Search arXiv papers, download full text, semantic search, citation graphs, and alerts via MCP.
Nothing to run from here
VirtualFlyBrain is installed from its publisher's own source and answers where it runs, so this marketplace is not in the path of a single call. There is no address here to send one to, and a panel that pretended otherwise would be showing you an answer we made up. Install it and call it from your own client — the Installation tab has the entry for each one.
96/100
tool-list score
11
tools declared
remote
at its publisher
—
calls last 7d
What it does
MCP server for Drosophila neuroscience data from VirtualFlyBrain
Quickstart
# 1 — add it to Claude Code
claude mcp add --scope user --transport http virtualflybrain-mcp https://vfb3-mcp.virtualflybrain.org
# 2 — ask your agent for something these tools do
# get_term_info, run_query, search_terms and 8 more
VirtualFlyBrain costs nothing on mcprush: there is no plan to choose here, no cap to set and nothing mcprush can bill you for.
Publishernot claimed
VIAll 1 server
virtualflybrain1 server
1 category
Collected from a public index. Nobody has claimed this account, so nothing here was written by its author — claim it if it is yours.
Installation
Where are you running it?
Every route below installs the same thing and ends at the same approval screen. Nothing here runs on your machine and nothing runs on ours: this server answers at its publisher’s own address, and what you install is the connection straight to it.
Claude Codedeclared by this listing
This is a public server: it answers at its publisher’s own address and this marketplace is not in the path. Claude Code registers it in one command; --scope user makes it available in every project. The transport below is http, as the publisher's own manifest declares it.
claude mcp add --scope user --transport http virtualflybrain-mcp https://vfb3-mcp.virtualflybrain.orgReconnect, or start a new session, and the tools appear in the model’s tool list.
Free on mcprush, and it answers at its publisher’s own address: this marketplace is not in the path, so there is no key of ours to hold and no card to add.
What it writes
One config entry pointing straight at the publisher’s own address — this marketplace is not in the path, and nothing from this listing executes on your machine.
What you approve
11 tools, with what each one reads, writes and reaches shown before you agree — the same list on every route above. Read the tool surface.
Tool surface
What the model actually sees. Descriptions are diffed on every release — see version history.
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 before run_query unless you already obtained the query_type from a previous get_term_info call in this conversation. Returns: SuperTypes (classification), Tags (
| Parameter | Type | Required | Notes |
|---|---|---|---|
| id | yes | One or more VFB IDs to look up | |
| force_refresh | boolean | no | Bypass the response cache and recompute this result. Expensive — leave it unset on a first call. Set it ONLY to re-try a call that, earlier in this same conversation, returned a result that was clearl |
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 return an error. If a query returns empty rows or an error, the entity does not support that query_type or has no data for it — try a different query_type from the Q
| Parameter | Type | Required | Notes |
|---|---|---|---|
| id | no | One or more VFB IDs to query | |
| query_type | string | no | A valid query type from the Queries array returned by get_term_info. Used for single id or array of ids. |
| queries | array | no | Array of {id, query_type} pairs for mixed batch queries. When provided, id and query_type params are ignored. |
| limit | number | no | Max rows returned per call (default 25). The true total is always returned as "count"; broad queries (e.g. ListAllAvailableImages, or NeuronsSynaptic on a whole region) can have thousands to hundreds |
| offset | number | no | Row offset for paging (default 0). To get the next page, re-run with offset increased by limit; "count" gives the total. |
| include_images | boolean | no | Include the image/thumbnail column in result rows. Default false: the thumbnail is a long markdown image string that is rarely useful to reason over and greatly inflates every row, so it is stripped a |
| force_refresh | boolean | no | Bypass the response cache and recompute this result. Expensive — leave it unset on a first call. Set it ONLY to re-try a call that, earlier in this same conversation, returned a result that was clearl |
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 scRNAseq artifacts and developmental stages in with the entity the user wants. Common filter_types recipes: - Neuron classes: ["neuron", "class"] - Individual n
| Parameter | Type | Required | Notes |
|---|---|---|---|
| query | string | yes | Search query (e.g., medulla) |
| filter_types | array | no | Filter results to only include items matching ALL of these facets_annotation types (AND logic). Use list_search_facets for valid names. |
| exclude_types | array | no | Exclude results matching ANY of these facets_annotation types (OR logic). Deprecated terms are already excluded. |
| boost_types | array | no | Float results matching these facets_annotation types to the top of the ranked list without excluding others |
| demote_types | array | no | Sink results matching these facets_annotation types to the bottom of the ranked list without excluding them. Ignored for a type that also appears in boost_types. |
| unique | boolean | no | One row per term (default true). Set false to get a row per matching synonym, which shows WHICH name matched at the cost of repeating IDs. |
| start | number | no | Pagination start index (default 0) - use to get results beyond the first page |
| rows | number | no | Number of results to return (default 150, max 1000) - use smaller numbers for focused searches |
| minimize_results | boolean | no | When true, return at most 10 results with only the essential fields. For exact matches, return only the matching result. |
