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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. | ||
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<br> | <br> | ||
− | <b>2. <i>File Options</i></b> | + | <b>2. <i>File Options</i></b> |
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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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==How to do a mutant simulation== | ==How to do a mutant simulation== | ||
− | *You can access the '''Simulation''' option under the '''Plugins->Regulatory Tool''' menu or right clicking on the Integrated Model icon on the clipboard. | + | *You can access the '''Simulation''' option under the '''Plugins->Regulatory Tool->''' menu or right clicking on the Integrated Model icon on the clipboard. |
− | [[Image:PathForSimAndOpt.png]] | + | [[Image:PathForSimAndOpt.png]] |
<br> | <br> | ||
− | + | In the Integrated Simulation you can select the model/project to work, and set up your configuration.<br> | |
[[Image:IntegratedSimulationOperaion.png]] | [[Image:IntegratedSimulationOperaion.png]] | ||
<br> | <br> | ||
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If you have created [[Environmental conditions|environmental conditions]] you can select them to be used as constraints in the simulation. These can be used to define the values of drain fluxes, i.e. the rates at which metabolites are consumed or produced.<br> | If you have created [[Environmental conditions|environmental conditions]] you can select them to be used as constraints in the simulation. These can be used to define the values of drain fluxes, i.e. the rates at which metabolites are consumed or produced.<br> | ||
<br> | <br> | ||
− | <b>3. <i>Objective Function | + | <b>3. <i>Objective Function Configuration</i></b><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> | 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> | + | <b>4. <i>Objective Function Configuration</i></b><br> |
− | Here you can | + | 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> | + | <b>6. <i>Select Simulation Method</i></b><br> |
OptFlux can use several simulation methods for knockout simulations, namely:<br> | OptFlux can use several simulation methods for knockout simulations, namely:<br> | ||
BRN+FBA, BRN+ROOM, BRN+MOMA and SR-FBA<br> | BRN+FBA, BRN+ROOM, BRN+MOMA and SR-FBA<br> | ||
<br> | <br> | ||
− | + | And that's all!! You can press OK and the results will be loaded into the clipboard.<br> | |
[[Image:ClipboarIntegratedSi_mulation.png]] | [[Image:ClipboarIntegratedSi_mulation.png]] | ||
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[[Image:PathForCriticalGenes.png]] | [[Image:PathForCriticalGenes.png]] | ||
− | * | + | *Choose the name of the project and the model to where you want to load the critical information and also the file that have the critical genes. |
− | + | [[Image:LoadCriticalRegulatoryGenesOperation.png]] | |
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*Now press OK and you can see a new element on the clipboard with the loaded critical genes. | *Now press OK and you can see a new element on the clipboard with the loaded critical genes. | ||
[[Image:ClipboardAfterCriticalGenes.png]] | [[Image:ClipboardAfterCriticalGenes.png]] | ||
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===How to determining essential genes=== | ===How to determining essential genes=== | ||
− | *You can access the | + | *You can access the "Compute Critical Regulatory Genes" option under the "Plugins->Regulatory Tool->Critical Information" menu or by right clicking on the Integrated Model icon on the clipboard. |
− | [[Image:PathForCriticalGenes.png]] | + | [[Image:PathForCriticalGenes.png]] |
− | |||
*In the options you can select the model/project to work, and set up the process. | *In the options you can select the model/project to work, and set up the process. | ||
[[Image:ComputeCriticalGenesOperation.png]] | [[Image:ComputeCriticalGenesOperation.png]] | ||
− | + | '''1.Set Regulatory User Variables'''<br> | |
− | + | Choose the value of all regulatory user variables. | |
− | + | ||
− | + | '''2. Select Environmental Conditions'''<br> | |
− | If you have created environmental conditions you can select them to be used as constraints in the critical genes/reactions calculation. This means that in this case you will calculate essential genes in a given environment. | + | If you have created environmental conditions you can select them to be used as constraints in the critical genes/reactions calculation. This means that in this case you will calculate essential genes in a given environment. |
− | + | ||
*And that's all !! Now you can press OK and check the results in the clipboard. | *And that's all !! Now you can press OK and check the results in the clipboard. | ||
[[Image:ClipboardAfterCriticalGenes.png]] | [[Image:ClipboardAfterCriticalGenes.png]] | ||
+ | |||
==How to optimise the gene knockouts set== | ==How to optimise the gene knockouts set== | ||
− | + | [[Image:PathForSimAndOpt.png]] | |
− | [[Image:PathForSimAndOpt.png]] | + | |
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[[Image:IntegrateOptimizationOperation.png]] | [[Image:IntegrateOptimizationOperation.png]] | ||
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[[Image:ClipboardAfterIntegrateOptimization.png]] | [[Image:ClipboardAfterIntegrateOptimization.png]] |