Search, read, and analyze 8M+ biomedical papers from the command line.

Paperclip is a CLI and MCP server for AI agents where every paper is a directory containing full text, sections, figures, and supplements on a virtual filesystem at /papers/.

• Search with natural language or regex across 8M+ papers from bioRxiv, medRxiv, and PubMed Central
• Run parallel AI readers across papers with map and synthesize with reduce
• Pipe results through standard Unix tools (grep, awk, sed, jq, etc.)
• Ask questions about figures with vision AI
• Query the database directly with SQL

Full documentation: paperclip.gxl.ai

Community

This repository hosts the source code for the Paperclip CLI client. Use it to:

• Report bugs
• Request features
• Start discussions

Install

Python 3.8+ required.

curl -fsSL https://paperclip.gxl.ai/install.sh | bash

Installs to ~/.paperclip/ with a wrapper at ~/.local/bin/paperclip.

Or install via pip:

pip install https://paperclip.gxl.ai/paperclip.whl
paperclip setup

Sign in

Sign-in happens automatically on first use, or run manually:

paperclip login

Verify

paperclip config
# Server:  https://paperclip.gxl.ai
# Auth:    ✓ you@example.com
# Config:  ~/.paperclip

MCP Server (alternative)

Use Paperclip as an MCP server directly — no local install needed.

Claude Code

claude mcp add --transport http paperclip https://paperclip.gxl.ai/mcp

Then start claude, enter /mcp, and select Authenticate under the paperclip server.

Cursor

Add to ~/.cursor/mcp.json (or .cursor/mcp.json in your project):

{
  "mcpServers": {
    "paperclip": {
      "url": "https://paperclip.gxl.ai/mcp",
      "type": "http"
    }
  }
}

Then Cmd/Ctrl + Shift + P → Tools & MCPs, enable the paperclip server, and authenticate.

Quick Start

# Search for papers
paperclip search "CRISPR base editing efficiency"

# Read a paper's metadata
paperclip cat /papers/bio_4f78753a6feb/meta.json

# Preview the first 50 lines
paperclip head -50 /papers/bio_4f78753a6feb/content.lines

# Grep within a single paper
paperclip grep -i "binding affinity" /papers/bio_4f78753a6feb/content.lines

# Regex search across the entire corpus (sub-second)
paperclip grep "alphamissense" /papers/

# Map over search results with an AI reader
paperclip map --from s_abc123 "What methods were used?"

# Run SQL queries
paperclip sql "SELECT title, doi FROM documents WHERE authors ILIKE '%Doudna%' LIMIT 5"

# Save results to a local file
paperclip search "CRISPR" -n 5 > results.txt

Use paperclip bash '...' for pipes and chains:

paperclip bash 'search "protein folding" | grep "deep learning"'

Commands

Command	Description
search	Hybrid search (BM25 + vector) across 8M+ papers
searches	Run multiple queries in parallel and merge results
grep	Regex search within a paper or across the entire corpus
scan	Multi-pattern grep in a single pass
lookup	Find papers by DOI, PMC ID, PMID, author, title, journal
sql	Read-only SQL queries against the papers database
export	Export SQL results to CSV
map	Parallel AI reader across multiple papers
reduce	Synthesize map results into summaries, tables, or themes
filter	Filter search results for relevance
ask-image	Analyze figures with vision AI
cat	Read files from the paper filesystem
head / tail	Preview first or last lines
ls / tree	List directory contents
grep / scan	Search within papers
sed / awk / jq	Text processing
results	View, browse, and export saved results
pull	Download papers or files locally
config	Show or set configuration
install	Install agent skill for Claude Code, Cursor, or Codex
update	Update to the latest version

Agent Integration

Install a skill so your coding agent can use Paperclip automatically:

paperclip install

Supports Claude Code, Cursor, and Codex. The skill teaches the agent the full command set. Then just mention /paperclip in your prompt:

Using /paperclip, find recent papers on GLP-1 receptor agonists and summarize the primary endpoints.

Paper Filesystem

Each paper lives at /papers/<id>/:

meta.json        — title, authors, doi, date, abstract, journal
content.lines    — full text, line-numbered (L<n>: <text>)
sections/        — named section files (Introduction.lines, Methods.lines, ...)
figures/         — figure files (PMC papers)
supplements/     — supplementary files (PMC papers)

Paper IDs use prefixes by source: bio_ (bioRxiv), med_ (medRxiv), PMC (PubMed Central).

License

Apache-2.0 — see LICENSE.