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Bio-Agents MCP Server

@dogeplusplus

代码仓库

基本信息

分类

其他

传输方式

stdio

作者

dogeplusplus

关于 Bio-Agents MCP Server

MCP servers for Protein Data Bank, ChemBL, and other life science data (WIP), with Ollama client for local testing.

#biology#protein-data-bank#agents#chembl-web-client#ollama#model-context-protocol#mcp-server

Bio-Agents MCP Server 配置

使用下面的配置,将此服务器添加到你的 MCP 客户端。

{
  "mcpServers": {
    "bio-agents-mcp": {
      "command": "docker",
      "args": [
        "build",
        "-t",
        "<module-name>",
        "."
      ]
    }
  }
}

Bio-Agents MCP Server 工具

工具列表暂未提供

当前收录暂时没有可展示的工具列表，不代表服务没有工具。请查阅项目文档了解支持的能力。

工具是从 README 中自动提取的。维护者可以在 ## Tools 标题下列出工具,即可填充这部分内容。

概览

What is Bio-Agents MCP?

Bio-Agents MCP is a collection of microservices and clients for natural language interaction with biological databases, including the Protein Data Bank (PDB) and ChEMBL chemical database, built using the FastMCP framework.

How to use Bio-Agents MCP?

Copy the example environment file, build Docker images with make build, start all services with make up, then launch the web interface with make run-chainlit and visit http://localhost:8000 to query biological data.

Key features of Bio-Agents MCP

  • LLM client with web UI (Chainlit) and terminal modes
  • PDB MCP Server for Protein Data Bank API
  • ChEMBL MCP Server for chemical database API
  • Docker Compose to run all services together
  • Makefile for common tasks (build, up, down, restart)
  • Each module can run independently or together

Use cases of Bio-Agents MCP

  • Query protein structures and annotations from PDB using natural language
  • Search chemical compounds and bioactivity data via ChEMBL
  • Combine biological and chemical data through an LLM interface

常见问题

1

What components does it include?

It includes an LLM Client (web UI and terminal), PDB MCP Server, and ChEMBL MCP Server.

2

How do I start the system?

Configure environment with `cp .env.example .env`, then run `make build` and `make up`, followed by `make run-chainlit`.

3

What transport does it use?

The architecture uses FastMCP framework; services communicate via Docker networking (implied by Docker Compose).

4

What are the runtime requirements?

Docker and Docker Compose are required to run all services together. Each service has its own Dockerfile.

5

Where are configuration files located?

Configuration files are in the `conf/` directory. Detailed documentation for each service is in its own README.

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