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
The woman
3 years ago
I received a $2k bribe to replace another developer in an interview
I can't believe they’d even think it works!
Developers are usually interviewed before being hired, right? Every organization wants candidates who meet their needs. But they also want to avoid fraud.
There are cheaters in every field. Only two come to mind for the hiring process:
Lying on a resume.
Cheating on an online test.
Recently, I observed another one. One of my coworkers invited me to replace another developer during an online interview! I was astonished, but it’s not new.
The specifics
My ex-colleague recently texted me. No one from your former office will ever approach you after a year unless they need something.
Which was the case. My coworker said his wife needed help as a programmer. I was glad someone asked for my help, but I'm still a junior programmer.
Then he informed me his wife was selected for a fantastic job interview. He said he could help her with the online test, but he needed someone to help with the online interview.
Okay, I guess. Preparing for an online interview is beneficial. But then he said she didn't need to be ready. She needed someone to take her place.
I told him it wouldn't work. Every remote online interview I've ever seen required an open camera.
What followed surprised me. She'd ask to turn off the camera, he said.
I asked why.
He told me if an applicant is unwell, the interviewer may consider an off-camera interview. His wife will say she's sick and prefers no camera.
The plan left me speechless. I declined politely. He insisted and promised $2k if she got the job.
I felt insulted and told him if he persisted, I'd inform his office. I was furious. Later, I apologized and told him to stop.
I'm not sure what they did after that
I'm not sure if they found someone or listened to me. They probably didn't. How would she do the job if she even got it?
It's an internship, he said. With great pay, though. What should an intern do?
I suggested she do the interview alone. Even if she failed, she'd gain confidence and valuable experience.
Conclusion
Many interviewees cheat. My profession is vital to me, thus I'd rather improve my abilities and apply honestly. It's part of my identity.
Am I truthful? Most professionals are not. They fabricate their CVs. Often.
When you support interview cheating, you encourage more cheating! When someone cheats, another qualified candidate may not obtain the job.
One day, that could be you or me.
Ellane W
3 years ago
The Last To-Do List Template I'll Ever Need, Years in the Making
The holy grail of plain text task management is finally within reach
Plain text task management? Are you serious?? Dedicated task managers exist for a reason, you know. Sheesh.
—Oh, I know. Believe me, I know! But hear me out.
I've managed projects and tasks in plain text for more than four years. Since reorganizing my to-do list, plain text task management is within reach.
Data completely yours? One billion percent. Beef it up with coding? Be my guest.
Enter: The List
The answer? A list. That’s it!
Write down tasks. Obsidian, Notenik, Drafts, or iA Writer are good plain text note-taking apps.
List too long? Of course, it is! A large list tells you what to do. Feel the itch and friction. Then fix it.
But I want to be able to distinguish between work and personal life! List two things.
However, I need to know what should be completed first. Put those items at the top.
However, some things keep coming up, and I need to be reminded of them! Put those in your calendar and make an alarm for them.
But since individual X hasn't completed task Y, I can't proceed with this. Create a Waiting section on your list by dividing it.
But I must know what I'm supposed to be doing right now! Read your list(s). Check your calendar. Think critically.
Before I begin a new one, I remind myself that "Listory Never Repeats."
There’s no such thing as too many lists if all are needed. There is such a thing as too many lists if you make them before they’re needed. Before they complain that their previous room was small or too crowded or needed a new light.
A list that feels too long has a voice; it’s telling you what to do next.
I use one Master List. It's a control panel that tells me what to focus on short-term. If something doesn't need semi-immediate attention, it goes on my Backlog list.
Todd Lewandowski's DWTS (Done, Waiting, Top 3, Soon) performance deserves praise. His DWTS to-do list structure has transformed my plain-text task management. I didn't realize it was upside down.
This is my take on it:
D = Done
Move finished items here. If they pile up, clear them out every week or month. I have a Done Archive folder.
W = Waiting
Things seething in the background, awaiting action. Stir them occasionally so they don't burn.
T = Top 3
Three priorities. Personal comes first, then work. There will always be a top 3 (no more than 5) in every category. Projects, not chores, usually.
