What is Biomarker Mcp

biomarker-mcp is a natural language interface designed for querying cell type markers from the CellMarker database using natural language processing.

Use cases

Use cases include conducting cell cluster analysis in scRNA-Seq studies and enhancing applications that require querying cell markers.

How to use

To use biomarker-mcp, install it via PyPI with ‘pip install biomarker-mcp’. You can run it locally or remotely by configuring your MCP client appropriately.

Key features

Key features include the ability to query cell type markers using natural language, integration with various AI clients and agent frameworks, and support for future database expansions.

Where to use

biomarker-mcp can be used in AI clients like Cherry Studio, plugins like Cline, and agent frameworks such as Agno that support MCP.

biomarker-MCP

Natural language interface for celltype marker query through MCP.

🪩 What can it do?

• query celltype marker from CellMarker database by natural language
• will add more database

❓ Who is this for?

• Anyone who wants to do query celltype marker with natural language!
• Agent developers who want to query cell markers for their applications

🌐 Where to use it?

You can use biomarker-mcp in most AI clients, plugins, or agent frameworks that support the MCP:

• AI clients, like Cherry Studio
• Plugins, like Cline
• Agent frameworks, like Agno

🎬 Demo

A demo showing query celltype markers in a AI client Cherry Studio using natural language based on biomarker-mcp

https://github.com/user-attachments/assets/71268f6f-c74d-4142-ad7a-893b411d748a

📚 Documentation

scmcphub’s complete documentation is available at https://docs.scmcphub.org

🏎️ Quickstart

Install

Install from PyPI

pip install biomarker-mcp

you can test it by running

biomarker-mcp run

run biomarker-mcp locally

Refer to the following configuration in your MCP client:

check path

$ which biomarker 
/home/test/bin/biomarker-mcp

"mcpServers": {
  "biomarker-mcp": {
    "command": "/home/test/bin/biomarker-mcp",
    "args": [
      "run"
    ]
  }
}

run biomarker-server remotely

Refer to the following configuration in your MCP client:

run it in your server

biomarker-mcp run --transport shttp --port 8000

Then configure your MCP client in local AI client, like this:

"mcpServers": {
  "biomarker-mcp": {
    "url": "http://localhost:8000/mcp"
  }
}

🤝 Contributing

If you have any questions, welcome to submit an issue, or contact me([email protected]). Contributions to the code are also welcome!

Citing

If you use biomarker-mcp in for your research, please consider citing following work:

Congxue Hu, Tengyue Li, Yingqi Xu, Xinxin Zhang, Feng Li, Jing Bai, Jing Chen, Wenqi Jiang, Kaiyue Yang, Qi Ou, Xia Li, Peng Wang, Yunpeng Zhang, CellMarker 2.0: an updated database of manually curated cell markers in human/mouse and web tools based on scRNA-seq data, Nucleic Acids Research, Volume 51, Issue D1, 6 January 2023, Pages D870–D876, https://doi.org/10.1093/nar/gkac947