Holy Bio MCP

Instead of just listing functions, here's a look at the kind of research questions you can answer with each server.

This repository provides unified configuration files that enable all the included servers at once. Here's how to get started:

For immediate use without cloning this repository, copy and paste this configuration directly into your MCP client:

{ "mcpServers": { "biothings-mcp": { "command": "uvx", "args": ](https://github.com/longevity-genie/holy-bio-mcp/blob/HEAD/biostratum-eliza)["--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"] } } }

This method uses the configuration files from this repository.
- Prerequisite: Make sure you haveuvinstalled. If not, it's a one-line command:

curl -LsSf https://astral.sh/uv/install.sh | sh

That's it!You do not need to run anyuvxcommands manually. Your MCP client will automatically useuvxto launch the necessary servers in the background when a tool is called and manage them for you.

For a visual guide on setting up clients like Cursor with these configuration files, watch our[Configuration Tutorial Video.

- Interactive Research (Chat-based): Use with AI assistants like Claude for exploratory research.
- AI-Enhanced Development (IDE Integration): Integrate with Cursor or Windsurf to access biomedical data and generate analysis scripts while coding.
- Agentic Workflows (Automated Research): Build autonomous research agents using frameworks like AutoGen or -ElizaOS with our biostratum pluginfor seamless multi-server integration.

This framework unites the following specialized MCP servers and integration tools. Each is a powerful tool on its own, but together they form a comprehensive research platform.

- ](https://www.youtube.com/watch?v=HBwJQybjOa8)gget-mcp: A powerful bioinformatics toolkit for genomics queries and analysis, wrapping the popularggetlibrary.
- opengenes-mcp: A queryable database for aging and longevity research from the OpenGenes project.
- synergy-age-mcp: A database of synergistic and antagonistic genetic interactions in longevity from SynergyAge.
- biothings-mcp: Access to BioThings.io APIs for comprehensive gene, variant, chemical, and taxonomic data.
- pharmacology-mcp: Access to the Guide to PHARMACOLOGY database for drug, target, and ligand information.

- futurehouse-mcpto use future-house prediction models
- addgene-mcpto search plasmids (note: alpha stage)
- boltz-mcpto run Boltz structure predictions (note: alpha stage)
- benchling-mcpto interact with Bencling API (note: alpha stage)
- and some others

- [biostratum-eliza: An ElizaOS plugin that enables autonomous AI agents to seamlessly connect to and utilize all the MCP servers below, providing a unified interface for building complex agentic workflows in bioinformatics research.

Provides a rich set of tools for sequence analysis, functional genomics, and structural biology.

- "Find information about the humanTP53gene and get its protein sequence."
- "Perform enrichment analysis for a set of cancer-related genes:TP53, BRCA1, BRCA2, ATM, CHEK2."
- "Get the 3D structure information for the protein encoded by theEGFRgene from AlphaFold."
- "Find mutations in the COSMIC database for thePIK3CAgene."
- "Perform a BLAST search with the DNA sequence 'ATGGCGCCCGAACAGGGAC' to identify its origin."
- "Align multiple protein sequences to find conserved regions."