(New page: OptFlux provides a number of model simplification operations aiming at reducing the model size but keeping the model mathematically equivalent to the original. These simplified models are ...) |
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Revision as of 20:02, 16 November 2009
OptFlux provides a number of model simplification operations aiming at reducing the model size but keeping the model mathematically equivalent to the original. These simplified models are useful when performing strain optimization operations.
How to calculate a Simplified Model
You
can access
the "Calculate Simplified Model" option under the "Model Simplification" menu or right clicking on the Metabolic Model icon on the clipboard.
In
the options you can select the model/project
to work, and set up your simplification configuration.
1. Structural Simplification
In this case, some operations that only rely on the model structure (i.e. the contraints) are issued.
You
can define here the types of operations that will be performed to simplify the model: zero flux detections (the flux value is zero given the contraints) and the detection of sets of
equivalent fluxes.
2. FBA-Based Simplification
In this case, operations use simulation based on Flux Balance Analysis. So, a Linear Programming problem is solved to maximize and minimize each flux in the model.
In the options, the user can define if he wants to remove the fluxes where the calculated limits are zero, and if he wants the new bounds to be replaced by the calculated limits.
3. Select Environmental Conditions
If you have loaded/created environmental conditions you can select them to use as constraints in the simulation.
And that's all!! Now you can press OK and check the new Simplified Model in the clipboard.
