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How to do a mutant simulation - Reaction Deletions

You can access the "Reaction Mutant" option under the "Simulation -> Mutants Simulation" menu or right clicking on the Metabolic Model icon on the clipboard.
Mutant simulation.png

In the Reaction Mutant Simulation you can select the model/project to work, and set up your configuration.


Reaction simulation.png

1. Reaction knockout list
Selecting in the Reaction list you can add/remove (using the arrows buttons) reactions to the knockout list (the list of reactions to be deleted, on the right).

2. Select Simulation Method
OptFlux can use several simulation methods for knockout simulations, namely:
Flux-Balance Analysis, ROOM-LP, ROOM-MILP, MOMA

ROOM-LP stands for the Regulatory On-Off Minimization Method (ROOM), using a linear programming (LP) relaxation; ROOM-MILP is the original ROOM that uses a Mixed Integer LP (MILP) method; MOMA stands for the Minimization of Metabolic Adjustment method that uses quadratic programming.

3. Objective Function Configuration
Here you can select the reaction to optimize (biomass, by default), and you can also define if you will be maximizing or minimizing the flux.

4. Select Environmental Conditions
If you have created environmental conditions you can select them to be used as constrains in the simulation. 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.