PaperHacking Research Workbench

Read papers.
Then do science.

A desktop workbench that turns scattered paper reading into structured knowledge through guided note templates, automatic cross paper synthesis, and a growing personal glossary.

Download for macOS

Free. No account. No cloud.

The Problem

You read 50 papers.
You remember 5.

Highlighters scatter insights across PDFs. Notes live in ten different apps. Literature reviews become copy paste nightmares. And "I'll remember this" becomes "Where did I read that?"

Fragmented notes

Highlights in one app, notes in another, PDFs in Downloads. Nothing connects.

The blank page

You sit down to take notes. The cursor blinks. You have no idea where to start.

No synthesis

You read 30 papers on a topic. You still can't articulate where the field disagrees.

The Workflow

From paper to knowledge.
In seven fields.

Here's what it actually looks like to use PaperHacking.

Plan: Cognitive Control
Module 1: Theta Oscillations
Priority:
Schedule:
1
2
3
4
5
6
7
8
3 papers assignedDue: Week 8
1

Plan your attack.

Create a reading plan. Group papers into modules. Assign 1 to 5 star priorities. PaperHacking distributes them across weeks, highest priority first. No more "which paper should I read next?"

Plans → Modules → Papers → Weeks
Template: Original Paper
The Claim
What does this paper argue?
Their Experiment
What did they actually do?
The Gap
What did they miss?
Steal This
What can you borrow?
+ 3 more fields
2

Never face a blank page.

Seven guided fields transform reading into structured thinking. The Claim. Their Experiment. The Gap. Steal This. Schema Update. Each field asks a specific question, your notes become instantly searchable and comparable.

Original Paper and Review Paper templates, fully customizable
PDF Viewer
Summary Edit
The Claim
The ACC monitors conflict between competing responses and signals the need for increased cognitive control.
The Gap
No consideration of individual differences in baseline ACC activity.
5/8
paper.pdf / Page 3 of 12

The conflict monitoring hypothesis

Recent evidence suggests that the anterior cingulate cortex plays a significant role in the detection of processing conflict...

Figure 2
3

Read and note, side by side.

PDF on the right. Your structured notes on the left. No more alt tabbing. No more losing context. As you read, you fill each field, one insight at a time. Auto-save means you never lose a thought.

Split view editor / Auto save / PDF navigation
Overview
Papers
Consensus
Contested
Gaps
Contested: Is the ACC a conflict monitor or a learning signal?
Detected from 5 paper summaries
Position A (3 papers)
Conflict monitoring theory. The ACC detects response competition and signals cognitive control.
Position B (2 papers)
Reinforcement learning theory. The ACC encodes prediction errors and drives learning.
Your Note
The hybrid model seems most promising. Both theories capture part of the story but neither explains the full picture.
3
Claims Found
2
Gaps Found
1
Contradiction
3
Schema Updates
4

Watch your notes become arguments.

After 3 or more papers in a module, Synthesis Mode activates. It auto extracts claims, detects contradictions, and maps contested points across papers. Suddenly you can see where the field agrees, where it fights, and where your contribution lives.

Auto extraction / Contradiction detection / Position mapping
Your Glossary / 12 terms
Conflict adaptation
3 papers
Theta coupling
2 papers
Reactive control
4 papers
Total Score
450
4/10 papers → next milestone
Streak
4 wks
On Time
4
5

Build a language. Keep the fire.

Every paper you read adds terms to your personal glossary, automatically linked back to source papers. Meanwhile, reading streaks and milestone rewards turn consistency into a game. Not because points matter, but because showing up matters.

Auto growing glossary / Reading streaks / Milestone rewards
Everything stored locally
Your data lives in a folder on your Mac. PDFs, images, and a lean JSON file. Sync via Dropbox or iCloud if you want. No lock-in, ever.
paperhacking_data/
new mac/
6

Your work. Yours forever.

No cloud dependency. No subscription. No account. Your notes, your PDFs, your glossary, all in a folder you control. Auto-save on every keystroke. Import and export in seconds. This is software that respects your data.

Folder based storage / Full import and export / Fully offline
"The goal isn't to read more papers.
It's to think more clearly about what you've read."
The philosophy behind PaperHacking
PaperHacking Workbench

Ready to turn reading into thinking?

Whether you're an undergraduate doing your first lit review, a doctoral student mapping an entire field, or just someone who believes ideas deserve better than forgotten PDFs. This app was built for you.

Download for macOS

Free. No account. No cloud. No catch.