 Welcome to this brief introduction to the Arena 3D tool. Arena 3D web is, as the name suggests, a web-based tool designed for doing 3D visualization of networks. If you're not already familiar with the topic of network visualization, I suggest you go watch my introduction to the core concepts of the topic before continuing. So what is the core idea of Arena 3D? If you're working with network visualization using tools like Cytoscape, you have for sure worked with 2D layouts which for large networks typically end up looking something like this, which is referred to as a hairball. There are many ways of trying to circumvent the problem of hairballs including clustering, which I've covered in earlier presentations. However, an alternative approach is to go from 2D to 3D layouts. This of course gives you more space, one more dimension to spread out the notes in and therefore making it easier to look at hairballs. The problem is it comes at the price of it being much more difficult to navigate in 3D space and that you have the issue of occlusion, namely that things can hide behind other things. For this reason it's difficult in reality to work with 3D networks unless you go into virtual reality using tools such as VRNetsup. Arena 3D tries to find a middle ground between 2D and 3D networks. Using so-called multilayer network visualization, in which you have multiple 2D layers which are placed within a 3D space to produce a visualization like this. Here you have two 2D layouts of networks and interactions both within the layers and between the layers. So what is the functionality of Arena 3D? It's as I already mentioned a web-based tool and you use it via the web interface that looks like this. It allows you to load in the data and work with scenes, layers, nodes and edges and of course turn around the visualization and look at it from any angle you want. To import the data you need to import node data which would be the usual information that you would use for cytoscape as well such as the nodes, what are their names, which colors do you want them to have but also layer assignments which nodes should go into its layers. You also need edge data which would have both intralayer and interlayer interactions. It's important to realize that Arena 3D likes cytoscape is domain agnostic. That means it's designed to simply do the best job of visualizing the network. It doesn't know anything about biology and the network could be anything. For this it has 2D layout algorithms such as force directed layouts which you can apply to individual layers allowing you to lay out different layers in different ways. You can then place these layers in 3D to get figures that look in many different ways. You can have the layers stacked like this, you can have parallel layers next to each other like this and you can even place the layers in different orientations forming for example a cube. Arena 3D also has several different color schemes including a light background which is very useful if you're preparing publication figures. At this point you might be asking yourself but where do the layers come from? How do you define which nodes go into which layers? And there are really two options. Either it's based on the node type or it's based on the edge type. The bad news is that it is 100% your job to assign nodes to layers. Let's start with layers by node type. If you're working on something like a knowledge graph, a topic I've covered earlier, you will have multiple different node types in your network. This could be genes, diseases, compounds and many other things. And each type of node could be a different layer in Arena 3D. If you're working with signaling pathways, you may only have proteins in your network but you still have multiple protein types. So you could want to place receptors in one layer, kinases in another, transcription factors in another, so on and so forth. If you're working with interspecies networks, you have multiple different species and that means that you can look, for example, at a host parasite network and put the host in one layer and the parasite in another. Alternatively, you can assign layers by edge type. In this case, you will have the same nodes in all the layers but different edges between them. If, for example, you fetch a network from the Spring Database, it will have multiple different evidence types. So you might want to place experimentally determined edges in one layer, text mining in another, etc. Who's the target audience of Arena 3D? I believe the layout could have very broad appeal. However, the current tool is very much targeting computational researchers because you need scripting skills to be able to prepare the data, in particular assigning nodes to the right layers and simply creating the files in the right file formats. What is needed to bring it to the broad audience is more integration, both with network databases and other network tools such as Cytoscape to make it easier to import networks into Arena 3D. And we're currently working with the Arena 3D team to provide just this. That's all I want to say about Arena 3D. If you want to learn about how to use Cytoscape for laying out networks, have a look at this presentation next. Thanks for your attention.