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=Example file= | =Example file= | ||
− | You can download it here -> | + | You can download it here -> |
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[[Image:IntegrateRegulatoryModel.png]] | [[Image:IntegrateRegulatoryModel.png]] | ||
− | <b>1. <i>Select Project and Model</i></b | + | <b>1. <i>Select Project and Model</i></b> |
− | You can select the model/project to integrate the regulatory model. | + | |
+ | You can select the model/project to integrate the regulatory model. | ||
+ | |||
<br> | <br> | ||
− | <b>2. <i>File Options</i></b> | + | <b>2. <i>File Options</i></b> |
+ | |||
You can select the regulatory model file. In our example the regulatory model file name is '''toy.regNet'''. | You can select the regulatory model file. In our example the regulatory model file name is '''toy.regNet'''. | ||
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Here you can select the reaction to optimize (biomass, by default), and you can also define if you will be maximizing or minimizing that flux.<br> | Here you can select the reaction to optimize (biomass, by default), and you can also define if you will be maximizing or minimizing that flux.<br> | ||
<br> | <br> | ||
− | <b>4. <i>Set Regulatory Variables</i></b><br> | + | <b>4. <i>Set Regulatory User Variables</i></b><br> |
Here you can define the value of all regulatory user variables, and see the values of the model variables.<br> | Here you can define the value of all regulatory user variables, and see the values of the model variables.<br> | ||
<br> | <br> | ||
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[[Image:PathForSimAndOpt.png]]<br> | [[Image:PathForSimAndOpt.png]]<br> | ||
<br> | <br> | ||
− | * | + | *You can select the model/project to work, and set up your optimization configuration.<br> |
[[Image:IntegrateOptimizationOperation.png]] | [[Image:IntegrateOptimizationOperation.png]] | ||
<br> | <br> | ||
− | <b>1. | + | <b>1.Select Project and Model</b><br> |
In the Project combo box select the project where you want to perform the | In the Project combo box select the project where you want to perform the | ||
optimization, in the Model combo box select the model in the project | optimization, in the Model combo box select the model in the project | ||
that you want to use.<br> | that you want to use.<br> | ||
<br> | <br> | ||
− | <b>2. | + | <b>2.Select Simulation Method</b><br> |
− | OptFlux can use several simulation methods | + | OptFlux can use several simulation methods, namely Flux-Balance Analysis, ROOM-LP, ROOM-MILP, MOMA. <br> |
− | + | Check the Simulation How To's to find out more about these methods... <br> | |
<br> | <br> | ||
− | <b>3. | + | <i><b>3.Select Environmental Conditions</b></i><br> |
− | If you have created [[Environmental conditions|environmental conditions]] you can select them to be used as constraints in the simulation. | + | If you have created [[Environmental conditions|environmental conditions]] you can select them to be used as constraints in the simulationIf you have loaded/created environmental conditions you can select them to use as constraints in the simulation. |
<br> | <br> | ||
− | <b>4. | + | <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> | <br> | ||
The first calculates the product of the biomass flux and the compound production flux; the second, returns the value of the target compound production flux divided by the substrate consumption flux, if the biomass is larger than a minimum value, defined by the user<br> | The first calculates the product of the biomass flux and the compound production flux; the second, returns the value of the target compound production flux divided by the substrate consumption flux, if the biomass is larger than a minimum value, defined by the user<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 substrate that is in use.<br> | ||
<br> | <br> | ||
− | + | <b>6.Select Optimization Algorithm</b><br> | |
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− | <b>6. | ||
OptFlux allows you to perform optimizations using one of the following algorithms:<br> | OptFlux allows you to perform optimizations using one of the following algorithms:<br> | ||
Cellular Genetic Algorithm, Evolutionary Algorithm, Simulated Annealing<br> | Cellular Genetic Algorithm, Evolutionary Algorithm, Simulated Annealing<br> | ||
<br> | <br> | ||
− | <b>7. | + | <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 have a variable size.<br> | You can also set up the maximum number of knockouts and if the set of knockouts should be static or have a variable size.<br> | ||
<br> | <br> | ||
− | <b>8. | + | <i><b>8.Essential information</b></i><br> |
− | If you loaded/created some essential genes you can define if it is | + | If |
+ | you loaded/created some essential genes you can define if it is | ||
possible to knockout some critical genes.<br> | possible to knockout some critical genes.<br> | ||
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<br> | <br> | ||
[[Image:ClipboardAfterIntegrateOptimization.png]] | [[Image:ClipboardAfterIntegrateOptimization.png]] |