From Optflux
Warning: You are not logged in. Your IP address will be publicly visible if you make any edits. If you log in or create an account, your edits will be attributed to your username, along with other benefits.
The edit can be undone.
Please check the comparison below to verify that this is what you want to do, and then save the changes below to finish undoing the edit.
Latest revision | Your text | ||
Line 58: | Line 58: | ||
<br> | <br> | ||
===Examples=== | ===Examples=== | ||
− | The following figure shows a regulatory model in an excel file | + | The following figure shows a regulatory model in an excel format file containing only the genes with an associated regulatory rule. The first column contains the gene identifiers, the second column contains the gene names (optional), the third column contains the rule identifiers and the last column contains the regulatory rules. |
[[Image:excel_example.png]] | [[Image:excel_example.png]] | ||
<br> | <br> | ||
<br> | <br> | ||
− | The next figure, shows a regulatory model in a comma-separated values file format containing all genes (includes also all metabolic genes). However, the name of the genes are not described in the regulatory file. | + | The next figure, shows a regulatory model in a comma-separated values file format containing all genes (includes also all metabolic genes). However, the name of the genes are not described in the regulatory file. |
[[Image:csvfile_example.png]] | [[Image:csvfile_example.png]] | ||
<br> | <br> | ||
− | |||
− | |||
= Build a new project containing an integrated model = | = Build a new project containing an integrated model = | ||
Line 76: | Line 74: | ||
[[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]] | |
− | |||
− | |||
− | |||
* '''Step 2''' | * '''Step 2''' | ||
− | + | [[Image:SelectionModelFiles.png]] | |
− | + | ||
− | |||
− | |||
+ | 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]] | |
− | |||
− | |||
− | |||
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) | ||
Line 118: | Line 109: | ||
* 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> | ||
− | |||
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'''. |