The Powerful Way to take Notes as A PhD Student

Hi I'm Ben, I did a PhD and survived to tell the tale.
What got me through was my level of organisation and the system I built to collect and process information; it basically felt like a PhD in organisation (it wasn't it was in nanophysics). I wanted to share my note-taking approach as it's something I think about a lot at the moment and still use avidly in my day-to-day life and work.
Link to Protolyst here: www.protolyst.org
Quick stats.
I finished my PhD in 3.5 years.
I wrote 5 papers (and 1 paper that never got published) in 18 months starting ~in year 2 of the PhD.
My final thesis write up took 4 weeks.
My viva (thesis defence) took 1 hour (but I hated it 😅)
Very happy to answer any questions.
Join the Protolyst Community Slack here:
join.slack.com/t/protolystcom...
--A bit about me now---
🚀 I'm the CEO and founder of a company called Spin Up Science (www.spin-up.science). We help scientists turn their discoveries into start up companies to get breakthroughs into the hands of the public.
🧪 I'm the cofounder and director of the Science Angel Syndicate (www.scienceangelsyndicate.com). We invest in great science and great scientists looking to change the world.
📓 I'm the CEO of cofounder of Protolyst. The note-taking and linked knowledge app I mention in this video. Link to Protolyst here: www.protolyst.org
(we just entered BETA! 👋 yes there will be bugs)
0:00 Introduction
1:31 Learning About Knowledge Management
3:50 The Three Principles of Good Note Taking
5:26 How To Take Fleeting Notes
8:23 Introduction to My Knowledge System
10:02 How to Takes Notes from Research Papers
12:35 How to Take Permanent Notes
17:10 Linking Your Knowledge Base
20:42 Using Workflow Tools
21:45 Conclusion!
#gradschool #notetaking #phd #zettlekasten

[@velbixfilms]

Thank you for sharing! Amazing thoughts that I needed.

[@chane-nel]

I absolutely love this system for keeping track of research! Thank you for sharing!

[@rafaelkr]

I loved this tool. Thank you so much

[@user-zs1ws4qw5u]

Very useful! Thanks Dr. Miles! Three principle of good note taking - take notes in your own words - 'irreducible' notes - connect the idea to other knowledge How to take fleeting notes - the source - the context (digested version)

[@guillaume6373]

This was great, thanks for the video!

[@severine_aurelia]

Very helpful to see a specific, real-world example. The PDF integration capabilities of your app make it an attractive choice for people who read a lot of papers!

[@shevacharya1030]

This video is great! As a new incoming PhD student I have been looking for a great system to use to get a hang of all the reading! Thank you so much for this video, it was very helpful!

[@quantumofknowledge1981]

You're very welcome!

[@parizashah7305]

this explaining is very good thanks

[@PriDrummond]

You explained your system so clearly. It gave me ideas on how to improve my process. Thank you! (And great app!)

[@quantumofknowledge1981]

You're very welcome!

[@mahsammdz9340]

Wow I will save this for future. Your app is great 👍😃

[@teakrose8613]

This is wonderful! I'm 4 years into my program and this solves so many issues I've had with organizing.

[@quantumofknowledge1981]

You're welcome!

[@chloe_steward]

Great point about consistency and creating a work-flow that is effective but not high-maintence. Thanks for the time you invested in sharing this. Just subscribed to your channel for more great advice!

[@310cdarren]

I subscribed because I enjoy listening to credible sources with relevant experience.

[@williamstensen5586]

Starting my Masters in Psycholinguistics next year and hopefully PhD not too long after. I have been using Obsidian for quite some time now, but I have really been looking for a program that would let me read PDFs in the same program as I take notes. I love this!

[@filippo7349]

Currently you can read PDFs directly in the Obsidian and make notes on the side panel.

[@aleks0_o879]

i already use nimbus note. im impressed with your app, i checked it out. I appreciate you can choose any color you wantto color code a text, thats what I never like about most other apps with its limited color pallet. good luck on development on a mobile app

[@93bigelow]

Thanks for putting this together. I'm a seasoned Obsidian user but the examples you give will help me improve my workflows.

[@jimgrant1776]

I'm very impressed with the app you've developed. Apparently, my mind doesn't work at all like yours. I have difficulty understanding what are the different types of entities and how they relate in your system. It just looks like a mass of notes and details. More specifically, I couldn't detect any "hierarchical" structure, which I've found as typical in most note-taking systems. - - - I guess what seems to be missing (for me) is come approach to "categorizing" your notes. Also, when you search for something, I would think you would get a long list of "Items" covering a large variety of related matters and it would take you some time to home in on the specific "item" you want. I would think that Evernote or Apple Notes would do a great job for your needs. No response needed - - - just offering a different perspective.

