Mcpmed bioinformatics server
Skill bg-szy/TOP-SKILLS/skills/awesome-skills/mcpmed-bioinformatics-server
Model Context Protocol (MCP) server for bioinformatics web services like GEO, STRING, and UCSC Cell Browser.From its SKILL.md
npx -y skills add bg-szy/TOP-SKILLS --skill mcpmed-bioinformatics-serverAssembled from the repository path, not quoted from the project. Check it against their README if it does not work.
2 things 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.
- 5 stars5 stars. Stars are a popularity signal and not a quality one, but at this level it is likely that nobody has read this closely except its author, and you would be relying on your own review.
What its file declares
Copied from the file, not written here
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
- GEO Integration: Search and retrieve Gene Expression Omnibus metadata autonomously.
- STRING DB Access: Query protein-protein interaction networks contextually.
- UCSC Cell Browser: Programmatic access to single-cell datasets.
Workflow
- Step 1: Start the MCPmed server to expose the bioinformatics backend tools.
- 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
What ships with it
Read from the repository
Just SKILL.md. No reference files, no scripts.