Constraint-based metabolic models are currently the most comprehensive system-wide models of cellular metabolism. Several challenges arise when building an in silico constraint-based model of an organism that need to be addressed before flux balance analysis (FBA) can be applied for simulations. An algorithm called FBA-Gap is presented here that aids the construction of a working model based on plausible modifications to a given list of reactions that are known to occur in the organism. When applied to a working model, the algorithm gives a hypothesis concerning a minimal medium for sustaining the cell in culture. The utility of the algorithm is demonstrated in creating a new model organism and is applied to four existing working models for generating hypotheses about culture media. In modifying a partial metabolic reconstruction so that biomass may be produced using FBA, the proposed method is more efficient than a previously proposed method in that fewer new reactions are added to complete the model. The proposed method is also more accurate than other approaches in that only biologically plausible reactions and exchange reactions are used. 1. Introduction Flux balance analysis (FBA) is the use of a linear program (LP) to model the flow of metabolites through the network of reactions in a cell [1]. FBA simulations give insight into the relative rates at which reactions occur when the cell is optimized for a specific objective. A fundamental assumption of FBA is that organisms can function optimally (often as a result of adaptive evolution) in that they make optimal use of scarce resources to serve the needs of the organism. This characterization of cell behavior naturally leads to a math programming modeling paradigm. FBA has been used to predict growth rates, gene essentiality, and other features of multiple organisms [2–5]. Several related challenges are encountered in the building of metabolic reconstructions. To apply FBA to a constraint-based model, both a reaction network (representing organism-specific biochemical capabilities) and an objective (representing a desired or measurable physiological goal) need to be specified. Currently, complete reaction networks for organisms are not known. There may be reactions in a cell that must be active for the production of biomass that have not been cataloged in biological databases or documented in the literature. Another challenge is modeler error; the modeler can mistakenly omit a reaction or transport process that is necessary for the production of biomass. Aside from establishing a model that can
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