Virtual Fly Brain MCP Server

A Model Context Protocol (MCP) server for Virtual Fly Brain (VFB): query Drosophila melanogaster neuroanatomy, connectomics, expression and reagent data from Claude, Copilot or any other MCP client. Its 11 documented tools cover resolve, neurotransmitters. It is available as a remote MCP endpoint.

Teams that work with resolve and neurotransmitters and want a hosted endpoint instead of running a local process. The project is written in TypeScript.

VERIFIED ACTIVE

LAST COMMIT 2026-09-10 · ★ 5 · #781 OF 945 MAINTAINED OTHER · VERIFIED 2026-09-18

MIT · TypeScript servers · how we verify → /methodology

01 · Install Virtual Fly Brain

before you install - you'll need

MCP_MODE

Environment variables documented in the project's README - it lists which are required and which have defaults.

Claude Code

claude mcp add virtualflybrain-vfb3-mcp --transport http https://vfb3-mcp.virtualflybrain.org

Claude Desktop / Cursor / VS Code - add to config

{
  "mcpServers": {
    "virtualflybrain-vfb3-mcp": {
      "url": "https://vfb3-mcp.virtualflybrain.org"
    }
  }
}

Same JSON for Cursor. For VS Code, rename the top-level key from `mcpServers` to `servers`.

Using another client? Same JSON, different key

Claude Desktop · mcpServers

Cursor · mcpServers

VS Code · servers

Windsurf · mcpServers

Zed · context_servers

Cline · mcpServers

Roo Code · mcpServers

Continue · mcpServers

LibreChat · mcpServers

Gemini CLI · mcpServers

Codex CLI · mcp_servers

Full setup guides: every client.

02 · Evidence

https://vfb3-mcp.virtualflybrain.org

transport: streamable-http

endpoint alive - responded to MCP initialize · probed 2026-09-18

Security posture

What to check before giving this server access to your agent - from the registry, GitHub, and our own probes. We don't score safety; we show what's verifiable.

runs as remote - your agent's requests go to vfb3-mcp.virtualflybrain.org

endpoint auth accepted our unauthenticated MCP initialize - no credentials needed to connect

license MIT - declared in the repository

registry vendor namespace org.virtualflybrain - domain-verified with the official MCP registry

03 · What Virtual Fly Brain can do

Prose above is summarized from the project's README and registry record - no invented capabilities.

What you can build

With this server connected, an agent can get detailed metadata for a VFB ID, run a precomputed analysis query for a VFB ID (see the Queries field from get_term_info), resolve an unresolved split-GAL4 combination name or synonym into its component IDs, and list available connectome datasets (e.g., Hemibrain, FAFB).

Capability map

Tools grouped from the project's README - what Virtual Fly Brain lets an agent do.

read & search

8 tools - e.g. Get detailed metadata for a VFB ID; Search VFB entities by text with filtering / boosting options. This is the same search virtualflybrain.org itself runs; List the facets_annotation type names that…

get_term_info · search_terms · list_search_facets · list_connectome_datasets · query_connectivity · get_predicted_neurotransmitters…

Resolve

2 tools - e.g. Resolve an unresolved FlyBase-related query string (e.g., P{VT054895-GAL4.DBD} or a driver line / cell type label) to VFB/FlyBase IDs and metadata (not the same; Resolve an unresolved split-GAL4…

resolve_entity · resolve_combination

run & execute

1 tool - e.g. Run a precomputed analysis query for a VFB ID (see the Queries field from get_term_info)

run_query

Latest releases

v1.11.2 · 2026-09-10

Per-caller GA4 client IDs and MCP client info tracking · Fixes and extends the GA4 usage analytics added in earlier releases: · client_id is now derived from a hash of the caller's IP. In stateless HTTP mode there is…

v1.11.1 · 2026-08-17

Repository references point at the org repo · Metadata only. No tool, schema or behaviour changes - 1.11.1 is functionally · identical to 1.11.0. · VirtualFlyBrain/VFB3-MCP is the standalone home of this project.…

v1.11.0 · 2026-08-02

A failed query no longer looks like an empty one · run_query returns count: -1 when the query did not run - Owlery errored, or the retries were exhausted. It is not a "too many to count" sentinel, and it is unrelated…

04 · Who maintains Virtual Fly Brain

VirtualFlyBrain is maintained by virtualflybrain. It's the only MCP server we track from this author; the repo dates to Feb 2026.

05 · Facts

repository: github.com/virtualflybrain/vfb3-mcp
website: https://virtualflybrain.org/
category: other - ranked #781 of 945 actively-maintained other servers as of 2026-09-18.
release cadence: 6 releases in the last 90 days (latest 2026-09-10)
registry: org.virtualflybrain/vfb3-mcp (active, first published 2026-02-07 · 27 versions)

06 · Virtual Fly Brain FAQ

Is Virtual Fly Brain still maintained?

Yes - as of 2026-09-18, its last commit was 2026-09-10 and it shipped 6 releases in the last 90 days. We re-verify nightly.

What can Virtual Fly Brain do?

How do I install Virtual Fly Brain?

Run `claude mcp add virtualflybrain-vfb3-mcp --transport http https://vfb3-mcp.virtualflybrain.org`. The README documents one environment variable (MCP_MODE) to set first. You can also paste the ready-made client config above.

Does Virtual Fly Brain require authentication?

No - the endpoint accepted our unauthenticated MCP initialize when probed on 2026-09-18; you can connect without credentials.

07 · Alternatives to Virtual Fly Brain

Alternatives to Virtual Fly Brain

Maintained other servers if Virtual Fly Brain isn't the fit.

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