Build Module YAML from Research

When to Use

Use this skill after completing research on a mechanism to create the module YAML specification.

Workflow

1. •

   Read research notes — Load models/<disease>/research/<mechanism_name>.md

2. •

   Define compartments — List all compartments involved (e.g., BrainISF, CSF, Plasma)

   • •Use Elbert naming conventions
   • •Include volume parameters (V_<compartment>)
3. •

   Define species — List all molecular species with compartment suffixes

   • •Follow naming convention: {base}_{compartment} (e.g., AB42_BrainISF)
   • •Set initial amounts where known
4. •

   Define reactions — Create reaction specifications

   • •Choose appropriate rate type: MA, RMA, BDF, UDF, custom_conc_per_time, custom_amt_per_time, custom
   • •List reactants and products using full species names
   • •Specify rate parameters or custom rate equations
5. •

   Define parameters — List all rate constants and other parameters

   • •Set values where known (null if not yet determined)
   • •Set confidence levels: measured, estimated, assumed
   • •Include source citations
6. •

   Validate — Check the module YAML against the schema

   bash

   just validate-module models/<disease>/modules/<mechanism>.yaml
   

Rate Type Guide

• •MA: Simple mass action, k * [reactants] * V_compartment — use for simple degradation, production
• •RMA: Reversible mass action — use for binding/unbinding equilibria
• •BDF: Bidirectional flow — use for transport between compartments (same rate both ways)
• •UDF: Unidirectional flow — use for one-way transport, no volume multiplication
• •custom_conc_per_time: Custom rate in concentration/time — use for Michaelis-Menten, Hill equations
• •custom_amt_per_time: Custom rate in amount/time — use when rate is already in absolute units
• •custom: Custom expression used as-is — use for complex rate laws

Output

A module YAML file in models/<disease>/modules/<mechanism_name>.yaml.