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* Is possible to define a regulatory model by describing only the genes that have an associated regulatory rule, or a regulatory model containing all the genes that are present in the metabolic model and the regulatory model. | * Is possible to define a regulatory model by describing only the genes that have an associated regulatory rule, or a regulatory model containing all the genes that are present in the metabolic model and the regulatory model. | ||
− | + | * In the implementation of the regulatory model is mandatory the description of the following elements for each gene rule: | |
− | <b>1. <i>A column containing the identifiers for each gene</i></b><br> | + | <b>1. <i>A column containing the identifiers for each gene that have an associated regulatory rule</i></b><br> |
* The gene identifier must be the same that is used in the metabolic GPRs rules, to link a metabolic gene to a regulatory rule. | * The gene identifier must be the same that is used in the metabolic GPRs rules, to link a metabolic gene to a regulatory rule. | ||
<b>Example</b>: if you have a reaction R1 that have two associated genes b0536 and b2567 and they are affected by a regulatory rule, you must define a column containing the identifiers (b0536 and b2567) of these two genes. | <b>Example</b>: if you have a reaction R1 that have two associated genes b0536 and b2567 and they are affected by a regulatory rule, you must define a column containing the identifiers (b0536 and b2567) of these two genes. | ||
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= Build a new project containing an integrated model = | = Build a new project containing an integrated model = | ||
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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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* 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'''. |