Bringing data into Cytoscape

Choose a pathway that you would like to import into Cytoscape. In our case, we picked glutathione biosynthesis
In the top of the window, under the header, you see a menu-bar that gives you different export options. One of these options (surrounded in yellow on the screenshot) allows for your pathway (or custom network) to be exported to a Cytoscape-compatible XML-file (for the techies: the file format we use is XGMML). When you click on it, a "Save as" file dialog should open, since your browser doesn't know what to do with files of this type. Save the XML-file somewhere on your harddisk, and remember where you saved it.
Now that you have the file stored on your harddisk (you remember what folder it's stored in, right?), start up Cytoscape. Look at the File menu in Cytoscape. The first option you see is File > Open, but you can't use that one. The native Cytoscape file format is the Session-file and ends with a .cys extension (for the techies (again): it's a compressed file format, similar to .zip-files). As you may have noticed, the file that you just downloaded has a .xml extension. In fact, if you try File > Open with the .xml file, you'll see a bunch of Java giberish error messages.
The option that you're looking for is Import > Network (multiple types).

After choosing this option, you get a new dialog. Click the Select button next to browse your harddisk and pick the file that you just downloaded. After selecting the file, you can click the Import button on the original dialog to finish importing the file.
Hmm, not very impressive yet but that's okay. Each entity in the pathway is initially superimposed over one another because our website doesn't provide any layout-information to Cytoscape. Since the program itself contains so many great layout algorithms, it wasn't worth trying to outsmart the master. So once you see anything appear after importing your file, you should select a layout-algorithm from the Layout menu.
This is what the Window eventually looks like after resizing and applying to Layout > yFiles > Circular layout to it. As far as layout algorithms go, we use GraphViz/Dot ourselves for the website. So most layouts you choose in Cytoscape can be expected to look slightly or significantly different from the layout you see on on our site.

This concludes our tutorial on how to interaction with Cytoscape using the MetNet Online website. You can select another tutorial if you wish.

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