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

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

^*Corresponding author af dette arbejde

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

11 Citationer (Scopus)

28 Downloads (Pure)

Abstract

Arena3D web is an interactive web tool that visualizes m ulti-la yered netw orks 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 B ´ezier curves. It comes with different color schemes (light / gray / dark mode), custom channel coloring, four node clustering algo- rithms 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 navi- gation controls (mouse orbit controls, layer dragging and layer / node selection), while its ne wl y de veloped API allows integration with external applications as well as saving and loading of sessions in JSON f or - mat. Finally, a dedicated Cytoscape app has been de- veloped, through which users can automatically send their 2D networks from Cytoscape to Arena3D web for 3D m ulti-la yer visualization. Arena3D web is acces- sible at http://arena3d.pavlopouloslab.info or http: //arena3d.org

Originalsprog	Engelsk
Artikelnummer	lqad053
Tidsskrift	NAR Genomics and Bioinformatics
Vol/bind	5
Udgave nummer	2
Antal sider	8
DOI	https://doi.org/10.1093/nargab/lqad053
Status	Udgivet - 2023

Bibliografisk note

Funding Information:
Hellenic Foundation for Research and Innovation (to H.F.R.I.) under the ‘First Call for H.F.R.I. Research Projects to support faculty members and researchers and the procurement of high-cost research equipment grant’ [1855-BOLOGNA]; G.A.P. was also supported by the project ‘The Greek Research Infrastructure for Personalized Medicine (pMedGR)’ [MIS 5002802], which is implemented under the Action ‘Reinforcement of the Research and Innovation Infrastructure’, funded by the Operational Program ‘Competitiveness, Entrepreneurship and Innovation’ [NSRF 2014-2020]; Greece and the European Union (European Regional Development Fund); F.B. was supported by the Fondatión Sante; N.T.D. and L.J.J. were funded by the Novo Nordisk Foundation [NNF14CC0001]; S.P. was supported by the Hellenic Foundation for Research and Innovation (HFRI) under the 3rd Call for HFRI PhD Fellowships [Fellowship number: 5726].

Publisher Copyright:
© 2023 The authors.

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10.1093/nargab/lqad053Licens: CC BY-NC

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Citationsformater

Kokoli, M., Karatzas, E., Baltoumas, F. A., Schneider, R., Pafilis, E., Paragkamian, S., Doncheva, N. T., Jensen, L. J., & Pavlopoulos, G. A. (2023). Arena3D^web: interactive 3D visualization of multilayered networks supporting multiple directional information channels, clustering analysis and application integration. NAR Genomics and Bioinformatics, 5(2), Artikel lqad053. https://doi.org/10.1093/nargab/lqad053

Arena3D^web: interactive 3D visualization of multilayered networks supporting multiple directional information channels, clustering analysis and application integration. / Kokoli, Maria; Karatzas, Evangelos; Baltoumas, Fotis A. et al.
I: NAR Genomics and Bioinformatics, Bind 5, Nr. 2, lqad053, 2023.

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

Kokoli, M, Karatzas, E, Baltoumas, FA, Schneider, R, Pafilis, E, Paragkamian, S, Doncheva, NT, Jensen, LJ & Pavlopoulos, GA 2023, 'Arena3D^web: interactive 3D visualization of multilayered networks supporting multiple directional information channels, clustering analysis and application integration', NAR Genomics and Bioinformatics, bind 5, nr. 2, lqad053. https://doi.org/10.1093/nargab/lqad053

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