Generally, the steps for applying modeling software towards MFA include metabolic reconstruction to compile all desired enzymatic reactions and metabolites, provide experimental information such as the labeling pattern of the substrate, define constraints such as growth equations, and minimizing the error between the experimental and simulated results to obtain final fluxes.
In most cases, applying modeling software to MFA involves creating a detailed metabolic network through reconstruction, incorporating experimental data on substrate labeling, setting limitations based on growth equations, and iteratively refining the model to match experimental results and arrive at predicted flux values.