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=Example file= | =Example file= | ||
− | You can download it here -> | + | You can download it here -> |
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To start using all features present in Regulatory plug-in, you have to integrate a regulatory model with a metabolic model previous loaded in OptFlux. | To start using all features present in Regulatory plug-in, you have to integrate a regulatory model with a metabolic model previous loaded in OptFlux. | ||
− | *After loaded the metabolic model in OptFlux, accessing the '''Load Regulatory Net''' option under the '''Plugins->Regulatory | + | *1 - After loaded the metabolic model in OptFlux, accessing the '''Load Regulatory Net''' option under the '''Plugins->Regulatory Too''' menu |
[[Image:PathForIntegratedModel.png]] | [[Image:PathForIntegratedModel.png]] | ||
− | *The following dialog will be displayed. | + | *2 - The following dialog will be displayed. |
[[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'''. | ||
− | *After execution, the '''Metabolic Model''' datatype will replaced | + | *3 - After execution, the '''Metabolic Model''' datatype will be replaced for '''Integrated Model''' in the clipboard. |
[[Image:ClipBoardAfterIntegrateModel.png]] | [[Image:ClipBoardAfterIntegrateModel.png]] | ||
==How to do a mutant simulation== | ==How to do a mutant simulation== | ||
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− | [[Image:PathForSimAndOpt.png]] | + | [[Image:PathForSimAndOpt.png]] |
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[[Image:IntegratedSimulationOperaion.png]] | [[Image:IntegratedSimulationOperaion.png]] | ||
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[[Image:ClipboarIntegratedSi_mulation.png]] | [[Image:ClipboarIntegratedSi_mulation.png]] | ||
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===How to do load critical genes from a file=== | ===How to do load critical genes from a file=== | ||
− | *To load the information from a file just access the | + | *To load the information from a file just access the "Load Critical Regulatory Genes" option under the "Plugins->Regulatory Tool->Critical Information" menu in the Project Menu or right click on the Integrated Model icon in the clipboard. |
[[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]] |
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*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. | |
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− | + | '''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. |
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*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]] | ||
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==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]] |