(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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How to calculate a Simplified Model</b><br> | How to calculate a Simplified Model</b><br> | ||
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| − | You | + | You can access the "Calculate Simplified Model" option under the "Model Simplification" menu or by right clicking on the Metabolic Model icon on the clipboard.<br> |
| − | can access | ||
| − | the "Calculate Simplified Model" option under the "Model Simplification" menu or right clicking on the Metabolic Model icon on the clipboard.<br> | ||
<div style="display: block; text-align: left;">http://sites.google.com/site/optfluxhowtos/howtos/model-simplification/performing-fba-based-simplification/ModelSimplificationMenu.png</div> | <div style="display: block; text-align: left;">http://sites.google.com/site/optfluxhowtos/howtos/model-simplification/performing-fba-based-simplification/ModelSimplificationMenu.png</div> | ||
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<b>1. Structural Simplification</b><br> | <b>1. Structural Simplification</b><br> | ||
| − | In this case, some operations that only rely on the model structure (i.e. the | + | In this case, some operations that only rely on the model structure (i.e. the constraints) are issued.<br> |
| + | You can define here the types of operations that will be performed to simplify the model: zero flux detections (identification of reactions for which the flux value is always zero given the model constraints) and the detection of sets of equivalent fluxes (identification of sets of reactions for which the flux values is always the same given the model constraints). | ||
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<b>2. FBA-Based Simplification</b><br> | <b>2. FBA-Based Simplification</b><br> | ||
| − | In this case, operations use simulation based on Flux Balance Analysis. So, | + | In this case, operations use simulation based on Flux Balance Analysis. So, several Linear Programming problems are solved to maximize and minimize each flux in the model. In this way, new flux bounds (different from the ones that are loaded with the model) are computed. |
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| − | In the options, the user can define if he wants to remove the fluxes | + | In the options, the user can define if he wants to remove from the model the fluxes for which the new calculated limits are zero, and if he wants the bounds to be replaced by the new calculated limits. |
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<i><b>3. Select Environmental Conditions</b></i><br> | <i><b>3. Select Environmental Conditions</b></i><br> | ||
| − | If you have loaded/created environmental conditions you can select them to use as constraints in the simulation.<br> | + | If you have loaded/created environmental conditions you can select them to use as constraints in the simulation. This means that in this case you will calculate a simplified model for a given environment.<br> |
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And that's all!! Now you can press OK and check the new Simplified Model in the clipboard.<br> | And that's all!! Now you can press OK and check the new Simplified Model in the clipboard.<br> | ||
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<div style="display: block; text-align: left;">http://sites.google.com/site/optfluxhowtos/howtos/model-simplification/performing-fba-based-simplification/ModelSimplificationSolution.png</div> | <div style="display: block; text-align: left;">http://sites.google.com/site/optfluxhowtos/howtos/model-simplification/performing-fba-based-simplification/ModelSimplificationSolution.png</div> | ||
Latest revision as of 19:13, 17 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 by 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 constraints) are issued.
You can define here the types of operations that will be performed to simplify the model: zero flux detections (identification of reactions for which the flux value is always zero given the model constraints) and the detection of sets of equivalent fluxes (identification of sets of reactions for which the flux values is always the same given the model constraints).
2. FBA-Based Simplification
In this case, operations use simulation based on Flux Balance Analysis. So, several Linear Programming problems are solved to maximize and minimize each flux in the model. In this way, new flux bounds (different from the ones that are loaded with the model) are computed.
In the options, the user can define if he wants to remove from the model the fluxes for which the new calculated limits are zero, and if he wants the bounds to be replaced by the new calculated limits.
3. Select Environmental Conditions
If you have loaded/created environmental conditions you can select them to use as constraints in the simulation. This means that in this case you will calculate a simplified model for a given environment.
And that's all!! Now you can press OK and check the new Simplified Model in the clipboard.
