Natural language interface for celltype marker query through MCP.
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# 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 …
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