When generating a model of physiological systems in a patient, differential equations representing parameters and variables in the systems are linked together to form one or more sub-models (e.g., one for each physiological system), which in turn are linked together to form the patient model. Simulations of hypothetical clinical situations are then run on the model to solve for the variables, and the solutions are output as decision support data for review by a clinician to facilitate a determination of a treatment of diagnosis for the patient. Additionally, model predictions can be compared to actual measurements, when available, and the model can be refined or optimized as a function of the comparison.