Arena3Dweb: interactive 3D visualization of multilayered networks supporting multiple directional information channels, clustering analysis and application integration

Maria Kokoli; Evangelos Karatzas; Fotis A Baltoumas; Reinhard Schneider; Evangelos Pafilis; Savvas Paragkamian; Nadezhda T Doncheva; Lars Juhl Jensen; Georgios A Pavlopoulos

doi:10.1093/nargab/lqad053

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

NAR Genom Bioinform. 2023 May 30;5(2):lqad053. doi: 10.1093/nargab/lqad053. eCollection 2023 Jun.

Authors

Affiliations

¹ Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", Vari16672, Greece.
² University of Luxembourg, Luxembourg Centre for Systems Biomedicine, Bioinformatics Core, Esch-sur-Alzette, Luxembourg.
³ Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Former U.S. Base of Gournes, Heraklion 71003, Greece.
⁴ Department of Biology, University of Crete, Voutes University Campus, P.O. Box 2208, 70013 Heraklion, Crete, Greece.
⁵ Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen N DK-2200, Denmark.
⁶ Center of New Biotechnologies & Precision Medicine, Medical School, National and Kapodistrian University of Athens, Athens 11527, Greece.

Abstract

Arena3D^web is an interactive web tool that visualizes multi-layered networks in 3D space. In this update, Arena3D^web supports directed networks as well as up to nine different types of connections between pairs of nodes with the use of Bézier 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 Arena3D^web for 3D multi-layer visualization. Arena3D^web is accessible at http://arena3d.pavlopouloslab.info or http://arena3d.org.