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Holy Bio MCP - Bringing together all your favorite agentic biotools under the same framework
개요
Holy Bio MCP is a unified framework born during Bio x AI Hackathon-2025 from our practical experience building LLM-powered agents at the , , and the . Our goal is to make life easier for researchers by providing a suite of specialized, interoperable tools that seamlessly integrate into AI-driven IDEs (like Cursor, Windsurf), chat clients (like Anthropic's Claude Desktop), and serve as foundational building blocks for complex agentic workflows (using ElizaOS, Just-Agents, AutoGen, etc.). This project aggregates several powerful, standalone MCP servers into a single, cohesive ecosystem for advanced bioinformatics and longevity research, for building autonomous research agents. MCP is a protocol designed to bridge the gap between Large Language Models (LLMs) and specialized, domain-specific tools and databases. It provides a standardized way for AI assistants and agents to access complex functionalities through structured, type-safe interfaces.
README
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Holy Bio MCP: A Unified MCP Framework for Bioinformatics Research
Developed during Bio x AI Hackathon 2025
🎯 Our Mission
Holy Bio MCP is a unified framework born during Bio x AI Hackathon-2025 from our practical experience building LLM-powered agents at the Longevity Genie project, IBIMA (Institute for Biostatistics and Informatics in Medicine and Ageing Research), and the Systems Biology of Aging Group. Our goal is to make life easier for researchers by providing a suite of specialized, interoperable tools that seamlessly integrate into AI-driven IDEs (like Cursor, Windsurf), chat clients (like Anthropic’s Claude Desktop), and serve as foundational building blocks for complex agentic workflows (using ElizaOS, Just-Agents, AutoGen, etc.).
This project aggregates several powerful, standalone MCP servers into a single, cohesive ecosystem for advanced bioinformatics and longevity research, including a native ElizaOS plugin for building autonomous research agents.
What is the Model Context Protocol (MCP)?
MCP is a protocol designed to bridge the gap between Large Language Models (LLMs) and specialized, domain-specific tools and databases. It provides a standardized way for AI assistants and agents to access complex functionalities through structured, type-safe interfaces.
If you want to understand MCP in more detail and learn how to use it effectively, we recommend these resources:
- DeepLearning.AI Course: MCP: Build Rich-Context AI Apps
- Official Documentation: Model Context Protocol Website
- Community: Search for “Model Context Protocol” on YouTube and other platforms for tutorials and discussions.
🔬 Real-World Example in Action
Here’s a real conversation (that you can easily reproduce yourself as all MCP-es are working and covered with tests) showing Holy Bio MCP servers working together to answer complex research questions, demonstrating the power of this integrated approach:
🎬 Video Demo
Here is a video demo of Holy-Bio-MCP, this time including synergistic genetic interventions and small molecules:
설치
uvx --from biothings-mcp stdio설정
{
"mcpServers": {
"biothings-mcp": {
"command": "uvx",
"args": ["--from", "biothings-mcp", "stdio"]
},
"gget-mcp": {
"command": "uvx",
"args": ["gget-mcp", "stdio"]
},
"synergy-age-mcp": {
"command": "uvx",
"args": ["synergy-age-mcp"],
"env": {
"MCP_TRANSPORT": "stdio"
}
},
"opengenes-mcp": {
"command": "uvx",
"args": ["opengenes-mcp"],
"env": {
"MCP_TRANSPORT": "stdio"
}
},
"pharmacology-mcp": {
"command": "uvx",
"args": ["--from", "pharmacology-mcp", "stdio"]
}
}
}