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__TOC__ | __TOC__ | ||
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=Example file= | =Example file= | ||
− | You can download it here -> [ | + | You can download it here -> [[Media:IntegratedModelToy.zip|IntegratedModelToy.zip]] |
[[Image:IntegratedModel.png]] | [[Image:IntegratedModel.png]] | ||
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*At the metabolic level, the substrate (S) is utilized to produce biomass (B) and by-products P1 and P2. The cellular objective is to maximize biomass production (B) and the engineering objective is the production of P1. Reaction R2 converts the internal metabolite I1 into product P1 and 0.08 biomass (B), whereas reaction R5 converts the internal metabolite I2 into product P2 and 0.12 Biomass. The stoichiometric coefficients of all other reactions reflect a one-to-one relationship between molecule quantities. | *At the metabolic level, the substrate (S) is utilized to produce biomass (B) and by-products P1 and P2. The cellular objective is to maximize biomass production (B) and the engineering objective is the production of P1. Reaction R2 converts the internal metabolite I1 into product P1 and 0.08 biomass (B), whereas reaction R5 converts the internal metabolite I2 into product P2 and 0.12 Biomass. The stoichiometric coefficients of all other reactions reflect a one-to-one relationship between molecule quantities. | ||
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= Build a new project containing an integrated model = | = Build a new project containing an integrated model = | ||
− | + | The user can build a project with an integrated model in two distinctive ways: | |
===1. Through the "New Project Wizard Operation"=== | ===1. Through the "New Project Wizard Operation"=== | ||
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[[Image:MakeIntegratedProject.png]] | [[Image:MakeIntegratedProject.png]] | ||
− | + | At the moment it is only possible to build an integrated model using the wizard operation from Flat Files, (new Formats will be available in a near future version). | |
* '''Step 1''' | * '''Step 1''' | ||
− | + | [[Image:Loadprojectfrommodel.png]] | |
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* '''Step 2''' | * '''Step 2''' | ||
− | + | [[Image:SelectionModelFiles.png]] | |
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+ | The user have to choose the the ''toy.fluxes'' file as the '''Reactions File'''; the ''toy.matrix'' file as the '''Matrix File'''; the ''toy.metab'' file as the '''Metabolites File'''; the ''toy.gr'' file as the '''GPR Information''' and the ''toy.regNet'' file as the '''Regulatory Model File'''. | ||
* '''Reader Configuration''' | * '''Reader Configuration''' | ||
− | + | [[Image:ReaderConfiguration.png]] | |
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In this step some definitions can be selected (depending from the type of the delimiters that are used on user Flat Files) | In this step some definitions can be selected (depending from the type of the delimiters that are used on user Flat Files) | ||
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It's mandatory that the previous loaded metabolic model, have the GPR Rules information. | It's mandatory that the previous loaded metabolic model, have the GPR Rules information. | ||
− | [[Image: | + | [[Image:LoadModelOtherWay.png]] |
* The following dialog panel will be displayed | * The following dialog panel will be displayed | ||
− | [[Image: | + | [[Image:NewIntegratedModelProject.png]] |
<b>1. <i>Project</i></b><br> | <b>1. <i>Project</i></b><br> | ||
You can select the model/project to integrate the regulatory model.<br> | You can select the model/project to integrate the regulatory model.<br> | ||
<br> | <br> | ||
− | <b>2. <i> | + | <b>2. <i>Choose Regulatory model reader type</i></b><br> |
− | You can select the regulatory | + | You can select the type of reader for the regulatory network.<br> |
<br> | <br> | ||
− | <b>3. <i> | + | <b>3. <i>Choose Regulatory model file</i></b><br> |
− | You can select | + | You can select the regulatory model file. In our example the regulatory model file name is toy.regNet.<br> |
<br> | <br> | ||
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After pressing the ''Ok'' button the new project will be created, and the model components will be displayed on '''Clipboard'''. | After pressing the ''Ok'' button the new project will be created, and the model components will be displayed on '''Clipboard'''. | ||
