How to optimize optimize the knockout set - Gene knockouts
You can access
the "Gene Knockout Optimization" option under the "Optimization" menu.
To use this optimization you have to use with a model with GPR (gene-protein-reaction) information.
You can select the model/project to work, and set up your optimization configuration.
1.Select Project and Model
In
the Project combo box select the project where you want to perform the
optimization, in the Model combo box select the model in the project
that you want to use (if you have performed model simplification, the simplified models will be easier to handle by the optimization algorithms).
2.Select Simulation Method
OptFlux can use several simulation methods, namely Flux-Balance Analysis, ROOM-LP, ROOM-MILP, MOMA.
Check the Simulation How To's to find out more about these methods...
3.Select Environmental Conditions
If you have loaded/created environmental conditions you can select them to use as constraints in the simulation.
Check the Simulation and Environmental Conditions How To's to find out more...
4.Select Objective Function
OptFlux can use two types of objective function:
BPCY - Biomass-Product Coupled Yield, YIELD - Product Yield with Minimum Biomass.
The first calculates the product of the biomass flux and the compound production flux; the second, returns the value of the compound production flux, if the biomass is larger than a minimum value.
5.Objective Function Configuration
Here you can select the flux to be optimize (the compound you wish to produce), the flux that represents the biomass and the substract that is in use.
6.Select Optimization Algorithm
OptFlux allows you to perform optimizations using one of this algorithms:
Cellular Genetic Algorithm, Evolutionary Algorithm, Simulated Annealing
7.Optimization Basic Setup
Here you can configure the maximum number of solution evaluations (simulations) and check the expected time to perform that number of evaluations.
You can also set up the maximum number of knockouts and if the set of knockouts should be static or size variable.
8.Essential information
If
you loaded/created some essential genes you can define if it is
possible to knockout some critical genes.
And that's all, now you can press OK and check the results in the Clipboard.
