Mushtaq Bilal, PhD Profile picture
Feb 2, 2025 19 tweets 6 min read Read on X
How to organize and summarize research papers with Zotero and Scholarcy:

You can learn this workflow in 15 minutes.
1. Open your Zotero desktop app and click on "File" and select "New Collection."

Choose a name for your collection. Keep the collection open.
2. If you haven't already, you'd need to install the Zotero Connector.

Go to Chrome web store and look for "Zotero Connector."

Add it to your Chrome and then pin it.

The Connector is available for Edge, Firefox, and Safari.
3. Look up papers relevant to your project in Google Scholar.

Click on the Zoteor Connector in the top-right corner and it will open an "Item Selector."

Select the papers you find useful and click on "OK."

Selected papers will be added to the collection you just created.
4. You can also look up papers in your university's online library or a database like PubMed.

Then add papers to your collection using Zotero Connector.
5. Go your Zotero collection and you will see the papers have been added.

Zotero will retrieve open access PDFs and add them to the collection.

If Zotero doesn't retrieve, you can add a PDF yourself. Simply drag and drop the PDF.
6. Double-click on a paper to open it in Zotero. You can read the paper and take notes on it if you want to.
7. To summarize paper, go to scholarcy[.]com and sign up for an account.

Scholarcy offers both free and paid plans.
8. Once you've logged in to Scholarcy, click on "Profile" and scroll down a bit.

Click on "Connect Zoteor account" and then click on "Accept Defaults."

Now your Zotero is connected with Scholarcy.
9. Click on "Create library" in the top-right corner and choose a name for your library.
10. Click on the library you just created and select "Click to import."

Click on "Cloud storage" and select "Zotero."

Select "Collections" on the top and Scholarcy will show you all your Zotero collections.

Select the relevant collection.
11. Select the papers you want to import to Scholarcy and click on "Import."

Scholarcy will take a few seconds to process the imported papers.

If a paper doesn't get imported, you can simply drag and drop its PDF in your Scholarcy library.
12. Once the papers have been processed, click on a paper and Scholarcy will give you its summary.

You can navigate to different sections using the tabs in the left sidebar.
13. You can change reading levels of summaries by clicking on "Enhacne."

Scholarcy has different reading levels: general reader, highschool student, undergraduate, researcher, and bullet point lover.

You can also ask it to focus on a specific point by selecting "Focused on..."
14. Within the summaries, Scholarcy will hyperlink difficult words and terms to Wikipedia articles.

This feature will save you a lot of time.
15. Once you've read a few papers, open a Word file and start writing.

To insert a citation, place the cursor where you want it to be. Click on the Zotero tab and select "Add/Edit Citation."

Enter the name of the author you want to cite.

Zotero will prepare the citation. Hit Enter and it'll be added.
16. Once you are done drafting, place the cusor where you want to add bibliopgrahy.

Then click on "Add/Edit Bibliography."

Zotero will add the bibliograhy in your selected style.
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More from @MushtaqBilalPhD

Mar 5
A lot of academics still think AI apps generate fake references to papers that don't exist.

They are living in 2023.

You can easily integrate a database of 280M research papers with Claude and ChatGPT to get answers with references to published papers.

Here's how to do it:
1. Go to scite[.]ai/mcp and select Claude ai

Copy the URL given in the second line. Then click on the blue "Add Scite" button.

This will open Claude Connectors. Type in the name Scite and paste the URL in the "Remote MCP" field.

Then click on "Add."
2. This will add a Scite Connector to your Claude.

Scroll down a little and you will see a Scite Connector. Click on "Connect" and log in to your Scite account.

Give Claude permission to access Scite. And that's it.

You will need a paid subscription for Scite to do this.
Read 7 tweets
Mar 4
Claude Code will fundamentally change the nature of academic research.

But most academics don't know how to use it.

Here's how to get started on Claude Code (even if you've never coded).

Claude Code for Academics 101:
Before getting started, we need to understand what Claude Code (CC) is.

It's not a simple chatbot.

Think of it as a general-purpose work enviroment that lets you create customized features for your own specific purposes.

It'll become clear by the end of this thread.
1. To get started, go to claude[.]com/download and download the Claude desktop app.

You will need a paid plan.

Select the $20/m one. That'll be enough to get you started.
Read 17 tweets
Mar 3
Academics are abandoning ChatGPT for Claude, and for good reason.

Claude is way better than ChatGPT for intellectual work.

But moving to Claude risks losing your work history and memory in ChatGPT.

Here's how to move all your work history and memory from ChatGPT to Claude:
1. Open Claude and click on your profile in the bottom-left corner.

Then click on "Settings" and select "Capabilities."

In Capabilities, look for the "Start Import" button.

Click it and then copy the prompt given on the top.
2. Open ChatGPT and put it on "Thinking."

Then run the prompt you just copied from Claude.

ChatGPT will give you an answer. Copy that.
Read 6 tweets
Mar 2
Claude Cowork is set to revolutionize intellectual and academic work.

But most academics don't know how to use it.

Here's how to set up Claude Cowork as your research assistant:

(This workflow will take you only 15 min.) Guide on setting up Claude Cowork for academic research.
1. To use Claude Cowork, you'll need to download Claude desktop app.

Go to claude[.]com/download

and download the Claude desktop app.

You'll also need a paid plan for $20/m or $100/m.

Start with $20/m plan.
2. Once you've installed it, open Claude desktop app.

On the top, you will see three options: Chat, Cowork, Code.

Click on "Cowork." Claude user interface displays options for chat, coding, and co-working, with prompts for user interaction prominently featured.
Read 13 tweets
Jan 5
How to build an academic writing habit (to write a lot and publish a lot):
In his book "Atomic Habits," James Clear writes about habits that are so small we don’t even notice them, but the power they have over us is immense.

He calls them atomic habits.

Although they are small, building atomic habits is VERY DIFFICULT.

Why? A photo of James Clear's book "Atomic Habits."
Clear calls the time between the point we start a habit to the point we start seeing its first results "the plateau of latent potential."

Most people remain stuck within this plateau.

To see the results of any habit, we must cross the plateau of latent potential. A photo of "The Plateau of Latent Potential" from James Clear's book "Atomic Habits."
Read 21 tweets
Dec 25, 2025
Don't use Sci-Hub — it's a "controversial" website with 84M+ research papers freely available.

We should all try to make billion-dollar academic publishers richer.

Anyway, here's a thread on how to integrate Sci-Hub with Zotero to get free papers.

🚨DO NOT DO IT!
1. Don't go to this link:
github(dot)com/syt2/zotero-scipdf

But if you do, replace the word "dot" with an actual [.]

Don't scroll down and click on "latest release xpi file."

This will download an "xpi" file to your computer.
2. Don't open your Zotero. But if you do, click on "Tools."

In "Tools," click on "Plugins." This will open Zotero's Plugin Manager.

In the Plugin Manager, click on the gear-like icon and select "Install Plugin From File."

Navigate to the XPI file you downloaded and add it.
Read 6 tweets

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