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

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
Mar 14
6 Months ago my core tools barely included any AI.

Today things have shifted - a short update to this post:
1. Writing with 3 AI GPTs

When writing I consider 3 things:
- Finding citations to support the argument
- Putting ideas effectively on paper
- Skimming papers for logical relevance

ChatGPT can now do all of these with the help of GPTs:

effortlessacademic.com/a-complete-guiโ€ฆ
2. Semantic Search with SciSpace

Search for meaning not keywords. This is what AI enables us to do!

Check out this post:

Read 4 tweets
Mar 12
Webinar Apr 6th:
Literature Review & Academic Writing with AI

โ†’ Find the most impactful literature quickly
โ†’ Uncover reference gaps
โ†’ Aid your writing process faithfully & ethically with AI

Link:

All details below:
๐Ÿ‘‡effortlessacademic.com/elr3-webinar/Image
In this video I explain why the major changes in AI are such a big deal for literature reviews:
1. Semantic Literature Search

Semantic search allows you to obtain a comprehensive reading list on any literature review topic in under 1 minute.

This is brand new and released in January 2024.

We will look deeply at the caveats & solutions of this new method.
Read 11 tweets
Mar 5
How do you conduct a lit-review in 2024?

โŒ Old way: Searching for papers by keywords on Google
โœ… New way: Semantic search using AI tools like SciSpace

Here is a demo:
๐Ÿ‘‡ Image
1. AI Search

Internet search replaced tedious searches in libraries and journals.

Similarly, semantic search will replace the internet search.

AI allows to search answers to questions directly, rather than using keywords.

SciSpace is one such semantic search tool. Let's try!
2. @scispace_ on the GPT store

SciSpace is one of the top 10 GPTs (AI assistants) worldwide.

It harnesses the conversational abilities of ChatGPT and combines them with a database of 200 Million academic papers.

Start a conversation with this AI assistant:
Read 12 tweets
Feb 22
Overwhelmed with too many things for your paper or project?

Create an academic command center.

Here is how to do it:
๐Ÿ‘‡Image
1. In @obsdmd install the Kanban plugin

Kanban is a free community plugin.
2. Create a board

A board is just a special note in the vault. Right click any folder to get a new board.

Add as many columns or "categories" as you like.

Columns define the purpose of your board. e.g. organize literature, publication tasks or organization.
Read 8 tweets

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