piaso-mcp

piaso-mcp

mcp-name: io.github.genecell/piaso-mcp

A local stdio MCP server for the PIASO single-cell omics ecosystem — PIASO, COSG / COSGR, cytome (Python + R), LARIS, Emergene, cytorete, PIASO-data. 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)	Data-object contract (reads/writes, defaults) for a function; points at the live generated API reference	bundled components/*.md
compare_implementations(function)	COSG (Python) vs COSGR (R); "cytome" for the Python vs R cytome packages	bundled
resolve_install(components, language)	Exact install line(s) per language, incl. extras and the R routes (r-universe, conda-forge); never a matplotlib pin	bundled meta.yaml
list_tutorials(topic, component)	The piaso.org tutorial index (executed tutorials): title, URL, what it covers	bundled meta.yaml
version_matrix()	Versions this snapshot was tested against, roles, citations	bundled meta.yaml
check_versions()	Current PyPI release of each package vs the tested version — disclose drift	PyPI JSON (network)
list_datasets() / get_dataset(name)	The PIASO-data registry (id, format, size, cells, counts layer, md5, how to load)	live datasets.json from GitHub, cached 24 h; offline fallback to bundled data.md
query_marker_db(...) / get_markers(...)	Cell-type marker lookup	live PIASOmarkerDB REST API at piaso.org
list_studies()	Studies in PIASOmarkerDB (36)	live API

The marker tools give R / non-Python users their first programmatic path to PIASOmarkerDB (the piaso.tl client is Python-only). The registry, version and marker tools need network access; everything else works offline.

Run

uvx piaso-mcp            # zero-install
# 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"; Codex: TOML [mcp_servers.piaso]
{ "mcpServers": { "piaso": { "command": "uvx", "args": ["piaso-mcp"] } } }

Per-client details (uv prerequisite, PATH, Codex TOML, Zed shape) are in the repository README.

Versions

piaso-mcp 0.1.0 — snapshot tested against piaso-tools 1.2.3 · cosg 1.2.0 · cytome 0.3.1 · laris 0.13.0 · emergene 1.0.2 · cytorete 0.1.1 · COSGR 1.0.0 · cytome (R) 0.1.0 (2026-09-04). 0.0.x served the July 2026 snapshot (five packages, scanpy-based workflows).

License

BSD-3-Clause.