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

Kokoli, M.; Karatzas, E.; Baltoumas, F. A.; Schneider, R.; Pafilis, E.; Paragkamian, S.; Doncheva, N. T.; Jensen, L. J.; Pavlopoulos, G.

2022-10-05 bioinformatics
10.1101/2022.10.01.510435 bioRxiv
Show 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 Bezier 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

Matching journals

The top 3 journals account for 50% of the predicted probability mass.

1
Bioinformatics
◐ 1204 papers in training set
Top 0.4%
38.2%
Similar papers in this journal
2
Bioinformatics Advances
◐ 203 papers in training set
Top 0.3%
9.5%
Similar papers in this journal
3
Nucleic Acids Research
◐ 1281 papers in training set
Top 3%
7.0%
Similar papers in this journal
50% of probability mass above
4
BMC Bioinformatics
○ 457 papers in training set
Top 1%
6.5%
Similar papers in this journal
5
Computational and Structural Biotechnology Journal
● 242 papers in training set
Top 0.6%
5.3%
Similar papers in this journal
6
PLOS Computational Biology
● 1863 papers in training set
Top 8%
4.2%
7
PLOS ONE
● 5266 papers in training set
Top 37%
3.1%
8
Database
◐ 61 papers in training set
Top 0.2%
3.1%
9
NAR Genomics and Bioinformatics
◐ 242 papers in training set
Top 2%
2.6%
10
GigaScience
◐ 212 papers in training set
Top 2%
2.3%
11
SoftwareX
○ 15 papers in training set
Top 0.1%
1.8%
12
Patterns
○ 78 papers in training set
Top 1%
1.7%
13
iScience
○ 1154 papers in training set
Top 29%
1.1%
14
F1000Research
○ 88 papers in training set
Top 3%
1.0%
15
iMeta
○ 10 papers in training set
Top 0.2%
1.0%
16
Journal of Molecular Biology
○ 232 papers in training set
Top 3%
1.0%
17
Briefings in Bioinformatics
◐ 354 papers in training set
Top 7%
0.8%
18
Scientific Reports
○ 3612 papers in training set
Top 75%
0.8%
19
Biology
○ 45 papers in training set
Top 1.0%
0.8%
20
Genomics
○ 64 papers in training set
Top 2%
0.6%
21
Genomics, Proteomics & Bioinformatics
188 papers in training set
Top 3%
0.6%

"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.