Parameterize Module

When to Use

Use this skill to fill in missing parameter values for a module, drawing from Elbert reference model, BioModels, and literature.

Workflow

1. •

   Identify missing parameters — Check module YAML for null-valued parameters

   bash

   just validate-params <disease>
   

2. •

   Search Elbert model — Primary source for parameter values

   • •Check ../Elbert_Esguerra_model_v2026b/ for matching parameters
   • •Match by reaction name and species names
3. •

   Search BioModels — Secondary source

   • •Download reference models and extract parameter values
   • •Convert units if needed
4. •

   Literature search — Tertiary source

   • •Search PubMed for kinetic parameters
   • •Record PMIDs for all values
5. •

   Assign values — Update module YAML with:

   • •value: the numeric value
   • •units: parameter units
   • •confidence: measured / estimated / assumed
   • •source: where the value came from
   • •evidence: PMIDs supporting the value
6. •

   Validate — Check completeness

   bash

   just validate-params <disease>
   

Confidence Levels

• •measured: Value directly measured in relevant biological system
• •estimated: Value estimated from related data or fitted from model
• •assumed: Placeholder value, needs verification

Output

Updated module YAML with all parameter values filled in and cited.