[@pipeg.3611]

Nice video, i am in the last stretch of my PhD and would have loved to have found this a few years back. Anyway, I noticed that when you show you notes on a table and assign categories and other properties, it resembles tagging said notes. I've never thought of tags as a table of variable columns but it was very nice to link the two concepts. Thanks for the nice video, I've been looking for a starting point to manage the scientific literature I have to deal with and this is a good tutorial for those interested. About you app, is the PDF reader included in the whole thing? I noticed that once you make a fleeting note on the paper it remains highlighted, however in ZK (afaik) you want to "upgrade" the fleeting notes to permanent ones and then delete those fleeting ones. In the video you don't show that, what happens if you delete that fleeting note associated to the paper?

[@jaw0449]

Thank you so much! I wish I had found this at the beginning of my PhD, but it's still very useful and especially a fellow physicist as there's differences between us and many other fields

[@liyanaazman4712]

I like how it's cloud based and how it can be traced to the original pdf source (unlike obsidian). And the interface can display permenant notes more clearly !

[@user-uo2wr5ys2b]

you can just embed PDFs in obsidian tho

[@zachariahprajeeyachat3436]

How do you keep track of permanent notes in relation to each other as the system becomes larger?

[@LearnWithJake]

Hi Dr Ben. I'm excited to finish my MBA so that I can pursue my PDH right after!

[@quantumofknowledge1981]

Awesome! Hope it goes well!

[@pradeep.s]

great system

[@quantumofknowledge1981]

Hey, I'd love to know what you think! How do you manage your knowledge base, PhD or otherwise?

[@knw-seeker6836]

thanks for sharing your approach Its really interesting how people take notes individually Could recommend anything in terms of preparing for an exam?

[@quantumofknowledge1981]

Totally, I'll add it to the list of video topics 👍👍

[@work_in_progress161]

Hi, I am going into my second degree and have a few quick questions that my teachers never answered. I will appreciate the clarification if you find the time. I have noticed that your citation was from a secondary source. Which one would you cite? I always get confused by going into the secondary source and trying to find what the original article got from it as sometimes authors use different words and their interpretation of the information differs. Also sometimes authors write a paragraph and put in only one caution at the end, how do I know if the rest from that source or only the last sentence preceding the citation is?

[@sorcererstone3303]

This way of rewriting the highlighted/captured segments of the paper using your own words (in permanent note video segment) will work when we are reading "normal length" papers. I am reading a report cited by a thesis. That report is 250 pages long & full of ideas. In this case (reading a very lengthy document), what is the most efficient & effective way to capture key ideas from it. Probably not by writing fleeting notes + permanent notes methodology. Correct? Because this approach may not be efficient at all for long documents. Any thoughts?

[@laulaja-7186]

A word is used several times in this video, and for those like me who want to know the spelling: Zettelkasten.

[@theverasilva]

Hi, thank you for sharing! So, I know you mentioned this, but I just wanted to confirm, did you use 'Protolyst' in during your thesis writing? How did you go from your notes to writing?

[@quantumofknowledge1981]

Hi! Great question. Protolyst wasn't around when I was writing up my thesis. I used a very early version of the app that I had written. I'll do a video soon showing exactly how to go to from atoms and notes to literature reviews and thesis writing!

[@theverasilva]

@@quantumofknowledge1981 sounds good, thanks! I’m a third year PhD student and I’ve created my own note taking system in Notion and my notes are also called atoms and there’s a lot of other similar terminology around my system haha! Looking forward to the next video.

[@GarlicTime]

Hi, Ben. Is there a way to work offline with Protolyst, that perhaps syncs when a connection is available? Thanks

[@quantumofknowledge1981]

Hey, I'll chat with the dev team on Tuesday and let you know 👍

[@quantumofknowledge1981]

Hey so response from the dev team: Ric - 8 minutes ago Yes this is on the roadmap for this year. As a 'collaborative-first' platform, we have to consider edit conflicts that arise from multiple users editing offline, which is why we have not implemented offline capabilities to date. We'll keep you posted Feel free to join the Slack channel that just launched to chat directly to the devs join.slack.com/t/protolystcommunity/shared_invite/zt-1u9lm8q7q-0Dj261friyoTlsjI8F7mZA

[@mattiek7526]

Oh my gosh, you are so nice 😋

[@anitamaylone]

Is there a transcript to this

[@rajanvk939]

is it similar to the notion?

[@quantumofknowledge1981]

Sort of, yes. The page-based system is similar, but the focus of Protolyst is the knowledge or "atom" layer, that let's you collect insights from across your documents and collate them together.