From FBA to self-contained models

The tutorial presents a systematic procedure, commencing with a basic biochemical network devoid of a biomass compartment. It delves into thermodynamic properties and introduces methods for a proper description. Conforming to the dimensions mentioned earlier, the tutorial confines itself to detailed quantitative models for an average cell, analyzing static properties. In all cases, one (or two) objective functions are utilized to yield meaningful solutions. The examples provided adhere strictly to quantitative principles, employing physiologically meaningful parameters and standard units such as g grams, mol moles, g\, DW grams of dry weight (gDW), and h hours for time constants. All simulations are executed using Matlab, and the tutorial offers live-script access for replicating the examples.