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=How to perform a mutant simulation= | =How to perform a mutant simulation= | ||
− | * You can access the Simulation option under the ''' | + | * You can access the Simulation option under the '''Plugins->Regulatory Tool->Simulation''' menu or right clicking on the Integrated Model icon on the clipboard. |
− | [[Image: | + | [[Image:MenuIntegratedSimulation.png]] |
* In both simulation types you can select the project to work, and set up your configuration. | * In both simulation types you can select the project to work, and set up your configuration. | ||
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==Critical Genes== | ==Critical Genes== | ||
− | The regulatory plug-in allows the users to define which are the genes present on the integrated model that are essential for the strain to survive, i.e. to keep a value of growth (biomass reaction flux) different from zero. The essential genes can be calculated using | + | The regulatory plug-in allows the users to define which are the genes present on the integrated model that are essential for the strain to survive, i.e. to keep a value of growth (biomass reaction flux) different from zero. The essential genes can be calculated using BRN+FBA method. Also, the software allows the user to load these genes or reactions from a file (if they are available). The list of essential genes can be manually edited, allowing users to add or remove elements, given their knowledge or the purpose of their experiments. |
===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 '''Load Critical Regulatory Genes''' option under 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: | + | [[Image:MenuCriticalInformation.png]] |
<br> | <br> | ||
<br> | <br> | ||
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===How to determining essential genes=== | ===How to determining essential genes=== | ||
− | *You can access the '''Compute Critical Regulatory Genes''' option under 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: | + | [[Image:MenuCriticalInformation.png]]<br> |
<br> | <br> | ||
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<br> | <br> | ||
<b>4. <i>Select Simulation Method</i></b><br> | <b>4. <i>Select Simulation Method</i></b><br> | ||
− | The critical genes operation can be performed using the same simulation methods, described in the | + | The critical genes operation can be performed using the same simulation methods, described in the [[OptFlux3:RT/Integrated Model Simulation]] <br> |
<br> | <br> | ||
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[[Image:CriticalGenesClipboard.png]] | [[Image:CriticalGenesClipboard.png]] | ||
− | ==How to | + | ==How to optimise the gene knockouts set== |
− | *You can access the '''Optimization''' option under the ''' | + | *You can access the '''Optimization''' option under the '''Plugins->Regulatory Tool''' menu.<br> |
− | [[Image: | + | [[Image:PathForSimAndOpt.png]]<br> |
<br> | <br> | ||
*The following dialog will be displayed.<br> | *The following dialog will be displayed.<br> | ||
− | [[Image: | + | [[Image:IntegrateOptimizationOperation.png]] |
<br> | <br> | ||
− | + | <b>1. <i>Select Project and Model</i></b><br> | |
− | <b>1. <i>Select Project </i></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.<br> | + | optimization, in the Model combo box select the model in the project |
+ | that you want to use.<br> | ||
<br> | <br> | ||
<b>2. <i>Select Simulation Method</i></b><br> | <b>2. <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> | |
<br> | <br> | ||
<b>3. <i>Select Environmental Conditions</i></b><br> | <b>3. <i>Select Environmental Conditions</i></b><br> | ||
If you have created [[Environmental conditions|environmental conditions]] you can select them to be used as constraints in the simulation.<br> | If you have created [[Environmental conditions|environmental conditions]] you can select them to be used as constraints in the simulation.<br> | ||
<br> | <br> | ||
− | <b>4 | + | <b>4. <i>Select Objective Function</i></b><br> |
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OptFlux can use two types of objective function:<br> | OptFlux can use two types of objective function:<br> | ||
− | + | <b>BPCY - Biomass-Product Coupled Yield</b>; <b>YIELD - Product Yield with Minimum Biomass</b>. | |
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<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> | ||
<br> | <br> | ||
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