More on Productivity
Leonardo Castorina
3 years ago
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
David G Chen
3 years ago
If you want to earn money, stop writing for entertainment.
When you stop blogging for a few weeks, your views and profits plummet.
Because you're writing fascinating posts for others. Everyone's done ithat…
If I keep writing, the graph should maintain velocity, you could say. If I wrote more, it could rise.
However, entertaining pieces still tend to roller coaster and jump.
this type of writing is like a candle. They burn out and must be replaced. You must continuously light new ones to maintain the illumination.
When you quit writing, your income stops.
A substitute
Instead of producing amusing articles, try solving people's issues. You should answer their search questions.
Here's what happens when you answer their searches.
My website's Google analytics. As a dentist, I answer oral health questions.
This chart vs. Medium is pretty glaring, right?
As of yesterday, it was averaging 15k page views each day.
How much would you make on Medium with 15k daily views?
Evergreen materials
In SEO, this is called evergreen content.
Your content is like a lush, evergreen forest, and by green I mean Benjamins.
Do you have knowledge that you can leverage? Why not help your neighbors and the world?
Answer search inquiries and help others. You'll be well rewarded.
This is better than crafting candle-like content that fizzles out quickly.
Is beauty really ephemeral like how flowers bloom? Nah, I prefer watching forests grow instead (:
wordsmithwriter
2 years ago
2023 Will Be the Year of Evernote and Craft Notetaking Apps.
Note-taking is a vital skill. But it's mostly learned.
Recently, innovative note-taking apps have flooded the market.
In the next few years, Evernote and Craft will be important digital note-taking companies.
Evernote is a 2008 note-taking program. It can capture ideas, track tasks, and organize information on numerous platforms.
It's one of the only note-taking app that lets users input text, audio, photos, and videos. It's great for collecting research notes, brainstorming, and remaining organized.
Craft is a popular note-taking app.
Craft is a more concentrated note-taking application than Evernote. It organizes notes into subjects, tags, and relationships, making it ideal for technical or research notes.
Craft's search engine makes it easy to find what you need.
Both Evernote and Craft are likely to be the major players in digital note-taking in the years to come.
Their concentration on gathering and organizing information lets users generate notes quickly and simply. Multimedia elements and a strong search engine make them the note-taking apps of the future.
Evernote and Craft are great note-taking tools for staying organized and tracking ideas and projects.
With their focus on acquiring and organizing information, they'll dominate digital note-taking in 2023.
Pros
Concentrate on gathering and compiling information
special features including a strong search engine and multimedia components
Possibility of subject, tag, and relationship structuring
enables users to incorporate multimedia elements
Excellent tool for maintaining organization, arranging research notes, and brainstorming
Cons
Software may be difficult for folks who are not tech-savvy to utilize.
Limited assistance for hardware running an outdated operating system
Subscriptions could be pricey.
Data loss risk because of security issues
Evernote and Craft both have downsides.
The risk of data loss as a result of security flaws and software defects comes first.
Additionally, their subscription fees could be high, and they might restrict support for hardware that isn't running the newest operating systems.
Finally, folks who need to be tech-savvy may find the software difficult.
Evernote versus. Productivity Titans Evernote will make Notion more useful. medium.com
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Jared Heyman
2 years ago
The survival and demise of Y Combinator startups
I've written a lot about Y Combinator's success, but as any startup founder or investor knows, many startups fail.
Rebel Fund invests in the top 5-10% of new Y Combinator startups each year, so we focus on identifying and supporting the most promising technology startups in our ecosystem. Given the power law dynamic and asymmetric risk/return profile of venture capital, we worry more about our successes than our failures. Since the latter still counts, this essay will focus on the proportion of YC startups that fail.
Since YC's launch in 2005, the figure below shows the percentage of active, inactive, and public/acquired YC startups by batch.
As more startups finish, the blue bars (active) decrease significantly. By 12 years, 88% of startups have closed or exited. Only 7% of startups reach resolution each year.
YC startups by status after 12 years:
Half the startups have failed, over one-third have exited, and the rest are still operating.
In venture investing, it's said that failed investments show up before successful ones. This is true for YC startups, but only in their early years.
Below, we only present resolved companies from the first chart. Some companies fail soon after establishment, but after a few years, the inactive vs. public/acquired ratio stabilizes around 55:45. After a few years, a YC firm is roughly as likely to quit as fail, which is better than I imagined.
I prepared this post because Rebel investors regularly question me about YC startup failure rates and how long it takes for them to exit or shut down.
Early-stage venture investors can overlook it because 100x investments matter more than 0x investments.
YC founders can ignore it because it shouldn't matter if many of their peers succeed or fail ;)
CyberPunkMetalHead
2 years ago
I talked to ChatGPT about the adoption of cryptocurrencies.
OpenAI's ChatGPT is an amazing AI-powered chatbot. It can write poetry, fiction, and marketing ideas. I was impressed how well ChatGPT followed the interview, albeit there were a few classics “I’m afraid I can’t do that”.
