Arena3D statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Arena3D

Tool usage distribution map

This map represents all the scientific publications referring to Arena3D per scientific context
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Associated diseases


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Arena3D specifications


Unique identifier OMICS_04116
Name Arena3D
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Maria Secrier

Publications for Arena3D

Arena3D citations


Urinary proteomics and metabolomics studies to monitor bladder health and urological diseases

BMC Urol
PMCID: 4802825
PMID: 27000794
DOI: 10.1186/s12894-016-0129-7

[…] e summarized. The major network-based visualization tools include VANTED (, VisAnt (, Metscape2 (, Arena3D ( and MetaMapR []. In order to construct a disease-perturbed network, several softwares and integrative querying systems for interaction information (PSICQUIC), network modeling a […]


The Human Plasma Membrane Peripherome: Visualization and Analysis of Interactions

Biomed Res Int
PMCID: 4095733
PMID: 25057483
DOI: 10.1155/2014/397145

[…] ating the layer of diseases. The drugs were also classified in 28 groups based on the drug category in which they belong (e.g., anticoagulants). The network created by these data was visualized using Arena3D [, ]. Arena3D uses staggered layers in 3D space, allowing the user to group related data into separate layers, in this case, the proteins, the drugs, and the indications/diseases. All data fro […]


Visualization of protein interaction networks: problems and solutions

BMC Bioinformatics
PMCID: 3548679
PMID: 23368786
DOI: 10.1186/1471-2105-14-S1-S1

[…] th an appropriate syntax and structure to define nodes and edges). The outcomes produced by Medusa can be exported as image or postscript files, html parameters, or in a format compatible with Pajek, Arena3D, Cytoscape and GraphViz.• Extensibility: At the moment the latest Medusa version does not have some functionality such as a plug-in manager that allows users to add further features in order t […]


Using graph theory to analyze biological networks

BioData Min
PMCID: 3101653
PMID: 21527005
DOI: 10.1186/1756-0381-4-10

[…] xpression profiles and coexpression detection. Many visualization tools [] such as Medusa [], Cytoscape [], Pajek [] and many others [] visualize networks in both 2D and 3D, but very few of them like Arena3D [] try to bridge the gap between clustering analysis and visualization. […]


A survey of visualization tools for biological network analysis

BioData Min
PMCID: 2636684
PMID: 19040716
DOI: 10.1186/1756-0381-1-12

[…] r biological pathways [], Pathway Studio [], GenePath [], PathScout [], MAPMAN [], MetaShark [], CnPlot [], CLANS [], GSCope [], BicOverlapper [], Celestial3D [], MetaNetter[], HyperGraph, VANTED [], Arena3D, SpectralNET [], TouchGraph Google Browser, VisLink [], SpectralNET [], CnPlot []. Before this new generation of visualization tools became available Otter [], Plankton [], GraphViz, Tulip[], […]

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Arena3D institution(s)
Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany

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