S = Soon
This part is action-oriented. It's for anything you can accomplish to finish one of the Top 3. This collection includes thoughts and project lists. The sole requirement is that they should be short-term goals.
Some of you have probably concluded this isn't for you. Please read Todd's piece before throwing out the baby. Often. You shouldn't miss a newborn.
As much as Dancing With The Stars helps me recall this method, I may try switching their order. TSWD; Drilling Tunnel Seismic? Serenity After Task?
Master List Showcase
My Master List lives alone in its own file, but sometimes appears in other places. It's included in my Weekly List template. Here's a (soon-to-be-updated) demo vault of my Obsidian planning setup to download for free.
Here's the code behind my weekly screenshot:
## [[Master List - 2022|✓]] TO DO
![[Master List - 2022]]FYI, I use the Minimal Theme in Obsidian, with a few tweaks.
You may note I'm utilizing a checkmark as a link. For me, that's easier than locating the proper spot to click on the embed.
Blue headings for Done and Waiting are links. Done links to the Done Archive page and Waiting to a general waiting page.
Read my full article here.
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Ian Writes
3 years ago
Rich Dad, Poor Dad is a Giant Steaming Pile of Sh*t by Robert Kiyosaki.
Don't promote it.
I rarely read a post on how Rich Dad, Poor Dad motivated someone to grow rich or change their investing/finance attitude. Rich Dad, Poor Dad is a sham, though. This book isn't worth anyone's attention.
Robert Kiyosaki, the author of this garbage, doesn't deserve recognition or attention. This first finance guru wanted to build his own wealth at your expense. These charlatans only care about themselves.
The reason why Rich Dad, Poor Dad is a huge steaming piece of trash
The book's ideas are superficial, apparent, and unsurprising to entrepreneurs and investors. The book's themes may seem profound to first-time readers.
Apparently, starting a business will make you rich.
The book supports founding or buying a business, making it self-sufficient, and being rich through it. Starting a business is time-consuming, tough, and expensive. Entrepreneurship isn't for everyone. Rarely do enterprises succeed.
Robert says we should think like his mentor, a rich parent. Robert never said who or if this guy existed. He was apparently his own father. Robert proposes investing someone else's money in several enterprises and properties. The book proposes investing in:
“have returns of 100 percent to infinity. Investments that for $5,000 are soon turned into $1 million or more.”
In rare cases, a business may provide 200x returns, but 65% of US businesses fail within 10 years. Australia's first-year business failure rate is 60%. A business that lasts 10 years doesn't mean its owner is rich. These statistics only include businesses that survive and pay their owners.
Employees are depressed and broke.
The novel portrays employees as broke and sad. The author degrades workers.
I've owned and worked for a business. I was broke and miserable as a business owner, working 80 hours a week for absolutely little salary. I work 50 hours a week and make over $200,000 a year. My work is hard, intriguing, and I'm surrounded by educated individuals. Self-employed or employee?
Don't listen to a charlatan's tax advice.
From a bad advise perspective, Robert's tax methods were funny. Robert suggests forming a corporation to write off holidays as board meetings or health club costs as business expenses. These actions can land you in serious tax trouble.
Robert dismisses college and traditional schooling. Rich individuals learn by doing or living, while educated people are agitated and destitute, says Robert.
Rich dad says:
“All too often business schools train employees to become sophisticated bean-counters. Heaven forbid a bean counter takes over a business. All they do is look at the numbers, fire people, and kill the business.”
And then says:
“Accounting is possibly the most confusing, boring subject in the world, but if you want to be rich long-term, it could be the most important subject.”
Get rich by avoiding paying your debts to others.
While this book has plenty of bad advice, I'll end with this: Robert advocates paying yourself first. This man's work with Trump isn't surprising.
Rich Dad's book says:
“So you see, after paying myself, the pressure to pay my taxes and the other creditors is so great that it forces me to seek other forms of income. The pressure to pay becomes my motivation. I’ve worked extra jobs, started other companies, traded in the stock market, anything just to make sure those guys don’t start yelling at me […] If I had paid myself last, I would have felt no pressure, but I’d be broke.“
Paying yourself first shouldn't mean ignoring debt, damaging your credit score and reputation, or paying unneeded fees and interest. Good business owners pay employees, creditors, and other costs first. You can pay yourself after everyone else.
