MCAS.Opensource

Add a pharma drug, herb, supplement, or biologic to the OpenMCAS curated compound library. Use when the user wants to extend data/compounds/seeds.json with a new compound. Triggers when the user says "add a compound", "I want to add X to the library", "include curcumin", or similar.

Scaffold a new experiments/EXP-NNN-*.md from the standard template and prefill it with the user's hypothesis, method, inputs, parameters, environment, and reproduction steps. Triggers when the user says "new experiment", "create an experiment report", "document this run", "EXP-006", or similar.

Capture a new MCAS trigger pattern (food, smell, physical, chemical, stress, infection, toxin, hormonal, medication) and add it to data/triggers/MCAS_Triggers_v1.csv with pathway mapping and linked counter-compounds. Triggers when the user says "report a trigger", "add this trigger", "I noticed when I'm around X I flare", or similar.

Run the full OpenMCAS computational pipeline end-to-end (build library, generate analogs, score warheads, screen targets, QSAR, rank) and produce a clean diff for review. Triggers when the user says "run the pipeline", "regenerate the rankings", "rerun everything", or similar.