Ilya Shabanov Profile picture
Dec 21, 2022 โ€ข 10 tweets โ€ข 8 min read โ€ข Read on X
Create the perfect digital Lab Notebook ๐Ÿ“’๐Ÿงช๐Ÿงฌ that links to your Reference Manager and Notes!

A Step by Step guide using Obsidian + Calendar Plugin:

โฌ‡๏ธ

#phdlife #phdchat #phdvoice #phdforum #phd #AcademicTwitter #AcademicTwitter Image
1. Install @obsdmd to create your first vault.

If you are in academia and have not worked with Obsidian yet, then your world is changed forever today ๐Ÿ˜ฎ (Check out why, here: buff.ly/3j8bl3d)

Let's move on to creating our lab notebook... Image
@obsdmd 2. Let's install the Calendar Plugin.

- Go to the Obsidian preferences
- Click "Community Plugins"
- Click "Browse"
- Search for "Calendar"
- Install and Enable the plugin ImageImageImage
@obsdmd 3. On your top right you can now access your calendar.

- Each day is simply a note in Obsidian.
- You can create a note for this day by clicking on it - super simple.

Here is a demo:
@obsdmd 4. The calendar will change as you add notes and todos into your daily entries.

Here is what each feature means: Image
@obsdmd 5. Make sure to setup a folder for your daily notes to avoid clutter in your vault

-> Go to preferences and select "Daily Notes" Image
@obsdmd 6. If you want to make weekly notes as well, you have to enable it.

-> Go to preferences and select "Calendar"
-> Check "Show week number"
-> Just like in the previous step, you can set a folder where the weekly notes will go Image
@obsdmd 7. There are many advanced features.

For example you can create tables from your daily notes that all relate to a certain experiment.

Or filter out unchecked TODOs inside those notes...

Too little space to fit that into a tweet ๐Ÿ˜‘ , but... Image
@obsdmd 8. In the next few days I am going to send out a newsletter to my subscribers!

I will go in depth on how to create the perfect lab notebook using the dreaded "dataview" plugin and many more tips on the process.

Please join, if this is relevant to you!

buff.ly/3j8bl3d
@obsdmd There is more!

๐Ÿ™ Follow @Artifexx for more hacks for academics
โ™ป๏ธ Share with your colleagues to help each other
๐ŸŽ„ Happy Holidays!

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More from @Artifexx

May 9
The best researchers aren't geniuses. They're well-organized.

This is my favorite system to organize 1000s of notes.

Simple, yet powerful:
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1. The Problem

Taking notes helps you remember only if you can find your notes.

My vault has almost 400k words over 1000+ notes (and countless PDFs/Screenshots).

To find things easier you need to have MULTIPLE layers of organization. Divide and conquer. Image
2. Folders do not work well.

In my experience folders just don't work. Because a note can't be part of multiple folders.

If you want to reuse notes for different "projects" inside your vault you need TAGS.

A Tag is just like a folder. But a note can be part of many tags! Image
Read 11 tweets
May 6
Struggling with remembering where you saved a note?

Use Rainbow Folders: A hidden feature in Obsidian.

Here is how:
๐Ÿ‘‡ Image
Obsidian (@obsdmd) is a free software if you are serious about organizing knowledge (e.g. academics)

Organize by: Folders, Tags or Maps of Content

Rainbow folders gives every folder a color making them easier to find.

There are two modes: Backgrounds(Left) or Titles (Mid) Image
@obsdmd 1. Installing the right theme

Not every theme supports rainbow folders.

You will have to try out.

These two popular themes do support it.
- Chime (my recommended theme at the moment).
- AnuPpuccin Image
Read 7 tweets
Apr 27
Plagiarism is a serious problem in academia.

Even a misplaced citation can massively damage your reputation.

Luckily AI is great at spotting plagiarism. Here is how:
๐Ÿ‘‡ Image
1. Plagiarism is complex

If you look at the Harvard Guide it identifies 6 types of plagiarism.

"Uncited paraphrase" might be the most difficult to spot.

Here you might mention established findings from older papers without citing them. Image
2. Check for Plagiarism

After you have written your manuscript (yourself!). You might still end up with a few unintended instances of plagiarism.

