Flux balance analysis

Constraint-based flux balance analysis (FBA) is a mathematical approach that enables to provide a holistic view of the cellular metabolism in pro- and eukaryotes and predict flux distribution in a global (on a genome-scale level) metabolic network both under a range of environmental conditions and genetic perturbations. The maximization of the biomass equation is typically used as an objective function of the model for FBA.

FBA via Analysis tab

FBA can be also conducted via the Flux Balance Constraint analysis in the BioUML. Firstly, move to Analysis tab in the Tree Area by a single click with the right mouse button on the corresponding tab.

FBC data table creation

To start the analysis via the tab it is required to create the table with flux balance constraint data. It can be created via Building Flux Balance Data Table analysis. It is worth noting, that the Building Flux Balance Data Table analysis and "FBC table" tab work only with SBML L3v1 diagrams with special fbc package. Thus, if the diagram does not satisfy these conditions it should be transformed before using this analysis. For example, if the diagram does not use fbc package but contains all necessary information about fluxes, it should be preprocessed by Recon transformer firstly.

Figure 4. View of Building Flux Balance Data Table analysis.

FBC analysis usage

To start work with the Flux Balance Constraint analysis one needs a diagram and a special table with data about its fluxes (names, bounds, objective function coefficients, etc.). Analysis enables to select path to the diagram, to the data table and to the table with results. Also it has an expert mode where user can select type of the objective function, solver type (GLPK, Apache simplex solver and Gurobi solver are available) and some solver's properties.

Figure 2. Solver type selection in the FBC analysis.

If the diagram contains fluxes properties written as fbc extension of the SBML "FBC table" tab can be used. Advantage of this tab usage is lack of necessity in creation table with data about fluxes: it will be created automatically using diagram.

Figure 3. Example of "FBC table" tab usage for Recon model.