One of the exciting new features in the Pathway Tools 15.0 release is a Flux Balance Analysis (FBA) module.  FBA models are steady-state quantitative models of the metabolic network that can be used for predicting growth phenotypes under different nutrient conditions and under gene knock-outs.  An FBA model predicts the steady-state flux rates of metabolic reactions given a set of nutrients, secretions, and metabolites to produce (i.e. the biomass reaction), and the set of reactions in a PGDB.

There are two main tasks involved in flux balance analysis: developing a model, and then solving it.  Pathway Tools can aid in both of these tasks.  Developing an accurate FBA model might require the addition of new reactions to a PGDB, altering the directionality of some reactions, modifying the biomass reaction (which lists all the chemical components of the cellular biomass), and adding new nutrients and secretions. The Pathway Tools FBA module can guide the user by suggesting changes, such as possible new reactions to add to produce a needed compound.
Solving an FBA model involves determining the correct fluxes of reactions given a set of nutrients, secretions, and biomass metabolites to produce, and is performed once a feasible FBA model has been generated.  Pathway Tools uses the SCIP solver for this task.  Since the results of solving the model can point out problems in the original model, these two tasks, model-generation and solving, are often invoked in an iterative fashion. Results can also be viewed on the Cellular Overview Diagram.