OptFlux allows the user to perform a simulation of the "wild-type" strain, i.e. of the model with no genetic modifications.
Access the "Wild Type" option either through the "Simulation" menu or right clicking on the model icon in the clipboard.
Wild-type simulations can be performed using Flux-Balance Analysis (FBA), where a Linear Programming problem is defined by the maximization of one flux of the model, usually the biomass formation, or Parsimonious Flux-Balance Analysis (pFBA) where the same principle applies, but the objective function is the minimization of the sum of the fluxes.
Choose the Project to do the simulation.
2.Objective Function Configuration
In the objective function section, you have select a reaction (typically the biomass/ growth reaction, selected by default) to maximize or minimize the corresponding flux.
3.Select the simulation method
Select between the two simulation methods available for wild type: FBA and pFBA
4.Select Environmental Conditions
If you have created environmental conditions you can select them to be used as constraints in the optimization. These can be used to define the values of drain fluxes, i.e. the rates at which metabolites are consumed or produced.
And that's all!! You can press OK and the results will be loaded into the clipboard.