Difference between revisions of "Flux balance analysis"
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| − | [https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC3108565/ <b><i>Constraint-based flux balance analysis (FBA)</i></b>] 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. | + | [https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC3108565/ <b><i>Constraint-based flux balance analysis (FBA)</i></b>] 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. |
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Revision as of 00:30, 16 March 2022
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.
Contents |
FBA via Diagram
FBA via Analysis tab
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
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 (apache simplex solver and gurobi solver are available) and some solver's properties. 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.
FBC data table creation
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 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 firtsly preprocessed by Recon transformer.
