
I use a conceptual and practical system I developed decades ago as an example.
Since childhood, I've been interested in the brain-mind connection, so I developed a system using scientific breakthroughs, experiments, and the experiences of successful people in my circles.
This story provides a high-level overview of a custom system to inform and inspire readers. Creating a mind gym was one of my best personal and professional investments.
Such a complex system may not be possible for everyone or appear luxurious at first. However, the process and approach may help you find more accessible and viable solutions.
Visualizing the brain as a muscle, I learned to stimulate it with physical and mental exercises, applying a new mindset and behavioral changes.
My methods and practices may not work for others because we're all different. I focus on the approach's principles and highlights so you can create your own program.
Some create a conceptual and practical system intuitively, and others intellectually. Both worked. I see intellect and intuition as higher selves.
The mental tools I introduce are based on lifestyle changes and can be personalized by anyone, barring physical constraints or underlying health conditions.
Some people can't meditate despite wanting to due to mental constraints. This story lacks exceptions.
People's systems may vary. Many have used my tools successfully. All have scientific backing because their benefits attracted scientists. None are unethical or controversial.
My focus is cognition, which is the neocortex's ability. These practices and tools can affect the limbic and reptilian brain regions.
A previous article discussed brain health's biological aspects. This article focuses on psychology.
Thinking, learning, and remembering are cognitive abilities. Cognitive abilities determine our health and performance.
Cognitive health is the ability to think, concentrate, learn, and remember. Cognitive performance boosting involves various tools and processes. My system and protocols address cognitive health and performance.
As a biological organ, the brain's abilities decline with age, especially if not used regularly. Older people have more neurodegenerative disorders like dementia.
As aging is inevitable, I focus on creating cognitive reserves to remain mentally functional as we age and face mental decline or cognitive impairment.
My protocols focus on neurogenesis, or brain growth and maintenance. Neurons and connections can grow at any age.
Metacognition refers to knowing our cognitive abilities, like thinking about thinking and learning how to learn.
In the following sections, I provide an overview of my system, mental tools, and protocols.
This system summarizes my 50-year career. Some may find it too abstract, so I give examples.
First, explain the system. Section 2 introduces activities. Third, how to measure and maintain mental growth.
1 — Developed a practical mental gym.
The mental gym is a metaphor for the physical fitness gym to improve our mental muscles.
This concept covers brain and mind functionality. Integrated biological and psychological components.
I'll describe my mental gym so my other points make sense. My mental gym has physical and mental tools.
Mindfulness, meditation, visualization, self-conversations, breathing exercises, expressive writing, working in a flow state, reading, music, dance, isometric training, barefoot walking, cold/heat exposure, CBT, and social engagements are regular tools.
Dancing, walking, and thermogenesis are body-related tools. As the brain is part of the body and houses the mind, these tools can affect mental abilities such as attention, focus, memory, task switching, and problem-solving.
Different people may like different tools. I chose these tools based on my needs, goals, and lifestyle. They're just examples. You can choose tools that fit your goals and personality.
2 — Performed tasks regularly.
These tools gave me clarity. They became daily hobbies. Some I did alone, others with others.
Some examples: I meditate daily. Even though my overactive mind made daily meditation difficult at first, I now enjoy it. Meditation three times a day sharpens my mind.
Self-talk is used for self-therapy and creativity. Self-talk was initially difficult, but neurogenesis rewired my brain to make it a habit.
Cold showers, warm baths with Epsom salts, fasting, barefoot walks on the beach or grass, dancing, calisthenics, trampoline hopping, and breathing exercises increase my mental clarity, creativity, and productivity.
These exercises can increase BDNF, which promotes nervous system growth. They improve mental capacity and performance by increasing blood flow and brain oxygenation.
I use weekly and occasional activities like dry saunas, talking with others, and community activities.
These activities stimulate the brain and mind, improving performance and cognitive capacity.
3 — Measured progress, set growth goals.
Measuring progress helps us stay on track. Without data, it's hard to stay motivated. When we face inevitable setbacks, we may abandon our dreams.
I created a daily checklist for a spreadsheet with macros. I tracked how often and long I did each activity.
I measured my progress objectively and subjectively. In the progress spreadsheet, I noted my meditation hours and subjective feelings.
In another column, I used good, moderate, and excellent to get qualitative data. It took time and effort. Later, I started benefiting from this automated structure.
Creating a page for each activity, such as meditation, self-talk, cold showers, walking, expressive writing, personal interactions, etc., gave me empirical data I could analyze, modify, and graph to show progress.
Colored charts showed each area's strengths and weaknesses.
Strengths motivate me to continue them. Identifying weaknesses helped me improve them.
As the system matured, data recording became a habit and took less time. I saw the result immediately because I automated the charts when I entered daily data. Early time investment paid off later.
Mind Gym Benefits, Effective Use, and Progress Measuring
This concept helped me move from comfort to risk. I accept things as they are.
Turnarounds were made. I stopped feeling "Fight-Flight-Freeze" and maintained self-control.
I tamed my overactive amygdala by strengthening my brain. Stress and anxiety decreased. With these shifts, I accepted criticism and turned envy into admiration. Clarity improved.
When the cognitive part of the brain became stronger and the primitive part was tamed, managing thoughts and emotions became easier. My AQ increased. I learned to tolerate people, physical, mental, and emotional obstacles.
Accessing vast information sources in my subconscious mind through an improved RAS allowed me to easily tap into my higher self and recognize flaws in my lower self.
Summary
The brain loves patterns and routines, so habits help. Observing, developing, and monitoring habits mindfully can be beneficial. Mindfulness helps us achieve this goal systematically.
As body and mind are connected, we must consider both when building habits. Consistent and joyful practices can strengthen neurons and neural connections.
