DFBAlab

The Dynamic Flux Balance Analysis laboratory (DFBAlab) is a MATLAB-based code that performs numerical integration of dynamic flux balance analysis (dFBA) systems. It provides efficient simulation of multi-culture of microbial species based on genome-scale metabolic network reconstructions for analysis, control and optimization of biochemical processes. As such, it generates dynamic predictions of substrate, biomass, and product concentrations for growth in batch or fed-batch cultures.

dFBA provides a structured model of a biochemical process, where the reaction pathways within the microorganism change depending on the environmental conditions, which is effectively represented by changes in the functional dependency on the substrate concentrations. These predictions result from the solution of linear programs (LPs). Common challenges involve the LPs becoming infeasible or nonunique solution sets. DFBAlab addresses both difficulties using the LP feasibility problem and lexicographic optimization, respectively.