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Mcpmed bioinformatics server

Skill BioTender-max/awesome-bio-agent-skills/skills/openclaw/mcpmed-bioinformatics-server

A curated collection of AI agent skills for biomedical research, covering genomics, proteomics, single-cell analysis, clinical AI, and protein design.

Install
npx -y skills add BioTender-max/awesome-bio-agent-skills --skill mcpmed-bioinformatics-server

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

One thing to look at

  • no licenseNo license file was found in the repository. Code published without one is not open source by default, so using it at work is a question for whoever answers licensing questions where you are.

What its author says it does

Copied from the file, not written here

Model Context Protocol (MCP) server for bioinformatics web services like GEO, STRING, and UCSC Cell Browser.

The file declares its own license as MIT. That is the author’s claim about this one file, and it is not the same thing as the license GitHub reports for the repository, which is listed with the other numbers below.

SKILL.md

1.4 KB, 250 tokens by cl100k_base, as published. Nobody here has run it

MCPmed Bioinformatics Web Services

Adapts the Model Context Protocol (MCP) to bioinformatics web server backends. This creates a standardized, machine-actionable layer for LLMs to interact with external biological resources, matching the 2026 standard for agentic tools.

When to Use This Skill

  • "Query STRING database for protein-protein interactions via MCP"
  • "Fetch dataset metadata from GEO using MCPmed"
  • "Access UCSC Cell Browser data through MCP"

Core Capabilities

  1. GEO Integration: Search and retrieve Gene Expression Omnibus metadata autonomously.
  2. STRING DB Access: Query protein-protein interaction networks contextually.
  3. UCSC Cell Browser: Programmatic access to single-cell datasets.

Workflow

  1. Step 1: Start the MCPmed server to expose the bioinformatics backend tools.
  2. Step 2: Connect the LLM client using MCP to query the integrated databases.

Example Usage

User: "Query the STRING database for interactions with TP53."

Agent Action:

python3 -m mcpmed.cli query string --gene TP53

Gives 0 of the 12 instructions most mcp tooling skills give in 250 tokens

Counted across 638 of the 750 authors here whose files we hold, read 2026-08-06

  • create ten complex read-only evaluation questionsin 71 of 638, across 17 files
  • test servers using MCP Inspectorin 60 of 638, across 18 files
  • provide actionable error messagesin 56 of 638, across 14 files
  • prioritize comprehensive API coverage over specific workflowsin 54 of 638, across 12 files
  • use TypeScript and Streamable HTTP for remote serversin 53 of 638, across 7 files
  • define structured output schemas where possiblein 51 of 638, across 9 files
  • use Zod or Pydantic for input schemasin 48 of 638, across 6 files
  • fetch MCP specification pages with markdown suffixin 46 of 638, across 4 files
  • load framework documentation using WebFetchin 45 of 638, across 3 files
  • verify each evaluation answer independentlyin 45 of 638, across 3 files
  • implement API client with authentication and paginationin 45 of 638, across 3 files
  • Define input schemas with validationin 28 of 638, across 10 files

Grouped from the skills themselves: near-identical wordings counted once, and counted by distinct author, so one author publishing three of these counts once. Length counted with cl100k_base; the agent that loads this file may tokenize it differently.

Keep looking

Skills are one crate of 328,083. Ordering is by how many stacks a row turns up in, so the top of any crate is what has actually been picked rather than what has the most stars.