Habits help us accomplish more with less effort. Regularly using mental tools and processes can improve our cognitive health and performance as we age.
Creating daily habits to improve cognitive abilities can sharpen our minds and boost our well-being.
Some apps monitor our activities and behavior to help build habits. If you can't replicate my system, try these apps. Some smartwatches and fitness devices include them.
Set aside time each day for mental activities you enjoy. Regular scheduling and practice can strengthen brain regions and form habits. Once you form habits, tasks become easy.
Improving our minds is a lifelong journey. It's easier and more sustainable to increase our efforts daily, weekly, monthly, or annually.
Despite life's ups and downs, many want to remain calm and cheerful.
This valuable skill is unrelated to wealth or fame. It's about our mindset, fueled by our biological and psychological needs.
Here are some lessons I've learned about staying calm and composed despite challenges and setbacks.
1 — Tranquillity starts with observing thoughts and feelings.
2 — Clear the mental clutter and emotional entanglements with conscious breathing and gentle movements.
3 — Accept situations and events as they are with no resistance.
4 — Self-love can lead to loving others and increasing compassion.
5 — Count your blessings and cultivate gratitude.
Clear thinking can bring joy and satisfaction. It's a privilege to wake up with a healthy body and clear mind, ready to connect with others and serve them.
Thank you for reading my perspectives. I wish you a healthy and happy life.
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The FOMC meets 8 times a year to set the target FFR. This is supposed to promote economic growth. The overnight lending market sets the actual rate based on commercial banks' short-term reserves. If the market strays too far, the Fed intervenes.
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Alex Mathers
3 years ago
12 habits of the zenith individuals I know
Calmness is a vital life skill.
It aids communication. It boosts creativity and performance.
I've studied calm people's habits for years. Commonalities:
Have mastered the art of self-humor.
Protectors take their job seriously, draining the room's energy.
They are fixated on positive pursuits like making cool things, building a strong physique, and having fun with others rather than on depressing influences like the news and gossip.
Every day, spend at least 20 minutes moving, whether it's walking, yoga, or lifting weights.
Discover ways to take pleasure in life's challenges.
Since perspective is malleable, they change their view.
Set your own needs first.
Stressed people neglect themselves and wonder why they struggle.
Prioritize self-care.
Don't ruin your life to please others.
Make something.
Calm people create more than react.
They love creating beautiful things—paintings, children, relationships, and projects.
Don’t hold their breath.
If you're stressed or angry, you may be surprised how much time you spend holding your breath and tightening your belly.
Release, breathe, and relax to find calm.
Stopped rushing.
Rushing is disadvantageous.
Calm people handle life better.
Are aware of their own dietary requirements.
They avoid junk food and eat foods that keep them healthy, happy, and calm.
Don’t take anything personally.
Stressed people control everything.
Self-conscious.
Calm people put others and their work first.
Keep their surroundings neat.
Maintaining an uplifting and clutter-free environment daily calms the mind.
Minimise negative people.
Calm people are ruthless with their boundaries and avoid negative and drama-prone people.
Victoria Kurichenko
3 years ago
Updates From Google For Content Producers What You Should Know Is This
People-first update.
Every Google upgrade causes website owners to panic.
Some have just recovered from previous algorithm tweaks and resumed content development.
If you follow Google's Webmaster rules, you shouldn't fear its adjustments.
Everyone has a view of them. Miscommunication and confusion result.
Now, for some (hopefully) exciting news.
Google tweeted on August 18, 2022 about a fresh content update.
This change is another Google effort to remove low-quality, repetitive, and AI-generated content.
The algorithm generates and analyzes search results, not humans.
Google spends a lot to teach its algorithm what searchers want. Intent isn't always clear.
Google's content update aims to:
“… ensure people see more original, helpful content written by people, for people, in search results.”
Isn't it a noble goal?
However, what does it mean for content creators and website owners?
How can you ensure you’re creating content that will be successful after the updates roll out?
Let's first define people-first content.
What does "people-first-content" mean?
If asked, I'd say information written to answer queries and solve problems.
Like others, I read it from the term.
Content creators and marketers disagree. They need more information to follow recommendations.
Google gives explicit instructions for creating people-first content.
According to Google, if you answer yes to the following questions, you have a people-first attitude.
Do you have customers who might find your content useful if they contacted you directly?
Does your content show the breadth of your knowledge?
Do you have a niche or a focus for your website?
After reading your content, will readers learn something new to aid them in achieving their goals?
Are readers happy after reading your content?
Have you been adhering to Google's fundamental updates and product reviews?
As an SEO writer, I'm not scared.
I’ve been following these rules consciously while creating content for my website. That’s why it’s been steadily growing despite me publishing just one or two stories a month.
If you avoid AI-generated text and redundant, shallow material, your website won't suffer.
If you use unscrupulous methods to boost your website's traffic, including link buying or keyword stuffing, stop. Google is getting smarter and will find and punish your site eventually.
For those who say, “SEO is no longer working,” I dedicated the whole paragraph below.
This does not imply that SEO is obsolete.
Google:
“People-first content creators focus on creating satisfying content, while also utilizing SEO best practices to bring searchers additional value.”
The official helpful content update page lists two people-first content components:
meeting user needs
best practices for SEO
Always read official guidelines, not unsolicited suggestions.
SEO will work till search engines die.
How to use the update
Google said the changes will arrive in August 2022.
They pledged to post updates on Google's search ranking updates page.
Google also tweets this info. If you haven't followed it already, I recommend it.
Ranking adjustments could take two weeks and will affect English searches internationally initially.
Google affirmed plans to extend to other languages.
If you own a website, monitor your rankings and traffic to see if it's affected.