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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 can access the "Calculate Simplified Model" option under the "Model Simplification" menu or | + | You |
| + | 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 contraints) are issued.<br> |
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| + | 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.<br> | ||
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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, a Linear Programming problem is solved to maximize and minimize each flux in the model.<br> |
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| + | 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.<br> | ||
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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 | + | If you have loaded/created environmental conditions you can select them to use as constraints in the simulation.<br> |
<br> | <br> | ||
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> | ||