Help:Tutorial:Step 2 v2
From WikiPathways
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Open the editor in a separate window by clicking the {{TutorialImage|fullscreenbutton.png}} ''Switch to fullscreen mode'' button. This allows you to resize the editor and edit fullscreen. You can return to the original editor in your browser by clicking the {{TutorialImage|restorescreenbutton.png}} ''Switch to embedded mode'' button. | Open the editor in a separate window by clicking the {{TutorialImage|fullscreenbutton.png}} ''Switch to fullscreen mode'' button. This allows you to resize the editor and edit fullscreen. You can return to the original editor in your browser by clicking the {{TutorialImage|restorescreenbutton.png}} ''Switch to embedded mode'' button. | ||
| - | == Adding gene products | + | == Adding gene products, metabolites and interactions == |
| - | + | For the purposes of this tutorial, we will use the Statin pathway as our example. | |
| - | + | * To start, click the drop-down next to the ''GENE'' button and select ''Metabolite''. Place the metabolite on the drawing board by dragging and dropping it. | |
| + | * To annotate the node, double-click the metabolite to bring up the ''DataNode properties'' interface. Type in ''3-hydroxy-3-methylglutaryl-coA'' and click ''Search''. | ||
| + | * In the search results, select the node with the HMDB identifier ''HMDB01375''. Click ''OK''. | ||
| + | * Back in the ''DataNode properties'' window, you can alter the text label that will used for the metabolite. In this case, change it to ''HMG-CoA''. Click ''OK'' to save. | ||
| + | * Repeat the steps above and add another metabolite node for ''Mevalonate''. Place it under the ''HMG-CoA'' node. | ||
== Changing the color and style of interactions == | == Changing the color and style of interactions == | ||
== Saving changes and adding a description == | == Saving changes and adding a description == | ||
Revision as of 23:01, 12 November 2015
This step includes several aspects of pathway creation, from creating a pathway at WikiPathways, launching the Applet Editor, to adding data nodes, interactions and annotations. All the steps are visually represented in the below video.
Create a new pathway
Open a new browser window or tab, go to the WikiPathways main page and click the image under the header Create in the Contributing New Pathways section. You can also click the Create link in the left-hand side panel. Enter Demo_yourname under the Pathway name field and select Homo sapiens in the species menu. Now click the Create pathway button.
After clicking the button, a new page will open and the pathway editor will be loaded.
Open the editor in a separate window by clicking the 
Switch to fullscreen mode button. This allows you to resize the editor and edit fullscreen. You can return to the original editor in your browser by clicking the 
Switch to embedded mode button.
Adding gene products, metabolites and interactions
For the purposes of this tutorial, we will use the Statin pathway as our example.
* To start, click the drop-down next to the GENE button and select Metabolite. Place the metabolite on the drawing board by dragging and dropping it. * To annotate the node, double-click the metabolite to bring up the DataNode properties interface. Type in 3-hydroxy-3-methylglutaryl-coA and click Search. * In the search results, select the node with the HMDB identifier HMDB01375. Click OK. * Back in the DataNode properties window, you can alter the text label that will used for the metabolite. In this case, change it to HMG-CoA. Click OK to save. * Repeat the steps above and add another metabolite node for Mevalonate. Place it under the HMG-CoA node.
