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− | <b>How to calculate | + | <b>How to calculate a Critical Genes/Reactions</b><br> |
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− | OptFlux allows the users to define which are the genes or reactions that are essential for the strain to survive, i.e. to keep a value of growth | + | OptFlux allows the users to define which are the genes or reactions that are essential for the strain to survive, i.e. to keep a value of biomass/ growth significantly different from zero. The essential genes/ reactions can be calculated using Flux Balance Analysis. Also, the software allows the user to load thse genes or reactions from a file (if they are available). The list of essential genes/ reactions can be manually edited, allowing users to add or remove elements, given their knowledge or the purpose of their experiments.<br> |
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− | You can access the "Calculate Critical Genes/Reactions" option under the "Model Simplification" menu or | + | You |
+ | can access | ||
+ | the "Calculate Critical Genes/Reactions" 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-structural-simplification/CalculateCriticalMenu.png</div> | <div style="display: block; text-align: left;">http://sites.google.com/site/optfluxhowtos/howtos/model-simplification/performing-structural-simplification/CalculateCriticalMenu.png</div> | ||
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<b>1.Biomass Flux</b><br> | <b>1.Biomass Flux</b><br> | ||
− | Choose the | + | Choose the flux related to the biomass / growth.<br> |
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<b>2.Critical Information</b><br> | <b>2.Critical Information</b><br> | ||
− | Choose if you want to calculate essential reactions or | + | Choose if you want to calculate essential reactions or genes (if GPR information available).<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 created environmental conditions you can select them to | + | If you have loaded/created environmental conditions you can select them |
+ | to use as constraints in the critical genes/reactions calculation. This means that in this case you will calculate essential genes/reactions in a given environment.<br> | ||
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And that's all !! Now you can press OK and check the results in the clipboard.<br> | And that's all !! Now you can press OK and check the results in the clipboard.<br> | ||
<div style="display: block; text-align: left;">http://sites.google.com/site/optfluxhowtos/howtos/model-simplification/performing-structural-simplification/CalculateCriticalSolution.png</div> | <div style="display: block; text-align: left;">http://sites.google.com/site/optfluxhowtos/howtos/model-simplification/performing-structural-simplification/CalculateCriticalSolution.png</div> | ||
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