Paper Pilot

Your AI's research copilot.

An MCP server that gives Claude, Codex, and any AI agent real academic research: 6 databases, full-text PDFs, evidence with citations, figure rendering, and Zotero sync.

Your AI Googles when you say "research." Paper Pilot searches real academic databases, downloads the PDFs, reads them cover to cover, renders the figures, gives you evidence with citations, and files it all in your Zotero library.

Quick start

Try it in 30 seconds. No MCP client, no config:

# straight from GitHub (works today):
uvx --from git+https://github.com/aytzey/paper-pilot paper-pilot demo "retrieval augmented generation"

# once published to PyPI:
uvx paper-pilot demo "retrieval augmented generation"

This searches 6 academic databases, downloads the open-access PDFs, reads them, writes a structured report, and opens an interactive citation graph in your browser.

👉 See a real run, no install needed: sample report · interactive citation graph

Then plug it into your AI agent

Wire it into your MCP client (setup below), set a free OPENALEX_EMAIL, and ask:

Research retrieval-augmented generation, deep-read the top papers, and compare the methods.

How it works

graph LR
    A[Prompt] --> B[Search 6 databases]
    B --> C[Resolve OA PDFs]
    C --> D[Download & read]
    D --> E[Extract evidence]
    E --> F[Render figures]
    F --> G[Markdown report]
    G --> H[Zotero sync]

One prompt searches six academic databases, downloads the real PDFs, and returns real citations.

Research retrieval-augmented generation, deep-read the top papers, and compare the methods.

Your AI will:

1. Search Semantic Scholar, OpenAlex, arXiv, Crossref, Europe PMC, and DOAJ
2. Find the open-access PDFs, not abstracts
3. Download and read them cover to cover
4. Extract evidence chunks with source attribution
5. Render specific pages so it can see the figures and tables
6. Write a structured Markdown report
7. Save everything into your Zotero library

vs. alternatives

MCP client setup

Claude Desktop

Add to your claude_desktop_config.json:

{
  "mcpServers": {
    "paper-pilot": {
      "command": "uv",
      "args": ["--directory", "/path/to/paper-pilot", "run", "paper-pilot"],
      "env": {
        "OPENALEX_EMAIL": "[email protected]",
        "UNPAYWALL_EMAIL": "[email protected]",
        "ZOTERO_LOCAL": "true",
        "SCIHUB_ENABLED": "false"
      }
    }
  }
}

Claude Code

claude mcp add --scope user paper-pilot -- uv --directory /path/to/paper-pilot run paper-pilot

Codex

Add to ~/.codex/config.toml:

[mcp_servers.paper_pilot]
command = "uv"
args = ["--directory", "/path/to/paper-pilot", "run", "paper-pilot"]

[mcp_servers.paper_pilot.env]
OPENALEX_EMAIL = "[email protected]"
ZOTERO_LOCAL = "true"

Streamable HTTP mode

paper-pilot --transport streamable-http --host 127.0.0.1 --port 8000

Tools

Prefer the CLI? paper-pilot demo "<topic>" runs the whole pipeline and opens the citation graph. No MCP client required.

Sci-Hub integration (opt-in)

Sci-Hub access is disabled by default. To opt in:

SCIHUB_ENABLED=true

Once enabled, use search_scihub and download_scihub_paper directly, or pass include_scihub=True to research_topic / deep_read_topic for automatic fallback.

Disclaimer: Sci-Hub integration is provided strictly for educational and research purposes. Users are solely responsible for compliance with applicable laws and institutional policies.

Who uses this

PhD students that don't want to spend a week on a literature review. Point it at your thesis topic, get back a structured comparison with real citations and the PDFs already in Zotero.

Research labs that want to scan preprints weekly and auto-file them. Run research_topic on a schedule and keep your group library current.

AI builders that need their agents to work with real academic papers instead of web scraping snippets.

Configuration

[email protected]        # Required for polite API access
[email protected]       # Required for OA resolution
SEMANTIC_SCHOLAR_API_KEY=             # Optional, higher rate limits

# Local Zotero
ZOTERO_LOCAL=true
ZOTERO_LIBRARY_TYPE=user

# Web Zotero API (alternative)
ZOTERO_LIBRARY_ID=
ZOTERO_API_KEY=

# Sci-Hub (disabled by default)
SCIHUB_ENABLED=false
INSECURE_SHADOW_TLS=false              # opt in to skip TLS verification for Sci-Hub/LibGen mirrors

# Storage
PAPER_PILOT_DATA_DIR=./data
MAX_DOWNLOAD_MB=75                     # per-PDF download size cap

# Institutional networks
HTTP_PROXY=
HTTPS_PROXY=
SSL_CERT_FILE=

Project structure

src/paper_pilot/
  server.py              MCP tools and pipeline orchestration
  cli.py                 Server entry point + `demo` subcommand
  demo.py                Zero-config one-command demo runner
  config.py              Environment and settings
  services/
    academic.py          Multi-source scholarly search (6 databases)
    open_access.py       OA resolution and PDF downloads
    scihub.py            Sci-Hub paper resolution (opt-in)
    deep_read.py         Full-text extraction and page rendering
    zotero.py            Local and web Zotero integration
    reporting.py         Markdown report + synthesis comparison tables
    graphing.py          Interactive citation-graph HTML export
    libgen.py            Supplementary LibGen support
    net.py               SSRF guard + size-capped downloads

Architecture details: docs/ARCHITECTURE.md

For AI agents

• AGENTS.md -- shared operating guide
• CLAUDE.md -- Claude Desktop and Claude Code setup
• CODEX.md -- Codex setup
• docs/CLIENTS.md -- side-by-side client comparison

Contributing

PRs welcome. The most impactful areas:

• New scholarly source adapters
• Better OA resolution logic
• PDF parsing improvements
• More MCP client configs

See CONTRIBUTING.md.

Disclaimer

This tool is designed for academic research and educational purposes only. Open-access features use only legal, publicly available sources. Sci-Hub and LibGen integrations are disabled by default and provided as opt-in features.

License

MIT. Do whatever you want with it.

If this helps your research, star the repo and tell a colleague.