Research a Disease Mechanism

When to Use

Use this skill when you need to research a specific disease mechanism to gather quantitative data for building an Antimony module.

Workflow

1. •

   Read dismech YAML — Extract the mechanism description, cell types, downstream links, and evidence PMIDs

   bash

   uv run antimony-bootstrap read-dismech <dismech_yaml_path>
   

2. •

   Check Elbert reference model — Look for existing reactions, species, and parameters in ../Elbert_Esguerra_model_v2026b/

   • •Check module files in modules/ for relevant reaction creation code
   • •Check generated/ for reaction dictionaries with parameter values
   • •Note compartment names, species naming conventions, rate types
3. •

   Search BioModels — Find published ODE models for this mechanism

   bash

   uv run antimony-bootstrap search-biomodels "<mechanism name>"
   

4. •

   Literature search — Search PubMed for quantitative kinetic data

   • •Focus on rate constants, half-lives, concentrations, volumes
   • •Record PMIDs for all data sources
5. •

   Write research notes — Save to models/<disease>/research/<mechanism_name>.md

   • •Include: quantitative values found, species list, compartment list
   • •Include: rate constants with units, initial concentrations
   • •Include: all PMIDs and source attributions

Output

A research notes file in models/<disease>/research/ that provides all the information needed for the build-module skill.