This is where @teampaperpal comes in.

Make an account on paperpal . com and click "Plagiarism Check" in the sidebar. Image
Read 7 tweets
Apr 22
Want to get more done at the end of the week?

Use SCRUM - a scheduling technique most companies use. It's perfect for academics.

Details in text below:
๐Ÿ‘‡
Summary:

1. Create a backlog of tasks and assign a difficulty to each (1,2,4,8 for the number of hours it takes to complete)

2. Plan meetings and seminars etc as they also take time.

3. Before starting your week distribute the tasks from the backlog to the days of the week. Don't plan more than 8hr of work a day (or less if you have other commitments).

4. During the week: Check off what you have completed (and how long it took you).

5. At the end of the week: Understand what you got done and what you didn't.

Understand that if you didn't get everything done it is a planning error. It does not mean you need to work harder/more (this is just recipe for burnout and I have been there myself). It just means you need to plan better. Efficiency comes in relaxation.

Every day you manage to accomplish what you planned you will feel great about yourself.

6. Next week you can copy and paste the open tasks to the next week and start the process again. Some people prefer to have a bi-weekly instead.
What tools can you use?

There are dozens of tools for kanban boards. The simplest one is of course Trello.

Read 5 tweets
Apr 2
Don't have time to read a paper in detail?

Here is how to extract relevant information instantly:
๐Ÿ‘‡ Image
The setup:

You have a rather large and relevant conceptual paper.

There are others and you are not sure if it's worth reading it.

You are however more interested in the "big picture" not the methods and details.
1. Upload the PDF to MyAIDrive(dot)com

Copy the link to the PDF.

MyAiDrive will analyze the PDF and make the results available in ChatGPT. Image
Read 8 tweets
Mar 26
Want to remember every paper you read?

Replace Zotero with a reference map and leverage your spatial memory.

Here is how:
๐Ÿ‘‡

1. Reference manager vs map

Take a look at this screenshot: Which one looks more approachable and interesting? On the right is Zotero displaying all your papers in an endless list. On the left is a reference map.

Reference maps lay out your papers or PDFs in 2D on an endless surface called a "canvas" or "whiteboard". There are many tools that are capable of doing it: Obsidian is an obvious choice, Heptabase is great too, DrawIO is more complex but also good.

2. Zooming in and out / Finding things

Using the scroll wheel or pinch gesture you can fluidly navigate between the bird's eye view and the detailed view with your own notes on a single paper. Left: Detail, Right: All Papers.

To find papers you "fly up" and then "land on" the paper you are looking for. It feels incredibly natural and easier than scrolling through a list.

3. Why it works: Spatial Memory
Humans evolved moving around as hunter gatherers and spatial memory is a key trait needed for navigation. You leverage it by laying out your papers in a landscape, not a list. Your papers gain location and relation.

4. Headers and Topics: Location
Now that your papers are on a landscape or map you can have "countries" on this map. Every country is a topic, further subdivided in sub-topics. Here is the "Machine Learning Country" in the far south west of my map:

I can refer to "papers in the south west" - this is spatial memory being leveraged to remember where things are.

5. Semantic Connections: Relation

The next step is to build the "roads" between locations on the map. Simply draw an arrow and write on it what this relation signifies.

In the above example Swenson 2020 (top) wrote "the trait-demography relationship is weak (Yang 2018)".
So I read Yang 2018 (left) and added a connection. Later I found that (Lynn 2023) suggested a few solutions and linked those two as well.

By just looking at this map you can immediately write a sentence for your literature review. A narrative emerges and synthesis begins.

Summary:

Lay out papers on a spatial canvas using e.g. Obsidian instead of Zotero. Remembering them will be much easier because you can use your spatial memory. Synthesis starts happening automatically when you annotate connections between papers.

Do you do something like this?
Share a screenshot with us!Image
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This is one of the methods you can learn about in my upcoming webinar:

In this post I mentioned Heptabase and Obsidian as tools to achieve this results.

Here is a comparison between those two:

effortlessacademic.com/note-taking-toโ€ฆ
Read 4 tweets

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