Monocle3 Remote Tool (MCP Server)

Serves Monocle3 (Cao et al., Nature 2019; Trapnell lab) — single-cell pseudotime / trajectory inference — as the ToolUniverse remote tool run_monocle3_pseudotime.

Monocle3 learns a principal graph through a UMAP embedding (capturing branches and loops) and orders cells in pseudotime from a chosen root. Unlike Slingshot (which orders pre-computed clusters), Monocle3 learns its own graph, and is the standard Trapnell-lab pseudotime tool.

Served remotely because the engine is R/Bioconductor (monocle3). The Python side reads the .h5ad with scanpy and hands the raw count matrix to the bundled monocle3_pseudotime.R (MatrixMarket interchange — no zellkonverter/basilisk). The R script runs the standard new_cell_data_set → preprocess_cds → reduce_dimension → cluster_cells → learn_graph → order_cells pipeline.

Root the trajectory with root_cluster (all cells of a named input cluster — requires cluster_key) or explicit root_cells.

Deploy

pip install -r requirements.txt            # scanpy + scipy (Python side)
# R side — monocle3 needs Bioconductor deps + system libs (gdal/geos/proj via terra):
Rscript -e 'BiocManager::install(c("SingleCellExperiment","batchelor","terra","ggrastr","leidenbase"))'
Rscript -e 'remotes::install_github("cole-trapnell-lab/monocle3")'
python monocle3_tool.py                      # starts the MCP server on 127.0.0.1:8031

Rscript must be on PATH (or set RSCRIPT_BIN). Expose remotely only behind TOOLUNIVERSE_API_TOKEN (SMCP bind guard).

Register in ToolUniverse

Tool definition: src/tooluniverse/data/remote_tools/monocle3_tools.json (type: RemoteTool).