If you follow Robert Kiyosaki's financial and business advice, you might as well follow Donald Trump's, the most notoriously ineffective businessman and swindle artist.
This book's popularity is unfortunate. Robert utilized the book's fame to promote paid seminars. At these seminars, he sold more expensive seminars to the gullible. This strategy was utilized by several conmen and Trump University.
It's reasonable that many believed him. It sounded appealing because he was pushing to get rich by thinking like a rich person. Anyway. At a time when most persons addressing wealth development advised early sacrifices (such as eschewing luxury or buying expensive properties), Robert told people to act affluent now and utilize other people's money to construct their fantasy lifestyle. It's exciting and fast.
I often voice my skepticism and scorn for internet gurus now that social media and platforms like Medium make it easier to promote them. Robert Kiyosaki was a guru. Many people still preach his stuff because he was so good at pushing it.
Dani Herrera
3 years ago
What prevents companies from disclosing salary information?
Yes, salary details ought to be mentioned in job postings. Recruiters and candidates both agree, so why doesn't it happen?
The short answer is “Unfortunately, it’s not the Recruiter’s decision”. The longer answer is well… A LOT.
Starting in November 2022, NYC employers must include salary ranges in job postings. It should have started in May, but companies balked.
I'm thrilled about salary transparency. This decision will promote fair, inclusive, and equitable hiring practices, and I'm sure other states will follow suit. Good news!
Candidates, recruiters, and ED&I practitioners have advocated for pay transparency for years. Why the opposition?
Let's quickly review why companies have trouble sharing salary bands.
💰 Pay Parity
Many companies and leaders still oppose pay parity. Yes, even in 2022.
💰 Pay Equity
Many companies believe in pay parity and have reviewed their internal processes and systems to ensure equality.
However, Pay Equity affects who gets roles/promotions/salary raises/bonuses and when. Enter the pay gap!
💰Pay Transparency and its impact on Talent Retention
Sharing salary bands with external candidates (and the world) means current employees will have access to that information, which is one of the main reasons companies don't share salary data.
If a company has Pay Parity and Pay Equity issues, they probably have a Pay Transparency policy as well.
Sharing salary information with external candidates without ensuring current employees understand their own salary bands and how promotions/raises are decided could impact talent retention strategies.
This information should help clarify recent conversations.
Rishi Dean
3 years ago
Coinbase's web3 app
Use popular Ethereum dapps with Coinbase’s new dapp wallet and browser
Tl;dr: This post highlights the ability to access web3 directly from your Coinbase app using our new dapp wallet and browser.
Decentralized autonomous organizations (DAOs) and decentralized finance (DeFi) have gained popularity in the last year (DAOs). The total value locked (TVL) of DeFi investments on the Ethereum blockchain has grown to over $110B USD, while NFTs sales have grown to over $30B USD in the last 12 months (LTM). New innovative real-world applications are emerging every day.
Today, a small group of Coinbase app users can access Ethereum-based dapps. Buying NFTs on Coinbase NFT and OpenSea, trading on Uniswap and Sushiswap, and borrowing and lending on Curve and Compound are examples.
Our new dapp wallet and dapp browser enable you to access and explore web3 directly from your Coinbase app.
Web3 in the Coinbase app
Users can now access dapps without a recovery phrase. This innovative dapp wallet experience uses Multi-Party Computation (MPC) technology to secure your on-chain wallet. This wallet's design allows you and Coinbase to share the 'key.' If you lose access to your device, the key to your dapp wallet is still safe and Coinbase can help recover it.
Set up your new dapp wallet by clicking the "Browser" tab in the Android app's navigation bar. Once set up, the Coinbase app's new dapp browser lets you search, discover, and use Ethereum-based dapps.
Looking forward
We want to enable everyone to seamlessly and safely participate in web3, and today’s launch is another step on that journey. We're rolling out the new dapp wallet and browser in the US on Android first to a small subset of users and plan to expand soon. Stay tuned!