 Welcome to this Omix Visualizer tutorial. This will be a hands-on demonstration of how you can use a Cytoscape app to visualize complex Omix data on networks. If you've never heard of Omix Visualizer before, I recommend that you go watch my brief introduction to the app before continuing with this tutorial. Here, I'll use Omix Visualizer to first import an Omix dataset as a table. As an example, I will use a phosphoproteomic study, which can of course have multiple sites per protein, and happens to also compare three different experimental conditions, which makes it more complicated to visualize. After importing the data, I'll retrieve a network from string and then show the site-specific data on the protein nodes using the so-called donut visualization. In this visualization, each node is shown as usual in Cytoscape, but with donuts around it where each slice represents a different phosphorylation site and the different rings represent comparisons of different conditions, showing the lock-fold change values with a color gradient. Let's get on with it. Welcome to Cytoscape. To use Omix Visualizer, we must first install it by opening the app store, searching for it, selecting Omix Visualizer and clicking the Install button. A short moment after, the Omix Visualizer app will have been installed and we can close the app store again. If we now go to the File menu, we will find a new option that is called Import Omix Visualizer Table from File. Selecting that, we can now choose the file with the phosphoproteomic data and click Import. A preview window will show the data and clicking Import will import it into a data table in Cytoscape. As you can see, the table has many columns, including the uniproduct session numbers of the proteins, the modified residue numbers, that is the phosphorylated residues and two different lock-fold change values representing two different pairwise comparisons of the three conditions. If we click the string icon inside the Omix Visualizer table, we get a dialog allowing us to use string app to easily retrieve a string network. It has already selected human as the default organism and uniprod as the column to use to query with names from. I thus only need to adjust the confidence threshold, which I changed to 0.8 and click Retrieve Network. A short moment after, I get the string network. Since this is a rather big network, I need to go to the View menu and turn on Always Show Graphics Details. I adjust the side window of a string and turn off the string colors to make the visualization less confusing later and turn off similarly the show structure images. Having now a simpler view of the string network, I go and click the Donut button in Omix Visualizer, select a data set that I want to visualize, select the other column I want to visualize, select a column called AA Positions that I want to use as labels on my visualization, go to the next page in the dialog. Here, I adjust the color scale for the color gradient to go from minus 5 to plus 5 on the lock-fold change scale and when I click Draw, it will draw the Omix Visualizer Donut visualizations onto the nodes in the string network. The network is a bit dense, so to improve the layout, I use the Wi-Files option to reduce overlaps and further use the Layout Tools to scale up the network by a factor of 2 to spread out the nodes. If we zoom in on a part of the network, you can now see how for each protein I have a node with two different circles around it with different segments representing different phosphorylation sites, all of which have been colored according to the data from the Phosphor Projomics data set and labeled with amino acid residue numbers. That's all I'll be showing you today. If you want to learn more about how you can visualize Omix data on networks, I recommend that you go take a look at this presentation next. Thanks for your attention.