gsmm-validator

Overview

The gsmm-validator skill performs rigorous quality control on a COBRApy Model before it enters any flux analysis pipeline. An invalid model silently produces biologically meaningless fluxes; validation catches structural errors early.

Validation covers six categories: (1) mass/charge balance, (2) feasibility and biomass production, (3) dead-end metabolites, (4) stoichiometric consistency, (5) thermodynamic loop detection, and (6) GPR rule integrity.

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Workflow

Step 1 — Load the Model

import cobra
import cobra.io

model = cobra.io.load_json_model("my_model.json")
print(f"Loaded: {model.id} ({len(model.reactions)} reactions)")

Step 2 — Mass and Charge Balance Check

Unbalanced reactions are among the most common modelling errors. COBRApy computes elemental balance per reaction.

errors = []
warnings = []

print("=== Mass/Charge Balance ===")
for rxn in model.reactions:
    # Returns dict like {"C": -1, "H": 2} if imbalanced; empty dict if OK
    imbalance = rxn.check_mass_balance()
    if imbalance:
        # Exchange and demand reactions are expected to be imbalanced
        if rxn.id.startswith(("EX_", "DM_", "SK_", "BIOMASS")):
            warnings.append(f"WARN  [{rxn.id}] boundary reaction imbalanced "
                            f"(expected): {imbalance}")
        else:
            errors.append(f"ERROR [{rxn.id}] mass/charge imbalance: "
                          f"{imbalance}")

for msg in errors + warnings:
    print(msg)
print(f"  {len(errors)} error(s), {len(warnings)} warning(s)")

Step 3 — Biomass Producibility (FBA Feasibility)

print("\n=== Biomass Producibility ===")
solution = model.optimize()

if solution.status != "optimal":
    errors.append(f"ERROR Model is {solution.status} — "
                  f"cannot produce biomass under current medium.")
    print(f"  FAIL: {solution.status}")
elif solution.objective_value < 1e-6:
    errors.append("ERROR Growth rate is effectively zero "
                  "(< 1e-6 h^-1). Check medium and objective reaction.")
    print(f"  FAIL: growth = {solution.objective_value:.6f} h^-1")
else:
    print(f"  PASS: growth = {solution.objective_value:.4f} h^-1")