jpx

First-run setup for jpx. Installs prerequisites, downloads data, and launches a notebook. Use when someone says "help me get started", "set up this repo", "how do I run this", or opens the repo for the first time.

Add a new annotation source to the JUMP pipeline. Use when integrating external databases like ToxCast, BindingDB, or other compound annotation sources. Guides through notebook creation, workflow.py task wiring, and SQL schema.

Compose a new marimo notebook in jpx by reusing @app.function helpers from the existing catalog (notebooks/nb00_*.py onward) to answer a JUMP Cell Painting question - e.g. "compare these distance metrics", "show consistency for these targets", "plot activity across datasets", "visualize UMAPs colored by X". Trigger whenever the user asks for a notebook, analysis, figure, or vignette that touches JUMP profiles, copairs results, mAP values, target consistency, compound metadata, or morphological activity - even if they don't say "marimo". Use this instead of writing standalone scripts. Also trigger when the user says "write me a notebook that..." or asks to build on existing catalog notebooks.

Work with copairs and copairs-runner for phenotypic profiling analysis. Use when discussing mAP metrics, activity/consistency analysis, configuring copairs-runner YAML configs, reviewing copairs results, or strategizing Cell Painting data analysis.