How to use Multiobjective strain optimization - Reaction Deletions
You can access
the "Multiobjective Reaction Knockout Optimization" on the menu "Multiobjective" under the "Optimization" menu.
1.Select Project and Model
In
the Project combobox select the project where you want to perform the
optimization, in the Model combobox select the model in the project
that you want to use.
2.Select Simulation Method
OptFlux can use several simulation methods, you can use:
Flux-Balance Analysis, ROOM-LP, ROOM-MILP, MOMA
3.Select Environmental Conditions
If you have loaded/created environmental conditions you can select them to use as constrains in the optimization.
4.Create and Add Objective Configurations
Using the buttons add/remove you can create the list of objective functions.
4.1Select Objective Function
OptFlux can different types of objective function:
BPCY - Biomass-Product Coupled Yield
YIELD - Product Yield with Minimum Biomass
Max/Min of Reaction Flux value
Max/Min Number of Knockouts
4.2Objective Function Configuration
Here you can configure the specific objective function that you have chosen.
5.Select Optimization Algorithm
OptFlux allows you to perform optimizations using one of this multiobjective algorithms:
Non-Dominate Sorting Genetic Algorithm II, Strengh Pareto Evolutionary Algorithm 2
6.Optimization Basic Setup
Here you can configure the number of solution evaluations and check expected time to perform that number of evaluations.
You can also set up the max number of knockouts and if the genome (set of knockouts) should be static or size variable.
7.Essential information
If
you loaded/created some essential information you can define if it is
possible to knockout some special type of reactions like drains,
transport and critical reactions.
And that's all, now you can press OK and check the results in the end of the optimization that you configured.
