Arena3D^web: Interactive 3D visualization of multilayered networks supporting multiple directional information channels, clustering analysis and application integration

Abstract

Arena3Dweb is an interactive web tool that visualizes multi-layered networks in 3D space. In this update, Arena3Dweb supports directed networks as well as up to nine different types of connections between pairs of nodes with the use of Bezier curves. It comes with different color schemes (light/gray/dark mode), custom channel coloring, four node clustering algorithms which one can run on-the-fly, visualization in VR mode and predefined layer layouts (zig-zag, star and cube). This update also includes enhanced navigation controls (mouse orbit controls, layer dragging and layer/node selection) while its newly developed API allows integration with external applications as well as saving and loading of sessions in JSON format. Finally, a dedicated Cytoscape App has been developed, through which users can automatically send their 2D networks from Cytoscape to Arena3Dweb for 3D multi-layer visualization. Arena3Dweb is accessible at http://arena3d.pavlopouloslab.info or http://arena3d.org

Cytoscape stringApp 2.0: Analysis and Visualization of Heterogeneous Biological Networks

“…In the first we show how a published SARS-CoV-2 interaction map can be augmented and analyzed with stringApp, and in the second how a cross-species network for malaria can be retrieved and visualized. An example of how stringApp can be used to create and visualize networks of chemical compounds, proteins, and enriched terms can be found in the first stringApp publication and in the recent paper about the Arena3D web interactive web tool …”

“…An example of how stringApp can be used to create and visualize networks of chemical compounds, proteins, and enriched terms can be found in the first stringApp publication 3 and in the recent paper about the Arena3D web interactive web tool. 36 While the first one is based on the analysis of proteomics data described in the previous stringApp publication, 3…”

iTraNet: A Web-Based Platform for integrated Trans-Omics Network Visualization and Analysis

“…Various web applications have been developed for visualizing and analyzing multiomics data such as OmicsNet (2, 33), 3Omics (34), PaintOmics (35), MergeOmics (36), MiBiOmics (37), OmicsAnalyst (38), and Arena3D (39, 40). The detailed characteristics of these web-based tools were well summarized and compared previously (2, 38).…”

Exploring microbial functional biodiversity at the protein family level—From metagenomic sequence reads to annotated protein clusters

“…In the scope of metagenomics, interaction networks can be used to visualize the relationships between metagenomic components in the form of gene neighborhood networks, metabolic paths and gene-disease associations. Heterogeneous information with metadata from various sources can also be visualized at a network level with the help of multilayered graphs ( Karatzas et al, 2021a ; Kokoli et al, 2022 ; Zhou et al, 2022 ).…”