Below is the list of objective criteria that we propose for classification of computational models of cellular function. Each model is classified in each of the following categories as: (A) satisfies, (B) does not satisfy, or (NA) not applicable. This classification is not intended as a judgment on the validity of a given model or approach; but is intended to help define the scope and applicability of a model for potential users.
Objective characteristics of models
Biophysically based model criteria:
(1) Mass balance. The total mass of model variables leaving or entering the system is explicitly accounted for (and in the case of a closed system is conserved).
(2) Charge balance. Total charge of model variables leaving or entering the system is explicitly accounted for (and in the case of a closed system is conserved).
(3) Osmotic balance. Mass balanced model accounts for water fluxes and volume changes.
(4) Thermodynamic feasibility. Model components obey detailed balance and thermodynamic box constraints.
Criteria for comparing model to data:
(5) Initial conditions given for periodically driven models provide a beat-to-beat steady state (variables return to the initial condition after exactly one period).
(6) All parameter values are justified by cited experimental measurement, previous estimation based on model analysis, or based on model analysis in the current study, or qualitative commentary by the authors.
Computational documentation criteria:
(7) In addition to MIRIAM compliance, all model units are defined and used consistently and model initial and boundary conditions are unambiguously defined.
We now consider the models, from our own work, described above. The classification of each of the models against these criteria is given in Table 1
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