Flux balance analysis

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FBC analysis view in the BioUML

Flux balance analysis is a mathematical approach for analyzing the flow of metabolites through a metabolic network. In the BioUML it is represented in the Flux Balance Constraint analysis. This page contains brief instruction of how this analysis should be used.

FBC analysis usage

Solver type choosing in the FBC analysis
Example of "FBC table" tab usage for Recon model

To start work with the Flux Balance Constraint analysis one needs a Type-diagram-icon.png diagram and a special table with data about its fluxes (names, bounds, objective function coefficients, etc.). Analysis enables to select path to the Type-diagram-icon.png 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 (apache simplex solver and gurobi solver are available) and some solver's properties. If the Type-diagram-icon.png 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 Type-diagram-icon.png diagram.

FBC data table creation

View of Building Flux Balance Data Table analysis

Table with flux balance constraint data 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 Type-diagram-icon.png diagrams with special fbc package. Thus if the Type-diagram-icon.png diagram does not satisfy these conditions it should be transformed before using this analysis. For example, if the Type-diagram-icon.png diagram does not use fbc package but contains all necessary information about fluxes, it should be firtsly preprocessed by Recon transformer.

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