Virtual Fly Brain MCP server

• Registry nameorg.virtualflybrain/vfb3-mcpverified in the MCP registry

The registry name sits under virtualflybrain.org. The registry only lets a publisher use that namespace after proving control of the domain through DNS or HTTP.

• Stateanswerschecked 2026-10-16
• Tools11
• Server calls itselfvfb3-mcp-server
• Server version1.11.2
• Protocol version2025-06-18

On 2026-10-16 the server answered initialize and tools/list without a sign-in. First answer in 482 ms.

• Whether its tools do the product's job has not been judged yet.

Said by rules from the measurements above. The likely first call is a model's pick from the tool list; read its description before relying on it.

• INITE MCP score83 of 100answers 100 · definitions 83 · context 81 · use 25 · connects 100
• Use9 GitHub stars
• Answered100% of days9 of 9 daily checks
• Median first answer490 ms
• Space in an agent's context≈ 5,987 tokensthe definitions of all its tools (11), which an agent carries on every turn
• Tool definitionsB · 83 of 100
• Typed results0 of 11 toolsdeclared outputSchema: results come typed, read once

• Not saying whether it only reads or can destroy: 11 of 11

A program checks the server once a day: initialize and tools/list, no model. Tokens are the definitions' length at about four characters a token. The grade averages six checks of every tool's name, description, schema and annotations; it says how well the tools are described, not whether they work. The score weighs what was measured and nothing else: answering (25%), doing the product's job (25%), definitions (20%), context (10%), use (10%) and how readily a client connects (10%). A part that was not measured is left out, and a hidden instruction caps the score at 40. The state of vendors' MCP servers: method and numbers →

• get_term_info

  Get term info for a VFB or anatomy ontology entity (VFB_*, FBbt_*, etc.). THIS IS THE QUERY DISCOVERY TOOL: the response's "Queries" array lists the valid query_type values that run_query accepts for this entity. ALWAYS call get_term_info…

• run_query

  Run a pre-computed query on a VFB entity. REQUIRED WORKFLOW: (1) call get_term_info on the ID first; (2) read the response's "Queries" array; (3) pass one of those values as query_type. Calling run_query with a guessed query_type will…

• search_terms

  Search VFB terms. This is the search virtualflybrain.org itself runs — the same Solr query, the same ranking — so what comes back first here is what a user would see first on the site. USE filter_types BY DEFAULT. Unfiltered searches mix…

• list_search_facets

  List the type names search_terms can filter, exclude, boost or demote by, with the number of terms carrying each one. Call this instead of guessing: there are over 200 names, they are the index's own annotations rather than a curated…

• resolve_entity

  Resolve an unresolved FlyBase-related query string into VFB/FlyBase IDs and metadata. Pass the raw text exactly as the user wrote it (for example "P{VT054895-GAL4.DBD}", "Hb9-GAL4", "SS04495", "MB002B", "PAM cluster", or "dpp"). Do NOT…

• resolve_combination

  Resolve an unresolved split-GAL4 combination name or synonym into its FBco ID and component hemidrivers. Pass the raw combination text exactly as the user wrote it (for example "MB002B" or "SS04495"). Do NOT pass an FBco ID; if you…

• list_connectome_datasets

  List available connectome datasets with their labels and symbols. Use the returned symbols when constructing exclude_dbs arguments for query_connectivity. Common datasets include Hemibrain (hb), FAFB (fafb), MANC, and others. Call this…

• query_connectivity

  Query synaptic connectivity between Drosophila neuron classes across ALL connectome datasets simultaneously for comparative connectomics. This is NOT pre-cached — it runs live queries, so expect slow responses (up to several minutes). Set…

• get_predicted_neurotransmitters

  Get the PREDICTED neurotransmitter(s) for a Drosophila neuron class — itself or any subclass — from per-instance connectome predictions (each reconstructed neuron carries a predicted transmitter with a confidence). Use this for "what…

• get_known_neurotransmitters

  Get the KNOWN (curated) neurotransmitter(s) for a Drosophila neuron class and its subclasses, from the ontology's classification rather than per-instance predictions — so there is no confidence. Use this for "what neurotransmitter is…

• get_hierarchy

  Build a hierarchy tree for a VFB term, showing ancestors (parents) and/or descendants (children). Use relationship "part_of" for brain region structure (e.g. "what are the parts of the mushroom body?") and "subclass_of" for cell type…