Full interview below.
Me: I'm your interviewer. We'll discuss crypto. Thanks for being interviewed. What do you think about cryptocurrency?
CGPT: Cryptocurrency is an innovative technology that could transform money and financial activities. It might boost the efficiency and security of financial institutions and let consumers deal directly without banks. Cryptocurrency is still a new and untested technology with many unknowns and hurdles before it can be broadly accepted.
Me: Over 22,000 cryptocurrencies exist, and many have little use. We need how much cryptocurrencies?
CGPT: The appropriate quantity will rely on a multitude of factors, including each cryptocurrency's use cases, adoption rate, and market rivalry. Only a few cryptocurrencies will likely receive widespread adoption and be successful. Many existing cryptocurrencies may not survive since they can't deliver new or valued solutions or compete with more established cryptocurrencies.
Me: Will cryptocurrencies grow? What's next for worldwide adoption?
CGPT: It's hard to forecast the future of cryptocurrencies because the acceptance of new technologies is unpredictable. I believe cryptocurrencies will expand and acquire popularity in the future years. Regulatory ambiguity, security concerns, and scalability issues must be overcome for this to happen. Cryptocurrency companies and organizations must engage together with governments and authorities to address these obstacles and establish a growth-friendly climate. Continued innovation and improvement of the technology, including public education and awareness, will drive acceptance.
Me: Do bear markets affect bitcoin adoption?
CGPT: On the one hand, a bear market might induce uncertainty and hesitation among potential consumers. Bear markets can present opportunities for long-term investors who can acquire cryptocurrencies at cheaper prices and are more likely to hang onto their assets. A bear market can also test the tenacity and power of the underlying technology and community, which can boost long-term confidence and adoption. A bear market might have profound and nuanced effects on bitcoin adoption.
Me: What are some likely outcomes if Bitcoin reaches $100,000 by next year?
CGPT: If Bitcoin saw rapid growth, it would undoubtedly have repercussions for the cryptocurrency market and economy. Possible scenarios include increased public interest and awareness of cryptocurrency, a surge in demand for Bitcoin and other cryptocurrencies, and a growth in the cryptocurrency industry's market value. By shifting their focus and cash to the cryptocurrency market, investors and traders may also affect other asset classes, such as traditional equities and commodities. Governments and financial organizations may focus more on the cryptocurrency sector as they try to grasp Bitcoin's rapid rise.
Me: Will other countries accept crypto as currency?
CGPT: It's hard to say if additional governments will adopt cryptocurrencies as legal tender. Some countries have recognized the promise of bitcoin and are exploring its use, while others are cautious. Adoption of bitcoin as legal cash may vary by country, based on financial infrastructure, rules, and political atmosphere. As cryptocurrency technology evolves and becomes more accepted, more governments may embrace it as legal tender.
Me: Final question: will the recent cryptocurrency hacks affect long term adoption?
CGPT: Hacks might tarnish cryptocurrency's reputation and public faith in its security, the technology underpinning it is continually improving. Many cryptocurrency projects have developed strong security mechanisms to prevent hacks and other dangers, and these safeguards will undoubtedly improve over time. The decentralized nature of cryptocurrency makes it more resistant to attacks. Hacks and other security breaches are a concern, but they may not affect cryptocurrency adoption.
Jeff John Roberts
3 years ago
Jack Dorsey and Jay-Z Launch 'Bitcoin Academy' in Brooklyn rapper's home
The new Bitcoin Academy will teach Jay-Marcy Z's Houses neighbors "What is Cryptocurrency."
Jay-Z grew up in Brooklyn's Marcy Houses. The rapper and Block CEO Jack Dorsey are giving back to his hometown by creating the Bitcoin Academy.
The Bitcoin Academy will offer online and in-person classes, including "What is Money?" and "What is Blockchain?"
The program will provide participants with a mobile hotspot and a small amount of Bitcoin for hands-on learning.
Students will receive dinner and two evenings of instruction until early September. The Shawn Carter Foundation will help with on-the-ground instruction.
Jay-Z and Dorsey announced the program Thursday morning. It will begin at Marcy Houses but may be expanded.
Crypto Blockchain Plug and Black Bitcoin Billionaire, which has received a grant from Block, will teach the classes.
Jay-Z, Dorsey reunite
Jay-Z and Dorsey have previously worked together to promote a Bitcoin and crypto-based future.
In 2021, Dorsey's Block (then Square) acquired the rapper's streaming music service Tidal, which they propose using for NFT distribution.
Dorsey and Jay-Z launched an endowment in 2021 to fund Bitcoin development in Africa and India.
Dorsey is funding the new Bitcoin Academy out of his own pocket (as is Jay-Z), but he's also pushed crypto-related charitable endeavors at Block, including a $5 million fund backed by corporate Bitcoin interest.
This post is a summary. Read full article here