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.

CI PyPI License: MIT Python 3.11+ GitHub stars

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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.

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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. Give the model every PDF's local path to open on demand, and render pages as images or embed the PDF when you ask for it
6. Write a structured Markdown report
7. Save everything into your Zotero library

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vs. alternatives

	ChatGPT Deep Research	Gemini Deep Research	Perplexity Pro	Paper Pilot
Reads actual PDFs	Web summaries	Web summaries	Web summaries	Full text extraction
Figures and tables	Text only	Text only	Text only	Page rendering to PNG
Your library	Locked in their UI	Locked in Google	Locked in Perplexity	Syncs to Zotero
Sources	Generic web search	Generic web search	Web search	6 academic databases
Cost	$200/month	$20/month	$20/month	Free, MIT licensed
Your data	Their cloud	Their cloud	Their cloud	Your machine
Open source	No	No	No	Yes

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MCP client setup

Works on Claude Desktop, Cursor, Claude Code, and Codex, across Windows, macOS, and Linux. Full per-OS config-file locations, the Windows spawn uv ENOENT fix, and a per-client capability matrix are in docs/CLIENTS.md.

Claude Desktop

Add to claude_desktop_config.json (macOS: ~/Library/Application Support/Claude/, Windows: %APPDATA%\Claude\; Claude Desktop has no Linux build, so use Claude Code on Linux):

{
  "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"

Cursor

Put this at .cursor/mcp.json (this repo) or ~/.cursor/mcp.json (global), then enable it in Settings (Cmd/Ctrl+Shift+J) under Model Context Protocol. See examples/cursor.mcp.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" }
    }
  }
}

Windows note

Claude Desktop and Cursor spawn the command without a shell, so a bare uv/uvx can fail with spawn uv ENOENT. Wrap it ("command": "cmd", "args": ["/c", "uv", "--directory", "C:\\path\\to\\paper-pilot", "run", "paper-pilot"]) or use the full path from where uv.

Streamable HTTP mode

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

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Tools

Tool	What it does
research_topic	Full pipeline: search, download, report, optional citation graph + Zotero sync
deep_read_topic	Everything above + full-text extraction with evidence chunks
graph_topic	Render an interactive citation / relatedness graph (HTML) for a topic
render_pdf_pages	Render PDF pages as images the model can see (figures, tables, layout)
read_pdf_document	Return a downloaded PDF's local path and resource link (embed base64 only on request)
get_pdf_page_text	Exact text of specific PDF pages as JSON, for fine-grained lookups (no base64)
search_literature	Fine-grained multi-source academic search (6 databases)
find_similar_papers	Related work expansion from a seed paper
inspect_open_access_pdf	OA availability check and PDF preview
extract_local_pdf_text	Text extraction from any local PDF
list_zotero_collections	List collections in your local or web Zotero library
search_scihub	Search Sci-Hub by DOI, title, or keyword (opt-in)
download_scihub_paper	Download a paper via Sci-Hub by DOI (opt-in)
search_libgen	Supplementary shadow library search (opt-in)
inspect_libgen_item	Resolve a LibGen mirror item and preview its PDF (opt-in)
healthcheck	Verify all connections are up

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

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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.

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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.

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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
ZOTERO_DATA_DIR=                       # optional: relocated/sandboxed Zotero data dir (default ~/Zotero)

# 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
PAPER_PILOT_ALLOW_EXTERNAL_PDF=true   # read PDFs outside the data dir (set false on networked transports)
PDF_EMBED_MAX_MB=5                     # size cap for an embedded PDF resource
PDF_EMBED_MAX_PAGES=60                 # page cap for an embedded PDF resource

# Institutional networks
HTTP_PROXY=
HTTPS_PROXY=
SSL_CERT_FILE=

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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
    content.py           PDF/image MCP content blocks (pages as images, embedded PDF)
    libgen.py            Supplementary LibGen support
    net.py               SSRF guard + size-capped downloads

Architecture details: docs/ARCHITECTURE.md

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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

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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.

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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.

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License

MIT. Do whatever you want with it.

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