  Protein-protein interaction networks (PPIN) enable the study of cellular
processes in organisms. Visualizing PPINs in extended reality (XR), including
virtual reality (VR) and mixed reality (MR), is crucial for exploring
subnetworks, evaluating protein positions, and collaboratively analyzing and
discussing on networks with the help of recent technological advancements.
Here, we present BioNet-XR, a 3D visualization framework, to visualize PPINs in
VR and MR environments. BioNet-XR was developed with the Unity3D game engine.
Our framework provides state-of-the-art methods and visualization features
including teleportation between nodes, general and first-person view to explore
the network, subnetwork construction via PageRank, Steiner tree, and all-pair
shortest path algorithms for a given set of initial nodes. We used usability
tests to gather feedback from both specialists (bioinformaticians) and
generalists (multidisciplinary groups), addressing the need for usability
evaluations of visualization tools. In the MR version of BioNet-XR, users can
seamlessly transition to real-world environments and interact with protein
interaction networks. BioNet-XR is highly modular and adaptable for
visualization of other biological networks, such as metabolic and regulatory
networks, and extension with additional network methods.
