# Mcpmed Bioinformatics Server

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

- Skill: `gabrielmoreira/mcpmed-bioinformatics-server` (Agent Skill)
- Install (CLI): `npx skillmds@latest add gabrielmoreira/mcpmed-bioinformatics-server`
- Raw SKILL.md: https://api.skillmd.com/api/skills/gabrielmoreira/mcpmed-bioinformatics-server/raw
- Safety review: pending (external: skill-scanner PASS, skillspector PASS)
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: AI & ML
- License: MIT
- Author: gabrielmoreira (https://skillmd.com/u/gabrielmoreira)
- Updated: 2026-09-09
- Page: https://skillmd.com/skills/gabrielmoreira/mcpmed-bioinformatics-server

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# 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**:
```bash
python3 -m mcpmed.cli query string --gene TP53
```