From Optflux
Warning: You are not logged in. Your IP address will be publicly visible if you make any edits. If you log in or create an account, your edits will be attributed to your username, along with other benefits.
The edit can be undone.
Please check the comparison below to verify that this is what you want to do, and then save the changes below to finish undoing the edit.
| Latest revision | Your text | ||
| Line 3: | Line 3: | ||
You can access | You can access | ||
the "Reaction Knockout Optimization" option under the "Optimization" menu.<br> | the "Reaction Knockout Optimization" option under the "Optimization" menu.<br> | ||
| − | + | <div style="display: block; text-align: left;">http://sites.google.com/site/optfluxhowtos/howtos/12---how-to-optimize-the-knockout-set-1/a-reaction-deletions/OptimizationReactionsMenu.png</div> | |
<br> | <br> | ||
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> | ||
| − | + | <div style="display: block; text-align: left;">http://sites.google.com/site/optfluxhowtos/howtos/12---how-to-optimize-the-knockout-set-1/a-reaction-deletions/OptimizationReactionsOperation.png</div> | |
<br> | <br> | ||
<b>1.Select Project and Model</b><br> | <b>1.Select Project and Model</b><br> | ||
| Line 12: | Line 12: | ||
<br> | <br> | ||
<b>2.Select Simulation Method</b><br> | <b>2.Select Simulation Method</b><br> | ||
| − | OptFlux can use several simulation methods, namely Flux-Balance Analysis, ROOM-LP, ROOM-MILP, MOMA. Check the | + | OptFlux can use several simulation methods, namely Flux-Balance Analysis, ROOM-LP, ROOM-MILP, MOMA. Check the Simulation How To's to find out more about these methods...<br> |
<br> | <br> | ||
<i><b>3.Select Environmental Conditions</b></i><br> | <i><b>3.Select Environmental Conditions</b></i><br> | ||
| − | If you have created | + | If you have loaded/created environmental conditions you can select them to use as constraints in the simulation. Check the Simulation and Environmental Conditions How To's to find out more...<br> |
<br> | <br> | ||
<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.<br> | BPCY - Biomass-Product Coupled Yield, YIELD - Product Yield with Minimum Biomass.<br> | ||
| − | The first calculates the product of the biomass flux and the compound production flux; the second, returns the value of the | + | <br> |
| − | <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> |
| + | <br> | ||
<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> |
| − | <br><br> | + | <br> |
<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. | + | Cellular Genetic Algorithm, Evolutionary Algorithm, Simulated Annealing.<br> |
| − | <br><br> | + | <br> |
| + | For more informations please check the following reference: [ttp://www.biomedcentral.com/1471-2105/9/499/ Natural computation meta-heuristics for the in silico optimization of microbial strains]<br> | ||
| + | <br> | ||
<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 size.<br> |
| − | <br><br> | + | <br> |
<i><b>8.Essential information</b></i><br> | <i><b>8.Essential information</b></i><br> | ||
| − | + | If you loaded/created some essential reactions information you can define if it is possible to knockout some special type of reactions like drains, transport and critical reactions.<br> | |
<br> | <br> | ||
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/12---how-to-optimize-the-knockout-set-1/a-reaction-deletions/OptimizationReactionResults.png</div> | <div style="display: block; text-align: left;">http://sites.google.com/site/optfluxhowtos/howtos/12---how-to-optimize-the-knockout-set-1/a-reaction-deletions/OptimizationReactionResults.png</div> | ||