| auto_fetch_term_info | boolean | no | When true and an exact label match is found, automatically fetch and include term info in the response. |
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 list, and they change as data is added. Use contains to narrow (e.g. contains="lineage" for the ~120 lineage clones, contains="connectivity" to find the connectome fa
| Parameter | Type | Required | Notes |
|---|---|---|---|
| contains | string | no | Only return type names containing this text. Matched case- and separator-insensitively, so "nervous system" finds "Nervous_system". |
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 pass resolved IDs such as FBgn/FBal/FBti/FBco/FBst or VFB IDs; if you already have an ID, use the downstream tool directly. Uses tiered resolution: exact name → syn
| Parameter | Type | Required | Notes |
|---|---|---|---|
| name | string | yes | Unresolved FlyBase-related query string from the user. Pass the raw name/synonym exactly as written (e.g., "P{VT054895-GAL4.DBD}", "Hb9-GAL4", "SS04495", "MB002B", "PAM cluster", "dpp"). Do NOT pass a |
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 already have one, use the downstream tool directly. Uses tiered resolution: exact name → synonym → broad pattern match. Returns FBco ID, combination name, matched synon
| Parameter | Type | Required | Notes |
|---|---|---|---|
| name | string | yes | Unresolved split-GAL4 combination name or synonym exactly as written by the user (e.g., "MB002B", "SS04495"). Do NOT pass an FBco ID here. |
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 tool if unsure which dataset symbols are valid.
No parameter schema on file.
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 both upstream_type AND downstream_type to filter connections between two specific neuron classes (e.g., "What Tm1→T3 connections exist across all datasets?"). At
| Parameter | Type | Required | Notes |
|---|---|---|---|
| upstream_type | string | no | Upstream (presynaptic) neuron class — OWL ID (e.g., "FBbt_00003789") or full label (e.g., "transmedullary neuron Tm1"). Must be a neuron type/class, NOT an anatomical region. Use search_terms with fil |
| downstream_type | string | no | Downstream (postsynaptic) neuron class — OWL ID or full label. Must be a neuron type/class, NOT an anatomical region. If user asks about connectivity to a brain region, first find neuron classes in th |
| weight | number | no | Minimum synapse count threshold (recommended default: 5). Lower to 1 if initial query returns zero results as first relaxation step. |
| group_by_class | boolean | no | If true, aggregate by class rolled up over the subclass hierarchy: a row appears for the queried class AND each subclass with data (a connection counts toward every ancestor pair up to the queried ter |
| exclude_dbs | array | no | Dataset symbols to exclude (recommended default: ["hb", "fafb"] to focus on newer datasets). Pass empty array [] to include all datasets. Must be the exact symbol field from list_connectome_datasets |
| limit | number | no | How many connection rows to return, strongest first (default 50). The summary always covers every connection found, not just the returned rows. Pass 0 for all rows — only do this on a query you alread |
| offset | number | no | Row to start from within the strongest-first ranking (default 0). Re-running with the same limit and the next offset walks down the list. |
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 neurotransmitter does <cell type> use?" when you want the data-driven prediction and its confidence. By default results are aggregated to flat per-class rows (one per
| Parameter | Type | Required | Notes |
|---|---|---|---|
| neuron_type | string | yes | Neuron class — OWL ID (e.g. "FBbt_00003797") or label (e.g. "Tm9"). Means the class and all of its subclasses. |
| aggregate | boolean | no | If true (default), aggregate to flat per-class rows {cell_type_id, cell_type, nt_id, nt_label, instances, percent_of_class, mean_confidence}. If false, return one row per individual neuron {..., neuro |
| split_by_dataset | boolean | no | If true (aggregate only), emit one row per (cell type, neurotransmitter, dataset) with a dataset column, so cross-connectome agreement is visible. Default false aggregates over all included datasets. |
| exclude_dbs | array | no | Dataset symbols to exclude (default ["hb","fafb"]). Pass [] to include all datasets. Same symbols as query_connectivity / list_connectome_datasets. |
| min_confidence | number | no | Drop predictions below this confidence (0..1). Default 0 (keep all). |
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 <cell type> known to use?" when you want the curated/established answer. Returns one row per (cell type, neurotransmitter): {cell_type_id, cell_type, nt_id, nt_label}
| Parameter | Type | Required | Notes |
|---|---|---|---|
| neuron_type | string | yes | Neuron class — OWL ID (e.g. "FBbt_00003797") or label (e.g. "Tm9"). Means the class and all of its subclasses. |
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 hierarchies (e.g. "what types of Kenyon cell are there?"). Descendants are returned as a nested tree for both relationship types. Ancestors are returned as a nested c
| Parameter | Type | Required | Notes |
|---|---|---|---|
| id | string | yes | VFB term ID (e.g. FBbt_00005801 for mushroom body, FBbt_00003686 for Kenyon cell) |
| relationship | string | yes | Type of hierarchy: "part_of" for brain region structure, "subclass_of" for cell type taxonomies |
| direction | string | no | Which direction to explore (default: "both") |
| max_depth | number | no | Number of levels to expand. 1 = direct children/parents only. Higher values go deeper. -1 = full tree (use with caution on broad terms). Default: 1. |
Free
$0 forever
- Every tool — any call limit is its publisher’s, not ours
- No card, and mcprush charges nothing for it
- Runs at its publisher’s own address — this marketplace is not in the path
- Nothing to cap, because mcprush bills nothing
What counts against your monthly calls
| Tool | Unit | Calls used | Out of the allowance |
|---|
Nothing here is billable: mcprush charges nothing to install VirtualFlyBrain or to call it, at any volume.
