# Pinakes

> Pinakes — a deterministic, verifiable data layer for AI agents across domains (biology + literature). Same query → byte-identical records, complete-or-fail-loudly, re-runnable provenance manifest + verify().

- **Type:** MCP server
- **Install:** `agentstack add mcp-001tmf-pinakes`
- **Verified:** Pending review
- **Seller:** [001TMF](https://agentstack.voostack.com/s/001tmf)
- **Installs:** 0
- **Category:** [AI & ML](https://agentstack.voostack.com/c/ai-and-ml)
- **Latest version:** 0.1.0
- **License:** Apache-2.0
- **Upstream author:** [001TMF](https://github.com/001TMF)
- **Source:** https://github.com/001TMF/pinakes

## Install

```sh
agentstack add mcp-001tmf-pinakes
```

Requires the [AgentStack CLI](https://agentstack.voostack.com/docs/cli). Works with Claude Code, Cursor, and any MCP-compatible agent.

## About

Pinakes

Deterministic, verifiable data for AI agents.

  
  
  
  
  
  

  

---

Pinakes is a single signed static Go binary — with **zero runtime dependencies** — that gives AI agents reproducible, complete, and verifiable access to public scientific databases. It is a CLI, a [Model Context Protocol](https://modelcontextprotocol.io) stdio server, and a local REST server, all in one executable.

Named for the *Pínakes*, the catalogue of the Library of Alexandria — the first index of all knowledge.

> **The problem:** ask a public biological database the same question twice and you can get different result sets. Tools paginate and truncate differently, and the databases expose no stable order. An agent's analysis silently inherits that drift, and nothing flags it.
>
> **The fix:** every Pinakes query pins a content-addressed snapshot, so results are byte-identical forever; retrieval is **complete-or-fail** (the returned count is reconciled against the source's authoritative total — a short set fails loudly, never silently); and every result ships a re-runnable manifest that `pinakes verify` re-derives **offline** to prove the result is exactly what it claims. It is git for scientific data.

---

## Install

Install the single static binary:

```sh
curl -fsSL https://get.pinakes.sh | sh
```

No token, no Docker, no network at query time beyond the source databases themselves. The install script verifies the release's **SHA-256** checksum (and its **cosign** keyless signature when `cosign` is present) before installing anything.

Then register `pinakes mcp` with your MCP client — **any** client (Claude, Cursor, Cline, Windsurf, Zed, …); see [Add to any MCP client](#add-to-any-mcp-client) below. *(In Claude Code, for example, that's one line: `claude mcp add --scope user pinakes -- pinakes mcp`.)*

> **Homebrew (coming soon).** `brew install pinakes-sh/tap/pinakes` is pending the public Homebrew tap and is not live yet — use the `curl | sh` line above for now.

### Add to any MCP client

Most clients (Claude Desktop, Cursor, Windsurf, Zed, VS Code via `.mcp.json`, …) read a standard config block. Add Pinakes to it:

```json
{
  "mcpServers": {
    "pinakes": {
      "command": "pinakes",
      "args": ["mcp"]
    }
  }
}
```

No `env`, no token, no Docker — fully local and offline. If your GUI app can't find `pinakes` on its `PATH`, replace `"command": "pinakes"` with the absolute path from `which pinakes`.

### Other ways to install

Homebrew (coming soon)

```sh
brew install pinakes-sh/tap/pinakes
```

Pending the public Homebrew tap — **not live yet**. Until then, use the `curl | sh` line above.

Go toolchain

```sh
go install pinakes.sh/pinakes/cmd/pinakes@latest
```

After installing, confirm the server is wired up by listing the catalogue:

```sh
pinakes catalog
```

---

## API keys (optional)

Pinakes works fully **without any key**. The only sources that benefit today are the two NCBI sources (`ncbi-protein`, `ncbi-virus`): supplying a free NCBI api key raises *your own* upstream rate limit (E-utilities and the NCBI Datasets API both lift to ~10 requests/sec with a key, vs 3–5 without).

A key affects **rate limits only** — never the results, their order, or their hashes. Pinakes attaches the key to the outbound HTTP request alone; it never enters a snapshot, a record, or the reproducibility manifest, so a query is byte-identical and reproducible with or without a key.

The single `ncbi` alias covers both NCBI sources. Set it via the scoped CLI (the key is read from **stdin**, never passed as an argument, and stored at `~/.config/pinakes/config.yaml` with `0600` permissions):

```sh
pinakes config set-key ncbi      # paste at the prompt, or:  A future hosted tier (accounts, metering) will use `PINAKES_API_KEY`. The local binary in this repository needs **no key** — it is the open, local engine, fully usable offline.

---

## Versioning & stability

Pinakes follows [SemVer](https://semver.org). Tags are `vMAJOR.MINOR.PATCH`.

Two things version separately:

- **The determinism contract** is frozen at `ManifestSchemaVersion` **1.0.0**. A pinned query and the manifest `pinakes verify` re-derives stay reproducible across releases. See [CONTRACTS.md](CONTRACTS.md) for what the contract covers and the rules for ever changing it.
- **The CLI, MCP, and REST surfaces** are still on the `0.x` line. Flags, tool names, and endpoints may change before `1.0.0`; surface stability is promised only at `1.0.0`. The contract above does not move when a surface does.

---

## License

Apache License 2.0. See [LICENSE](LICENSE).

## Source & license

This open-source MCP server is cataloged on AgentStack and links to its original source — we do not rehost the code.

- **Author:** [001TMF](https://github.com/001TMF)
- **Source:** [001TMF/pinakes](https://github.com/001TMF/pinakes)
- **License:** Apache-2.0

Install and usage instructions live in the source repository linked above.

## Pricing

- **Free** — Free

## Security capabilities

Automated source analysis of v0.1.0 — what this tool can access:

- **Network access:** yes
- **Filesystem access:** no
- **Shell / process execution:** no
- **Environment & secrets:** no
- **Dynamic code execution:** no

*"Yes" means the capability is present in the source — more access means more to trust, not that it is unsafe.*


## Versions

- **0.1.0** — security scan: flagged — Imported from the upstream source.

## Links

- Listing page: https://agentstack.voostack.com/l/mcp-001tmf-pinakes
- Seller: https://agentstack.voostack.com/s/001tmf
- Browse the marketplace: https://agentstack.voostack.com/browse

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Listed on AgentStack — the marketplace for AI agent skills and MCP servers. Every listing is security-reviewed. Creators keep 70%.