Mirobody
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Runs on your computer✓ thetahealth.ai
Noodle Biomedical Literature Discovery MCP
Overview
Description from the maker (original English)
Search biomedical papers, inspect publication records, and traverse citation or semantic graphs.
PopNx MCP’s three pillars
These three are never merged into one score: opinions, measurements and popularity are different things.
- User voiceiNo reviews yetReviews open together with accounts in a later step
- Our basic checksi1 of 1 passedChecked from public information; code not scanned yet
- UsageiVery new★ –
What you can do with it
We have not written a plain-language summary for this one yet. Below are the facts we read from the registry.
- Connection: Runs in the cloud
- Transport: Streamable HTTP
- Category: Clinics & health
Install
Pick the AI app you use, then copy the settings.
Before you install
- Basic checks: 1 of 1 passed
- Runs on the maker’s server: what you ask it goes through their server.
- The registry lists no key to fill in.
You need
- Runs in the cloudNothing to install; it connects over the internet
Which app do you use?
Pick your app above. We remember it, so next time the button says “Install in …”.
Works in Claude on the web, desktop and mobile:
- Open Settings → Connectors
- Press Add custom connector
- Paste the address below and press Add
- If it asks you to sign in, sign in with the maker
https://api.helena.bio/noodle/v1/mcpRun this in your terminal
claude mcp add --transport http noodle https://api.helena.bio/noodle/v1/mcpOr copy the settings yourself
Paste into .cursor/mcp.json in your project, or ~/.cursor/mcp.json
{
"mcpServers": {
"noodle": {
"url": "https://api.helena.bio/noodle/v1/mcp"
}
}
}Your browser asks to open the app, then the app shows the settings and asks you to confirm. Key values are left empty for you to fill in.
Or copy the settings yourself
Paste into .vscode/mcp.json in your project
{
"servers": {
"noodle": {
"type": "http",
"url": "https://api.helena.bio/noodle/v1/mcp"
}
}
}Your browser asks to open the app, then the app shows the settings and asks you to confirm. Key values are left empty for you to fill in.
ChatGPT connects only to servers on the internet:
- Open ChatGPT on the web → Settings → Connectors (Apps)
- Press Create or Add (some plans need Developer mode under Advanced first)
- Paste the address below, give it a name and save
- If it asks you to sign in, sign in with the maker
https://api.helena.bio/noodle/v1/mcpMenu names can differ slightly by plan and over time.
Your choice stays on this device in a cookie; no account needed.
These settings are generated from the maker’s registry entry. If the README says otherwise, follow the README.
What it can do
We have not read this server’s tool list yet; we check endpoints in rotation.
Basic checksi
We check information anyone can see; we have not read the code. Checks that do not apply are left out of the count. · Checked Nov 8, 2026
- ✓ Pass
Maker matches the repo
The registry name was verified with the GitHub account helena-bioinformatics, which owns the repo
- … Not checked yet
Still maintained
We have not read this repo from GitHub yet
- … Not checked yet
Has a licence
We have not read this repo from GitHub yet
- … Not checked yet
Endpoint responds
Not checked yet; we check endpoints in rotation
- … Not checked yet
Sign-in with OAuth
Not checked yet; we check endpoints in rotation
- … Not checked yet
No hidden instructions in tool descriptions
Not checked yet; we read the tool list when we check the endpoint
Compared with others in Clinics & healthi
- More stars than 0% of the other 1028 servers in this category
- Published to the registry more recently than 34% of the other 1028 servers in this category
- Basic checks equal to or better than 100% of the other 1028 servers in this category
Compared with every active server in this category in the registry. Stars count only when the publisher owns the repo.
Common questions
Is Noodle Biomedical Literature Discovery MCP safe?
It passed 1 of 1 applicable basic checks. We have not read the code. Before adding a key or token, see what access the server asks for and use a key with only the permissions you need.
What keys or codes does it need?
The registry does not list a required key, though some servers ask you to sign in on first use.
Does it run on my computer or in the cloud?
It runs in the maker’s cloud. Connect over the internet with nothing to install, but what you send passes through the maker’s servers.
Is it still maintained?
The GitHub repo last changed –, and the latest version (0.2.1) reached the registry 2 months ago.
Which apps can use it?
Apps that support MCP, such as Claude Desktop, Claude Code, Cursor and VS Code. It connects by URL, so apps that accept remote MCP servers work too, such as ChatGPT in developer mode.
What can I use instead?
In the same category: Mirobody, FHIR MCP Server, Google Health MCP
Alternatives
Servers in the same category from other makers, sorted by stars.
Reading a card:↓ Downloads per weeki★ GitHub starsiThree pillars: reviews · checks · usageiUpdated = latest version published to the registryi
FHIR MCP Server
MCP server providing seamless access to FHIR APIs for AI tools and healthcare applications
Runs on your computer
Google Health MCP
Privacy-first unofficial Google Health API v4 MCP server for health, sleep, activity, HR agents
Runs on your computer
README from the maker
Open the README
Copied from the maker’s repo as written. PopNx MCP has not reviewed or endorsed it. HTML, images and scripts are removed. Links lead off this site.
