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

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

Arena3Dweb : interactive 3D visualization of multilayered networks supporting multiple directional information channels, clustering analysis and application integration. / Kokoli, Maria; Karatzas, Evangelos; Baltoumas, Fotis A.; Schneider, Reinhard; Pafilis, Evangelos; Paragkamian, Savvas; Doncheva, Nadezhda T.; Jensen, Lars Juhl; Pavlopoulos, Georgios A.

In: NAR Genomics and Bioinformatics, Vol. 5, No. 2, lqad053, 2023.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Kokoli, M, Karatzas, E, Baltoumas, FA, Schneider, R, Pafilis, E, Paragkamian, S, Doncheva, NT, Jensen, LJ & Pavlopoulos, GA 2023, 'Arena3Dweb: interactive 3D visualization of multilayered networks supporting multiple directional information channels, clustering analysis and application integration', NAR Genomics and Bioinformatics, vol. 5, no. 2, lqad053. https://doi.org/10.1093/nargab/lqad053

APA

Kokoli, M., Karatzas, E., Baltoumas, F. A., Schneider, R., Pafilis, E., Paragkamian, S., Doncheva, N. T., Jensen, L. J., & Pavlopoulos, G. A. (2023). Arena3Dweb: interactive 3D visualization of multilayered networks supporting multiple directional information channels, clustering analysis and application integration. NAR Genomics and Bioinformatics, 5(2), [lqad053]. https://doi.org/10.1093/nargab/lqad053

Vancouver

Kokoli M, Karatzas E, Baltoumas FA, Schneider R, Pafilis E, Paragkamian S et al. Arena3Dweb: interactive 3D visualization of multilayered networks supporting multiple directional information channels, clustering analysis and application integration. NAR Genomics and Bioinformatics. 2023;5(2). lqad053. https://doi.org/10.1093/nargab/lqad053

Author

Kokoli, Maria ; Karatzas, Evangelos ; Baltoumas, Fotis A. ; Schneider, Reinhard ; Pafilis, Evangelos ; Paragkamian, Savvas ; Doncheva, Nadezhda T. ; Jensen, Lars Juhl ; Pavlopoulos, Georgios A. / Arena3Dweb : interactive 3D visualization of multilayered networks supporting multiple directional information channels, clustering analysis and application integration. In: NAR Genomics and Bioinformatics. 2023 ; Vol. 5, No. 2.

Bibtex

@article{eb4cff337ed048a5a8a279bad2fc6127,
title = "Arena3Dweb: 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 B{\'e}zier 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",
author = "Maria Kokoli and Evangelos Karatzas and Baltoumas, {Fotis A.} and Reinhard Schneider and Evangelos Pafilis and Savvas Paragkamian and Doncheva, {Nadezhda T.} and Jensen, {Lars Juhl} and Pavlopoulos, {Georgios A.}",
note = "Publisher Copyright: {\textcopyright} 2023 The authors.",
year = "2023",
doi = "10.1093/nargab/lqad053",
language = "English",
volume = "5",
journal = "NAR Genomics and Bioinformatics",
issn = "2631-9268",
publisher = "Oxford University Press",
number = "2",

}

RIS

TY - JOUR

T1 - Arena3Dweb

T2 - interactive 3D visualization of multilayered networks supporting multiple directional information channels, clustering analysis and application integration

AU - Kokoli, Maria

AU - Karatzas, Evangelos

AU - Baltoumas, Fotis A.

AU - Schneider, Reinhard

AU - Pafilis, Evangelos

AU - Paragkamian, Savvas

AU - Doncheva, Nadezhda T.

AU - Jensen, Lars Juhl

AU - Pavlopoulos, Georgios A.

N1 - Publisher Copyright: © 2023 The authors.

PY - 2023

Y1 - 2023

N2 - 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 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 Arena3Dweb for 3D multi-layer visualization. Arena3Dweb is accessible at http://arena3d.pavlopouloslab.info or http://arena3d.org

AB - 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 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 Arena3Dweb for 3D multi-layer visualization. Arena3Dweb is accessible at http://arena3d.pavlopouloslab.info or http://arena3d.org

U2 - 10.1093/nargab/lqad053

DO - 10.1093/nargab/lqad053

M3 - Journal article

C2 - 37260509

AN - SCOPUS:85161966346

VL - 5

JO - NAR Genomics and Bioinformatics

JF - NAR Genomics and Bioinformatics

SN - 2631-9268

IS - 2

M1 - lqad053

ER -

ID: 357770788