Call allowance · this installenforced at the gateway
Monthly allowance, in calls
—
—
Alert at 80% · then the tool returns a normal MCP error
Used this month: —
ATool-list grade · score 96 / 100
Release 1.11.3 · scanned 28 Oct 2026
Graded from the tools this server lists, not from its source code.
Two independent axes, because powerful and malicious are different questions. The grade is threat only. The capability level is blast radius, and it is never a penalty on the grade — it is priced as one subtract-only term in the score, where you can see it.
Threat score100
Client score96
Findings0 threat · 0 capability
Capabilityminimal
Coveragemanifest
Verificationnot in this report
Surface digest99e99a9d9718f892e835e0af6ca7c6255a7dff298c90a51e6564a0007c34f1a9
Score vectorthreat 100 → client 96
| Term | Level | What it prices | Points |
|---|---|---|---|
| capability-exposure | minimal | capability blast radius (minimal) — client exposure if the model is manipulated | −0 |
| coverage-honesty | manifest | inspection depth (manifest) — how much of the target the scan could see | −4 |
score = clamp(round(threatScore − E_cap − E_ver − E_cov), 0, 100). No model, no opinion, no network call at scoring time: the same methodology version against the same bytes always produces this number, and every line above is a field of the report rather than a summary of it.
What the scan could actually read
A grade is only as meaningful as its coverage, so the scanner publishes its own depth before it publishes its result.
The scan read each tool’s name, description, input schema and annotations exactly as the server listed them the last time it answered us; no code was reviewed. We ask the server again about once a month, and a list that changed is graded again.
Tool surfaceread
Implementation sourcenot available
Package metadatanot available
Live transportnot available
The implementation source was not read — this reflects the declared tool metadata only.
Capability — what it could do if the model were manipulated
Tags derived from each tool’s schema and the implementation, not from what the tool calls itself. minimal is the level these add up to.
| Tool | Capability tags | Why the tag was assigned |
|---|---|---|
| get_term_info | untrusted-input | untrusted-input: keyword "fetch" |
| run_query | no tags | |
| search_terms | untrusted-input | untrusted-input: keyword "fetch" |
| list_search_facets | no tags | |
| resolve_entity | no tags | |
| resolve_combination | no tags | |
| list_connectome_datasets | no tags | |
| query_connectivity | no tags | |
| get_predicted_neurotransmitters | no tags | |
| get_known_neurotransmitters | no tags | |
| get_hierarchy | no tags |
Toxic-flow graph
The lethal trifecta, checked as a graph rather than as a checklist: untrusted input, a sensitive source and an external sink have to meet before there is a path worth worrying about.
The public result for this release does not print the flow graph, so there is nothing to show here. That is not the same as "no paths were found": what the scan did read is above, under coverage.
Supply chain and provenance
Integrityfirst-seen
Surface digest99e99a9d9718f892
Scanned2026-10-28
This is the first scan of this surface here, so there is nothing yet to compare it against.
Every result on this tab comes from one deterministic pass over the published package — offline, rule by rule, and auditable line by line above. Same methodology version, same bytes, same score.
Release history
This is an address its publisher runs: which release it serves is theirs to choose, so there is nothing here to pin. The history below is for reading; the current release on file is 1.11.3.
1.11.3
undated
latestNo release note was published with this version.
—
no reviews yet
Who can review
One review per account, from a signed-in account that does not publish this listing. Nothing else is asked — you can say what you think before you install it. Publishers can reply once per review, and a review can be edited or deleted by whoever wrote it.
Sign in to write one
Any signed-in account that does not publish VirtualFlyBrain can review it, once — before installing it or after. A review from an account that has installed it is marked as one.
No reviews yet
Nobody has reviewed this listing. The rating on the card is the mean of the reviews written here and nothing else, so there is no rating until somebody writes the first — which takes a signed-in account that does not publish it, and nothing else.