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.

翻译：蛋白质-蛋白质相互作用网络（PPIN）能够研究生物体中的细胞过程。借助最新技术进展，在扩展现实（XR，包括虚拟现实VR和混合现实MR）中可视化PPIN，对于探索子网络、评估蛋白质位置以及协同分析和讨论网络至关重要。本文提出BioNet-XR——一个三维可视化框架，用于在VR和MR环境中呈现PPIN。BioNet-XR基于Unity3D游戏引擎开发，提供节点间瞬移、全局视角与第一人称视角探索网络等先进方法与可视化特性，并通过PageRank、Steiner树和全对最短路径算法针对给定初始节点集构建子网络。我们通过可用性测试收集了专家（生物信息学研究者）与普通用户（跨学科团队）的反馈，以回应可视化工具可用性评估的需求。在MR版本的BioNet-XR中，用户可无缝切换至真实环境并与蛋白质相互作用网络交互。该框架具有高度模块化和可扩展性，适用于代谢网络、调控网络等其他生物网络的可视化，并可扩展集成其他网络分析方法。