Noodle Biomedical Literature Discovery MCP
The official public, read-only Model Context Protocol adapter for biomedical literature discovery from Helena Bioinformatics. Agents can select it from a user task even when the user does not know the Noodle brand.
Public endpoint: https://api.helena.bio/noodle/v1/mcp
Official Registry identity: io.github.helena-bioinformatics/noodle
No account, API key, patient data, or private content is required or accepted.
What agents can do
- search a public PubMed-derived biomedical corpus by natural language, PMID, DOI, or PMCID;
- retrieve source-linked publication records by PMID or Noodle work ID;
- traverse bounded citation and semantic neighborhoods from a publication;
- continue graph exploration through returned work identifiers while preserving edge types and graph provenance;
- inspect corpus size, sources, freshness, coverage, and active graph metadata.
The seven published tools are search_biomedical_literature, get_publication_details, get_work_details, get_publication_neighborhood, get_work_neighborhood, get_corpus_summary, and the separate explicit opt-in support_helena information action.
Connect
Any MCP client that supports remote Streamable HTTP can use the endpoint. Exact recipes for ChatGPT, Claude, Codex, VS Code, Cursor, Windsurf, Gemini CLI, Grok, Perplexity, Microsoft Copilot Studio, Biomni, and Biorouter live under registry/platforms and integrations.
Ready-to-use ecosystem packages are included for:
- Dify, including a reproducible
.difypkg; - n8n, using the exact stateless MCP JSON-RPC contract supported by the hosted service;
- Galaxy, with a Planemo-linted ToolShed wrapper; and
- KNIME Analytics Platform, with a table-to-MCP Python Script node and prepared Hub listing; and
- Google Colab and Kaggle notebooks, plus a Cytoscape GraphML workflow; and
- the companion Galaxy Training Network tutorial for a Folklore-to-Noodle literature workflow.
The companion Agent Skill is in skills/noodle-biomedical-literature-discovery. It enables implicit, task-first selection for requests such as:
- “Find source-linked papers about BRCA1 homologous recombination.”
- “What publication is PMID 35008774?”
- “Show papers related to this article through citations and semantic similarity.”
- “Walk two bounded hops from this work ID and preserve the edge types.”
Build the deterministic skill archive with:
python3 ops/package_agent_skill.pyGraph boundary
Start from a resolved PMID or work ID and request one bounded neighborhood at a time. Report edges exactly as returned, keep a visited-ID set, and stop at a missing neighborhood. Search rank, citation proximity, semantic similarity, co-mention, and graph distance are discovery signals. They do not establish causality, scientific validity, diagnosis, or treatment.
Development
Python 3.12 is required.
python -m venv .venv. .venv/bin/activate python -m pip install -r requirements-dev.lock python -m pip install --no-deps -e . pytest ruff check . ruff format --check .
Run the brand-blind contract audit with:
python benchmarks/agent-discovery/audit_skill.pyThe benchmark contains 60 prompts that omit Noodle, Helena, and MCP. It covers all six scientific routes plus negative and safety controls.
Agent Plugin and Kiro Power
This repository is also a portable Agent Plugin and Kiro Power. plugin.json provides brand-blind activation keywords, the existing Agent Skill supplies the scientific routing and safety boundary, and mcp.json connects directly to the canonical hosted Streamable HTTP endpoint. The Power does not proxy, repackage, or reimplement Noodle.
Privacy policy: https://noodle.helena.bio/privacy
Cite Noodle
The persistent Research Resource Identifier is RRID:SCR_028920. Cite the resource in a methods section as Noodle (RRID:SCR_028920). Use the version DOI when a version-specific software citation is also needed. The RRID identifies the resource across publications, while the DOI identifies the archived 0.2.0 release.
Support: https://noodle.helena.bio/contact or contact@helena.bio
Public resources
- Hands-on tutorial: https://github.com/helena-bioinformatics/noodle-mcp/blob/main/docs/tutorials/biomedical-literature-discovery-and-graph-traversal.md
- Connector and agent-selection guide: https://noodle.helena.bio/mcp
- Client integrations: https://noodle.helena.bio/integrations
- Server Card: https://noodle.helena.bio/.well-known/mcp/server-card.json
- Official Registry: https://registry.modelcontextprotocol.io/v0/servers?search=io.github.helena-bioinformatics%2Fnoodle
- Citable release: https://doi.org/10.5281/zenodo.22166486
- Software Heritage archive request: https://archive.softwareheritage.org/api/1/origin/save/2457442/
- Software Heritage snapshot: https://archive.softwareheritage.org/swh:1:snp:09b8fb7c64de15487e873b4f77e3e4b57abc02fb/
- Methodology: https://noodle.helena.bio/methodology
License and security
Apache License 2.0. Report vulnerabilities privately as described in SECURITY.md. Do not submit patient, private case, clinical-record, credential, or private uploaded content to the public service or issue tracker.