BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data
Fig 2
BOFdat Step 1: Calculating the biomass objective function stoichiometric coefficients (BOFsc) for the 4 principal macromolecular categories of the cell.
(A) Impact of BOFdat Step 1 on the description of the cellular dry weight. (B) BOFsc are calculated using three data types: i) Macromolecular weight fractions, ii) Omic datasets, and iii) the genome sequence. (C) Comparison of the stoichiometric coefficients used in iML1515 (grey) with those generated by BOFdat (red) and SEED (green). (D) Experimentally measured growth rate, substrate uptake rate, and metabolic waste secretion rate across different conditions are used to constrain the model and generate growth-associated (GAM) and non-growth associated (NGAM) ATP maintenance costs. The GAM is represented by the slope (m) of the linear regression over the conditions, while the NGAM is the Y-intercept (b) of that slope.