Arena3D 3.0: a web server for exploring, analyzing, annotating and sharing multilayered networks in 3D
- 1Institute for Fundamental Biomedical Research, BSRC Alexander Fleming, 16672 Vari, Greece; Division of Biological and Life Sciences, Mohamed bin Zayed Universit
Abstract
Multilayer networks describe biological entities linked by several kinds of relation or measured under several conditions. Arena3D 3.0, a complete reimplementation of Arena3Dweb, gives each layer its own place in an interactive 3D scene. Networks are uploaded or imported from STRING, IntAct, OmniPath, NDEx, Reactome and the Gene Ontology. Twelve layouts, seven in 3D, are available, and node copies can be aligned across layers. Layers are drawn as floors or 3D containers in thirteen arrangements, including 3D hive plots. Communities and annotated groups can be laid out apart and outlined as hulls or fog clouds, and edges can be bundled. Analyses cover node and multilayer metrics, distributions and perturbation, with chord, Sankey, heatmap, UpSet and UMAP views. Networks go to Cytoscape, Gephi Lite, NORMA and JBrowse 2, gene lists to Flame, and a REST API gives programmatic access. Arena3D 3.0 is free at www.arena3d.org without login.
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BibTeX
@misc{karatzas2026arena3d,
title = {{Arena3D 3.0: a web server for exploring, analyzing, annotating and sharing multilayered networks in 3D}},
author = {E. Karatzas and F. Baltoumas and M. Kokoli and A. Galaras and E. Aplakidou and M. Itsios and I. N. Chasapi and M. N. Chasapi and E. Lamari and I. Georgakopoulos-Soares and N. Przulj and G. A. Pavlopoulos},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.23.761450},
url = {https://www.biorxiv.org/content/10.64898/2026.10.23.761450v1},
note = {CC BY-NC},
}
RIS
TY - UNPB
TI - Arena3D 3.0: a web server for exploring, analyzing, annotating and sharing multilayered networks in 3D
AU - E. Karatzas
AU - F. Baltoumas
AU - M. Kokoli
AU - A. Galaras
AU - E. Aplakidou
AU - M. Itsios
AU - I. N. Chasapi
AU - M. N. Chasapi
AU - E. Lamari
AU - I. Georgakopoulos-Soares
AU - N. Przulj
AU - G. A. Pavlopoulos
PY - 2026
DA - 2026/10/23
PB - bioRxiv
DO - 10.64898/2026.10.23.761450
UR - https://www.biorxiv.org/content/10.64898/2026.10.23.761450v1
AB - Multilayer networks describe biological entities linked by several kinds of relation or measured under several conditions. Arena3D 3.0, a complete reimplementation of Arena3Dweb, gives each layer its own place in an interactive 3D scene. Networks are uploaded or imported from STRING, IntAct, OmniPath, NDEx, Reactome and the Gene Ontology. Twelve layouts, seven in 3D, are available, and node copies can be aligned across layers. Layers are drawn as floors or 3D containers in thirteen arrangements, including 3D hive plots. Communities and annotated groups can be laid out apart and outlined as hulls or fog clouds, and edges can be bundled. Analyses cover node and multilayer metrics, distributions and perturbation, with chord, Sankey, heatmap, UpSet and UMAP views. Networks go to Cytoscape, Gephi Lite, NORMA and JBrowse 2, gene lists to Flame, and a REST API gives programmatic access. Arena3D 3.0 is free at www.arena3d.org without login.
ER -