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<b>How to optimize optimize the knockout set - Gene knockouts</b><br> | <b>How to optimize optimize the knockout set - Gene knockouts</b><br> | ||
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− | You can access the "Gene Knockout Optimization" option under the "Optimization" menu. | + | You can access |
− | + | the "Gene Knockout Optimization" option under the "Optimization" menu.<br> | |
− | + | <i><b>To use this optimization you have to use with a model with GPR (gene-protein-reaction) information.</b></i><br> | |
+ | <br><div style="display: block; text-align: left;">http://sites.google.com/site/optfluxhowtos/howtos/12---how-to-optimize-the-knockout-set-1/gen/OptimizationGenesMenu.png</div> | ||
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You can select the model/project to work, and set up your optimization configuration.<br> | You can select the model/project to work, and set up your optimization configuration.<br> | ||
− | + | <br> | |
+ | <div style="display: block; text-align: left;">http://sites.google.com/site/optfluxhowtos/howtos/12---how-to-optimize-the-knockout-set-1/gen/OptimizationGenesOperation.png</a></div> | ||
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<b>1.Select Project and Model</b><br> | <b>1.Select Project and Model</b><br> | ||
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<i><b>3.Select Environmental Conditions</b></i><br> | <i><b>3.Select Environmental Conditions</b></i><br> | ||
− | If | + | If you have loaded/created environmental conditions you can select them to use as constraints in the simulation.<br> |
+ | Check the Simulation and Environmental Conditions How To's to find out more...<br> | ||
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<b>4.Select Objective Function</b><br> | <b>4.Select Objective Function</b><br> | ||
OptFlux can use two types of objective function:<br> | OptFlux can use two types of objective function:<br> | ||
− | BPCY - Biomass-Product Coupled Yield, YIELD - Product Yield with Minimum Biomass. | + | BPCY - Biomass-Product Coupled Yield, YIELD - Product Yield with Minimum Biomass.<br> |
+ | <br> | ||
+ | The first calculates the product of the biomass flux and the compound production flux; the second, returns the value of the compound production flux, if the biomass is larger than a minimum value.<br> | ||
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<b>5.Objective Function Configuration</b><br> | <b>5.Objective Function Configuration</b><br> | ||
− | Here you can select the flux to be optimize (the compound you wish to produce), the flux that represents the biomass and the | + | Here you can select the flux to be optimize (the compound you wish to produce), the flux that represents the biomass and the substract that is in use.<br> |
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<b>6.Select Optimization Algorithm</b><br> | <b>6.Select Optimization Algorithm</b><br> | ||
− | OptFlux allows you to perform optimizations using one of | + | OptFlux allows you to perform optimizations using one of this algorithms:<br> |
Cellular Genetic Algorithm, Evolutionary Algorithm, Simulated Annealing<br> | Cellular Genetic Algorithm, Evolutionary Algorithm, Simulated Annealing<br> | ||
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<b>7.Optimization Basic Setup</b><br> | <b>7.Optimization Basic Setup</b><br> | ||
Here you can configure the maximum number of solution evaluations (simulations) and check the expected time to perform that number of evaluations.<br> | Here you can configure the maximum number of solution evaluations (simulations) and check the expected time to perform that number of evaluations.<br> | ||
− | You can also set up the maximum number of knockouts and if the set of knockouts should be static or | + | You can also set up the maximum number of knockouts and if the set of knockouts should be static or size variable.<br> |
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<i><b>8.Essential information</b></i><br> | <i><b>8.Essential information</b></i><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> | ||
+ | <br> | ||
<div style="display: block; text-align: left;">http://sites.google.com/site/optfluxhowtos/howtos/12---how-to-optimize-the-knockout-set-1/gen/OptimizationGenesResults.png</div> | <div style="display: block; text-align: left;">http://sites.google.com/site/optfluxhowtos/howtos/12---how-to-optimize-the-knockout-set-1/gen/OptimizationGenesResults.png</div> |