Here we, 1) discuss the computation of cellular yields and growth rates and how they differ, 2) outline the formulation of a detailed biomass objective function, and 3) review several studies that have focused on the use of the objective function.

Unlike FBA, in which the analysis depends on the choice of a specific objective function, network methods rely on the metabolic stoichiometry alone. Metabolic modularity is an area where network science has shown promising results.

Jul 10, 2007 · Using reconstructed genome-scale metabolic models, the group of Palsson has shown on several occasions that a well suited guiding principle—the so-called ‘objective function' in the terminology used in metabolic flux balance analysis—for operation of metabolic networks is optimization of growth ( Price et al, 2004 ).

Metabolic networks for multiple plant tissues were derived from the generic model and combined in an organism framework. FBA was done by minimizing photon usage as the objective function for the entire network. Two additional Arabidopsis GSMNMs have been developed.

May 23, 2016 · Genome-scale flux balance models of metabolism provide testable predictions of all metabolic rates in an organism, by assuming that the cell is optimizing a metabolic goal known as the objective function.

Feb 10, 2021 · Objective Functions. FBA can be applied to predict the optimal growth rate. In such case, the objective function is a biomass objective function. Biomass objective function takes the contributions of multiple biomass components and biomass precursors made to cell’s growth into account. Formulation of a biomass objective function is introduced ...

Feb 6, 2025 · Results: Recent advances in single-cell omics, metabolic modeling, and machine/deep learning methods have enabled the inference of cellular objectives at both the transcriptomic and metabolic levels, bridging gene expression …

We present a novel method called Biological Objective Solution Search (BOSS) for the inference of an objective function of a biological system from its underlying network stoichiometry as well as experimentally-measured state variables.

objective: optlang.interface.Objective: Before introduction of the optlang based problems, this function returned the objective reactions as a list. With optlang, the objective is not limited a simple linear summation of individual reaction fluxes, making that return value ambiguous.

May 23, 2016 · Genome-scale flux balance models of metabolism provide testable predictions of all metabolic rates in an organism, by assuming that the cell is optimizing a metabolic goal known as the objective function.