Flux Variability Analysis

Use this tool to explore metabolic state of the system. The program computes minimal and maximal flux through the reaction (range of fluxes) consistent with maximal theoretical flux towards selected metabolite. These values are unique and can be used to draw conclusions about internal flux distribution. Calculations will take about 10 minutes. The program will set the flux towards selected metabolite to maximal theoretical value and compute the minimal and maximal flux through each reaction. Results will be displayed, as calculation progresses.

The output of the Flux Variability Analysis run contains maximal theoretical growth rate, status of the optimisation (OPTIMAL if the model is feasible) and the table of metabolic flux ranges. Each row contains reaction name, computed minimal flux, computed maximal flux, reaction formula and gene annotation linked to ScoDB, ScoCYC and KEGG.

Experimental conditions. The form below shows definition of glucose minimal medium. Media conditions are defined by specifying nutrient transport reactions in the following format: Reaction_name lower_bound upper_bound comment. You can modify experimental conditions by changing their maximal uptake rates. You can also constrain any reaction in the system by stating its name, lower bound and upper bound. See model file and the list of metabolite names.

Optimisation criterion. Optimisation criterion is specified as the name of metabolite. The program computes maximal theoretical flux towards this metabolite. Default optimisation criterion is a BIOMASS. The maximal flux towards BIOMASS represents maximal theoretical growth rate under given media conditions.

Optimisation criterionMedia conditions

The model: The GSMN model file including reaction formulas and gene/reaction associations can be found here. Follow this link for the list of metabolite names.