Single Flux Balance Analysis run.

Use this tool to compute maximal flux towards selected metabolite and metabolic flux distribution. Remember, that most probably there are many possible metabolic flux distributions that could sustain maximal production rate of the metabolite. Use Flux Variability Analysis to explore metabolic state of the model.

The output of the Flux Balance Analysis run will contain maximal flux towards selected metabolite, status of the optimisation (OPTIMAL if the model is feasible) and metabolic flux distribution. Each line in the distribution contains reaction name, computed flux value, active bounds on reaction capacity (input data) 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.