piaso-mcp 0.0.1

Local stdio MCP server for the PIASO single-cell omics ecosystem — serves knowledge and public data (PIASOmarkerDB via the live piaso.org API), never compute or user data.

piaso-mcp

A local stdio MCP server for the PIASO ecosystem. Serves knowledge and public data only — never compute, never user data, never your expression matrices.

Generated artifact. The doc tools read a snapshot of canonical/ that build.py writes into piaso_mcp/data/. Do not hand-edit that snapshot — edit canonical/ and re-run build.py.

Tools

Tool	What it does	Source
search_docs(query)	Search the ecosystem knowledge pack — works with zero packages installed	bundled canonical/
get_api(function)	Exact current signature + data-object contract	bundled api-map.md
compare_implementations(function)	COSG (Python) vs COSGR (R) divergences	bundled components/cosg.md
resolve_install(components, language)	The exact install line for a chain, per language	bundled meta.yaml
list_datasets()	PIASO-data fixtures (URLs + loading code)	bundled data.md
query_marker_db(...) / get_markers(...)	Cell-type marker lookup	proxies the live PIASOmarkerDB REST API at piaso.org
list_studies()	Studies in PIASOmarkerDB	proxies the live API

The marker tools give R / non-Python users their first programmatic path to PIASOmarkerDB (the piaso.tools query API is Python-only). They require network access to piaso.org; everything else works offline.

Run

uvx piaso-mcp            # zero-install, once published
# or from source:
pip install -e mcp/ && piaso-mcp
python -m piaso_mcp      # equivalent

Configure your agent

// Claude Code / Cursor / Windsurf: "mcpServers"; VS Code: "servers"; Zed: "context_servers"
{ "mcpServers": { "piaso": { "command": "uvx", "args": ["piaso-mcp"] } } }

License

BSD-3-Clause.