By name: bio-mcpmed-bioinformatics-server description: Model Context Protocol (MCP) server for bioinformatics web services like GEO, STRING, and UCSC Cell Browser. tool_type: mixed primary_tool: Unknown measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools:
- read_file
- run_shell_command
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