Through COBRA for OptFlux plugin it is possible to perform optimizations using the OptKnock formulation.
This formulations aims to optimize the model to maximize a certain product through a set of possible knockout reactions.
Access the Cobra OptKnock option either through the Optimization -> COBRA menu or right clicking on the model icon in the clipboard.
The following window will be displayed.
Select Project
You can select the project to work.
Optimization Basic Parameters:
- Product Flux
You can select the desired product.
- Minimum Growth
You can define the minimum growth of the model.
- Maximum Knockouts
You can define the maximum number of knockouts to be performed.
- Time Limit
You can define the time limit that the optimization must take to be performed.
Selected Environmental Conditions
You can define the environmental conditions if you have created any.
Selected Reactions to Knockout:
- Select Reactions
Here a list of all model's reactions is presented.
You must select the ones that will be the OptKnock's search landscape to knockout and give as result.
For the consistency of the model system normally the critical reactions are not select.
- Critical Reactions
Here you can select the Critical Reactions already created and remove them from the search landscape list.
Also the Drain Reactions and Transport Reactions can be also removed.
Selected Reactions Constraints
You can select the flux value that you want for the reaction to have.
The flux can be greater, smaller or equal to the selected Constraint Value.
e.g. You can define that the OptKnock must find a list of knockouts which ensure that the R_FUM is greater than 0.5.
Note that with a large number of restrictions the OptKnock may never find a proper result
And that's all!! You can press OK and after MATLAB perform the optimization the results will be loaded into the clipboard.
The following figure represent the MATLAB session after performing the OptKnock:
This happens when you have the Show MATLAB Console Only option disabled.
Optimization solution[edit]
When the optimization procedure completes, the solutions will be sent to the OptFlux clipboard:
Clicking it will launch the following view:
- Pressing the << Add to simulation results button, will send the selected solutions to the list of simulations in the clipboard
Aftewards, each simulation can be individually analysed with full detail using the simulation view.
