Arena3D 3.0: a web server for exploring, analyzing, annotating and sharing multilayered networks in 3D

Arena3D 3.0 reimplements Arena3Dweb to let users explore multilayer biological networks in an interactive 3D scene with layer-specific layouts and aligned node copies.

• Why it matters: Multilayer networks need ways to compare multiple relation types or conditions without losing context, and existing tools make 3D, annotation, and sharing workflows difficult.
• What they did: The web server supports uploads/imports from STRING, IntAct, OmniPath, NDEx, Reactome, and the Gene Ontology, offers twelve layouts (seven in 3D), and includes analyses like multilayer metrics, distributions, perturbation, and UMAP views.
• The result: Users can lay out communities and annotated groups, bundle edges, and export to Cytoscape, Gephi Lite, NORMA, and JBrowse 2, with gene lists to Flame and a REST API for programmatic access.

AI summary of the abstract · may contain errors · not medical advice · read the paper.