Arena3D and Cytoscape: A brief introduction to combining the two with Arena3DwebApp
Channel: Lars Juhl Jensen
Date: 21/11/2022

A brief introduction to how Arena3D and Cytoscape can be combined. I first introduce the Arena3D is a web tool for 3D visualization of multilayer networks, which can be useful for displaying, e.g., multiomics data but requires scripting skills to prepare the data. Next, I quickly cover the Cytoscape tool, which allows data to be integrated and mapped onto networks, e.g., from STRING, through a graphical user interface. I present the newly developed Arena3DwebApp for Cytoscape, which allows networks to be easily sent from Cytoscape to Arena3D. I explain how one can prepare a network in Cytoscape, define which nodes should go into which layers, and then send the network to Arena3D, preserving visual properties such as coloring. Finally, I briefly talk about the Arena3Dweb API, which is what receives the networks sent by the app.

If you are are not already familiar with the tools discussed, I suggest that you first watch my separate videos on Arena3D (https://youtu.be/4qnNBcQb1q8) and Cytoscape (https://youtu.be/Ohf9IPUJ82w).

0:00 Introduction: Arena3D, multilayer networks, Cytoscape, and Cytoscape apps
1:26 Arena3DwebApp: install from app store, user interface, defining layers, and retention of visual properties
2:32 Arena3Dweb API: receiving the networks, default 3D layout, and user customization of layout