mcpmed-bioinformatics-server
Model Context Protocol (MCP) server for bioinformatics web services like GEO, STRING, and UCSC Cell Browser.
Best use case
mcpmed-bioinformatics-server is best used when you need a repeatable AI agent workflow instead of a one-off prompt.
Model Context Protocol (MCP) server for bioinformatics web services like GEO, STRING, and UCSC Cell Browser.
Teams using mcpmed-bioinformatics-server should expect a more consistent output, faster repeated execution, less prompt rewriting.
When to use this skill
- You want a reusable workflow that can be run more than once with consistent structure.
When not to use this skill
- You only need a quick one-off answer and do not need a reusable workflow.
- You cannot install or maintain the underlying files, dependencies, or repository context.
Installation
Claude Code / Cursor / Codex
Manual Installation
- Download SKILL.md from GitHub
- Place it in
.claude/skills/mcpmed-bioinformatics-server/SKILL.mdinside your project - Restart your AI agent — it will auto-discover the skill
How mcpmed-bioinformatics-server Compares
| Feature / Agent | mcpmed-bioinformatics-server | Standard Approach |
|---|---|---|
| Platform Support | Not specified | Limited / Varies |
| Context Awareness | High | Baseline |
| Installation Complexity | Unknown | N/A |
Frequently Asked Questions
What does this skill do?
Model Context Protocol (MCP) server for bioinformatics web services like GEO, STRING, and UCSC Cell Browser.
Where can I find the source code?
You can find the source code on GitHub using the link provided at the top of the page.
SKILL.md Source
# 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 ```
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