MCP server

Allen Brain

io.github.pipeworx-io/allen-brain

Checked 26 Oct 2026, 08:29 UTC · Connected to it and listed its tools

Gene expression experiments and the brain structure ontology from the Allen Institute's Brain…

Working at last checkOfficial: pipeworx.io's GitHub account (pipeworx-io)About 27,485 tokens per request once connected45 tools

https://gateway.pipeworx.io/allen-brain/mcp

At a glance

Type: MCP server
Publisher: pipeworx.io (verified by the MCP Registry)
Status: Working at last check
Tools: 45
Token cost: About 27,485 tokens per request
Sets up in: Claude Code, Claude Desktop, Codex, Gemini CLI, Cursor, VS Code, Antigravity, ChatGPT, OpenAI API, Grok
Last checked: 26 Oct 2026, 08:29 UTC

Opens the app, which shows the server and asks you to confirm. For other apps, copy the setup below.

Claude Code

claude mcp add --transport http allen-brain https://gateway.pipeworx.io/allen-brain/mcp

Claude Desktop

Settings → Connectors → Add custom connector, and paste the URL.

Codex (config.toml)

[mcp_servers.allen-brain]
url = "https://gateway.pipeworx.io/allen-brain/mcp"

Gemini CLI

{"mcpServers":{"allen-brain":{"httpUrl":"https://gateway.pipeworx.io/allen-brain/mcp"}}}

Cursor

{"mcpServers":{"allen-brain":{"url":"https://gateway.pipeworx.io/allen-brain/mcp"}}}

VS Code

{"servers":{"allen-brain":{"type":"http","url":"https://gateway.pipeworx.io/allen-brain/mcp"}}}

Antigravity

agy mcp add allen-brain https://gateway.pipeworx.io/allen-brain/mcp

ChatGPT

Settings → Apps & Connectors → Advanced settings: turn on Developer mode, then Create a connector and paste the URL. Which plans can do this varies.

OpenAI API (Responses tools)

{"type":"mcp","server_label":"allen-brain","server_url":"https://gateway.pipeworx.io/allen-brain/mcp","require_approval":"always"}

Grok (xAI API tools)

{"type":"mcp","server_label":"allen-brain","server_url":"https://gateway.pipeworx.io/allen-brain/mcp"}

allen_expression_datasets ~441 tokens
List the Allen Brain Atlas in-situ hybridization expression experiments (SectionDataSets) for a gene — which atlas product they belong to (Mouse Brain, Developing Mouse, Human Brain, Mouse Spinal Cord), plane of section (coronal/sagittal), section thickness, and the dataset id used to fetch images a
allen_search_genes ~379 tokens
Look up genes in the Allen Brain Atlas gene catalog by symbol/acronym, name substring, or Entrez ID. AUTHORITATIVE for resolving a gene to the Allen internal gene id and organism that the atlas expression data is keyed on — note the atlas holds mouse and human as SEPARATE gene records with the same-
allen_structures ~362 tokens
Query the Allen Brain Atlas structure ontology — the canonical hierarchy of named brain regions (Field CA1, Primary visual area, Substantia nigra) with their acronyms, colors, parent structure, and full root-to-leaf structure_id_path. AUTHORITATIVE for resolving a brain-region name or acronym to the

Expression Atlas
EBI Expression Atlas MCP.
Health Data
Health data: NIH grants, WHO statistics, and genetic variants
Gtex
GTEx MCP.
Herb Tcm
HERB 2.0 (herb.ac.cn) — Traditional Chinese Medicine herb/ingredient/target/
Ncbi Eutils
NCBI E-utilities MCP — federated Entrez search/fetch.
Genomic Intelligence
Hosted DNA language models: promoter, splice, enhancer, chromatin, expression, annotation
The Cure Protocol
Agent research API for 15 disease areas, plus a T1D cure lab, sourced evidence ledger and models.
Quickgo
QuickGO (EBI) MCP — Gene Ontology browser.

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