Retrieve BioModels Reference Models

When to Use

Use this skill to search BioModels for published ODE models relevant to a disease mechanism, download them, and convert to Antimony format for reference.

Workflow

1. •

   Search BioModels

   bash

   uv run antimony-bootstrap search-biomodels "<query>"
   

   Try multiple queries: disease name, mechanism name, key proteins.

2. •

   Review results — Identify models that:

   • •Cover the mechanism of interest
   • •Have realistic parameter values
   • •Are well-cited
3. •

   Download and convert — For each useful model:

   python

   from antimony_bootstrap.retrieval.biomodels import fetch_and_convert
   ant_string = fetch_and_convert("BIOMD0000000123", output_dir="reference_models/")
   

4. •

   Extract useful information:

   • •Parameter values and units
   • •Species names and initial conditions
   • •Rate laws and kinetic expressions
   • •Compartment volumes
5. •

   Record attribution — Note the BioModels ID, original publication, and which parameters were borrowed.

Output

• •Antimony files in reference_models/ directory
• •Notes on which parameters/rate laws to use in the module