Journal: BMC Systems Biology

Article Title: Metabolic modeling of a chronic wound biofilm consortium predicts spatial partitioning of bacterial species

doi: 10.1186/s12918-016-0334-8

Figure Lengend Snippet: Formulation and solution of the multispecies biofilm metabolic model. a Schematic representation of the chronic wound biofilm model of constant thickness W with glucose provided at the tissue-biofilm interface ( z = 0), oxygen supplied at the biofilm-air interface ( z = W ) and the metabolic byproducts acetate, succinate and lactate removed at the tissue-biofilm interface. b Schematic representation of the biofilm metabolic model solution procedure. The multispecies biofilm with temporal and spatial variations is described by a spatiotemporal model that accounts for the diffusion of nutrients and byproducts. PDEs are written with respect to the bacterial species concentration ( X i ) and the metabolite concentrations ( M j ) assuming that spatial variations are limited to a single direction z . Lexicographic linear program solution of the genome-scale reconstruction of each species is performed to predict the growth rate, nutrient uptake rates and byproduct secretion rates. The PDEs are spatially discretized to yield a large-set of ODEs with embedded LPs that are integrated with the MATLAB code DFBAlab to generate time and spatially resolved predictions

Article Snippet: This ODE system was solved using DFBAlab [ ], a MATLAB tool that explicitly addresses problems associated with LP alternative optima and possible infeasibilities [ ].

Techniques: Formulation, Diffusion-based Assay, Concentration Assay

Journal: BMC Bioinformatics

Article Title: DFBAlab: a fast and reliable MATLAB code for dynamic flux balance analysis

doi: 10.1186/s12859-014-0409-8

Figure Lengend Snippet: Concentration profiles (left) and DFBAlab penalty function (right) of Example 1. The penalty function shows how the simulation becomes infeasible after approximately 8.1 hours. Simulation times: DyMMM = 6.6 seconds, DFBAlab = 7.7 seconds.

Article Snippet: In this paper, we implement the LP feasibility problem combined with lexicographic optimization in our Dynamic Flux Balance Analysis laboratory (DFBAlab), a MATLAB code that performs fast, reliable and flexible community simulations.

Techniques: Concentration Assay

Journal: BMC Bioinformatics

Article Title: DFBAlab: a fast and reliable MATLAB code for dynamic flux balance analysis

doi: 10.1186/s12859-014-0409-8

Figure Lengend Snippet: DFBAlab simulation results of example 2. Two cyclic steady states are presented. Simulation 1 (solid line) was performed with lexicographic objectives presented in Table , whereas simulation 2 (dashed line) used the negative of Objective 4 for algae. Significant differences can be observed in the predicted concentrations of yeast, glucose, and oxygen. Computation times for simulations 1 and 2 where 82 and 74 seconds, respectively.

Article Snippet: In this paper, we implement the LP feasibility problem combined with lexicographic optimization in our Dynamic Flux Balance Analysis laboratory (DFBAlab), a MATLAB code that performs fast, reliable and flexible community simulations.

Techniques: Algae

Journal: BMC Bioinformatics

Article Title: DFBAlab: a fast and reliable MATLAB code for dynamic flux balance analysis

doi: 10.1186/s12859-014-0409-8

Figure Lengend Snippet: DFBAlab simulation results of example 3. This example incorporates the pH balance (solid line). Simulation results were close to the ones obtained without a pH balance. Slight variations were observed for the CO 2 concentration profile. Computation time was 162 seconds.

Article Snippet: In this paper, we implement the LP feasibility problem combined with lexicographic optimization in our Dynamic Flux Balance Analysis laboratory (DFBAlab), a MATLAB code that performs fast, reliable and flexible community simulations.

Techniques: Concentration Assay