 Welcome to this brief introduction to the Cytoscape platform. Cytoscape is open source software that allows you to analyze networks and in particular visualize them. Since we will use it in the context of network biology, I highly recommend that you go watch my short introduction to the core concepts in network biology first if you have not already done so. Cytoscape is normally used via its graphical user interface. It looks like this. It's a bit overwhelming at first, but let's have a walk through it. In the upper right corner you see the network view. That is where you have a graphical layout of the network which you can interact with. Immediately below that you have the so-called table panel which is where all the actual data resides. It contains a note table in which you would store for example data about proteins and an edge table where you would store data about protein interactions for example. To the left of these you have the control panel. As the name implies, that's where you control most things. One thing that you will want to control is the visual styles. That includes the note properties such as size, shape and color and the edge properties such as width, line type and color. For each of these properties you have a triplet called default, mapping and bypass. This is a core concept of Cytoscape that you really need to understand. The default value for each specifies how this is going to be if there is no other information. So for example the default color would be the color that is used when you have missing values. The mapping tells you how the data maps into properties. We'll get back to that. The bypass allows you to select one or more notes and for example say I want these notes to be read. There are several types of mappings. You need to know about two of them mainly. There's the continuous mapping which is what you use for quantitative data like if you have lock fold change values and there's the discrete mapping which you use for categorical data such as if you want to mark different classes of proteins. Of course to use all of this you need to first get your data into Cytoscape. Cytoscape is able to import a wide range of tabular file formats including spreadsheets. There are two ways to import a table and it's very important to keep them separate. One is the import network functionality. That's what you use if you have a table of protein interactions so each row in the table tells you that A interacts with B. The other function is import table. That's the one you use to import additional note data. For example if you have expression data about your proteins that you want to subsequently visualize in the network. The data can come from anywhere. It could be your own experiment but it could also be data that you extracted from some database. This leads me to the next topic which is the Cytoscape app store. It works exactly like the app store on your phone. Except that everything is free. It allows you to install apps into Cytoscape that extend the functionality in a variety of ways. One example of an app is the String app. It allows you to import networks from the String database straight into Cytoscape so that you can come with a long list of proteins and pull a network from String without having to use the import functionality that I just described. Another example of an app is ClusterMaker 2. It provides a wide range of different clustering algorithms so that you can take the network that I just showed you and cut it up and make an arguably better layout like this. That's all I want to say about Cytoscape in this short introduction. If you have any questions feel free to ask them below and if you want to know more about network biology I've linked to a related presentation up here. Thanks for your attention.