FlyBase AI Tools

Tools for using FlyBase data from AI assistants.

• mcp/: the hosted FlyBase MCP server (Rust). Endpoint: https://mcp.flybase.org/mcp.
• plugins/flybase/: a Claude Code plugin that registers the MCP server. Skills will live here later.
• blast-jobs/: the BLAST job service behind the MCP's BLAST tools (Rust, NCBI BLAST+ 2.17.0).

The server's tools and their arguments are listed in docs/tools.md.

Install

The server is public at https://mcp.flybase.org/mcp. It speaks the Model Context Protocol over Streamable HTTP and needs no account, key or login. Pick your client below.

Claude Code, through the plugin marketplace

Inside a Claude Code session:

/plugin marketplace add FlyBase/flybase-ai-tools
/plugin install flybase@flybase

The same two steps work from a shell:

claude plugin marketplace add FlyBase/flybase-ai-tools
claude plugin install flybase@flybase

The plugin installs at user scope and registers the server. claude mcp list then shows plugin:flybase:flybase: https://mcp.flybase.org/mcp (HTTP) - ✔ Connected. Plugin tools are named mcp__plugin_flybase_flybase__<tool>. Skills will ship in the same plugin later.

Claude Code, without the plugin

claude mcp add --transport http flybase https://mcp.flybase.org/mcp

That adds the server for the current project on your machine only. Add --scope user for every project. To share it with everyone who clones a project, use --scope project, or commit this .mcp.json at the project root:

{
  "mcpServers": {
    "flybase": {
      "type": "http",
      "url": "https://mcp.flybase.org/mcp"
    }
  }
}

Claude Code asks each user to approve a project's .mcp.json servers the first time it starts there. For a one-off non-interactive run, save the same JSON as flybase.json and pass it in. Put the prompt before --allowedTools, which takes a list and would otherwise swallow it:

claude -p "What is the FlyBase ID for wingless?" --mcp-config flybase.json --allowedTools "mcp__flybase__*"

Codex

codex mcp add flybase --url https://mcp.flybase.org/mcp

Or add this to ~/.codex/config.toml:

[mcp_servers.flybase]
url = "https://mcp.flybase.org/mcp"

codex exec with an approval policy of never refuses MCP tool calls that need approval. The tools only read FlyBase data (blast_submit starts a search job and nothing else), so for scripted runs you can approve them up front. Add this line under the existing [mcp_servers.flybase] table, below its url line (do not repeat the table header):

default_tools_approval_mode = "approve"

Claude.ai and Claude Desktop

Add a custom connector: open Settings, then Connectors, choose "Add custom connector", paste https://mcp.flybase.org/mcp, and leave the OAuth fields empty. Free plans allow one custom connector. On Team and Enterprise plans an owner adds the connector for the organization first, then each member connects. Enable it per chat from the "+" menu under Connectors. See Anthropic's custom connector guide.

ChatGPT

Open ChatGPT's Plugins page (chatgpt.com/plugins), choose the plus button, then "Add custom MCP server". Give it a name such as FlyBase, choose "Public endpoint" and enter https://mcp.flybase.org/mcp, and set no authentication. Confirm the warning and choose "Create as a plugin". In a new chat, type @ and pick it. Workspace policies decide whether custom servers are allowed, and older accounts reach the same form through developer mode under Settings, Apps. OpenAI's connect from ChatGPT guide has the current steps.

Any other MCP client

Setting	Value
URL	https://mcp.flybase.org/mcp
Transport	Streamable HTTP (JSON-RPC over POST)
Authentication	none
Tools	25; they read FlyBase data and never change it

initialize is optional, so a bare tools/call works:

curl -s https://mcp.flybase.org/mcp \
  -H 'Content-Type: application/json' -H 'Accept: application/json, text/event-stream' \
  -d '{"jsonrpc":"2.0","id":1,"method":"tools/call","params":{"name":"resolve","arguments":{"query":"wingless"}}}'

What you can ask

Ask in plain language. For example:

• "What is the best human ortholog of wingless?"
• "Which genes are highly expressed in adult testis but off in the ovary?"
• "What genes and aberrations are in cytological band 89D?"
• "I want a GAL4 driver for wingless. What can I order?"
• "BLAST this protein fragment against D. melanogaster polypeptides and tell me what it is."

docs/examples.md has tested questions for every tool, with the call the assistant makes and what comes back. The server's 25 tools cover identifying symbols and IDs, reports, batch downloads, the genome (sequence, features in a range, cytology, release 5 to 6 coordinates), controlled vocabularies, homepage data (orthologs, gene groups, disease models, stocks, interactions), RNA-seq expression, BLAST, and the FlyBase wiki's help pages (what report fields mean, how tools and downloads work). Each is described in docs/tools.md.

Using the public server

• Data release. Every result names the FlyBase release it came from, currently FB2026_03.
• BLAST databases. BLAST searches the archived FB2023_04 database set, so BLAST results can lag the rest of the server. Each blast_submit response says so.
• Fair use. The server is shared and rate limited per client. Requests over the limit get HTTP 429; wait and retry. One assistant session stays well within it. Please be polite with scripts: pause between batches, use batch_download and validate_ids for bulk work, and cache what you fetch.
• Only /mcp is public. /health and /metrics are intentionally not exposed and return 404.

BLAST

The MCP's BLAST tools are clients of a private job API. blast-jobs/ implements it. The service is a small Rust process that runs NCBI BLAST+ 2.17.0 against a directory of BLAST databases described by a catalogue file, in its own container with the databases mounted read-only. Nothing in it is specific to FlyBase, so anyone with BLAST databases and a catalogue can run it. Configuration, the image and the run shape are in docs/blast-jobs.md.

Develop

See docs/deployment.md for running the server and mcp/README.md for the crate.

Private-side handoff: docs/handoff-private-side.md lists what a host must provide (database, runtime role, release runbook step, proxy and CDN requirements, and the BLAST job API contract).

Licence

The code in this repository is under the MIT License; see LICENSE. The bundled release 5 to 6 coordinate map, mcp/data/coordinates/dmel_r5_to_r6.tsv, is derived from FlyBase's published map and carries its BSD-3-Clause notice in mcp/data/coordinates/LICENSE.bulkfile-scripts.