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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


Empirical Comparison of Visualization Tools for Larger Scale Network Analysis

PMCID: 5540468
PMID: 28804499
DOI: 10.1155/2017/1278932

[…] the field, 2d standalone applications like graphvizdb [], ondex [], proviz [], vizant [], guess [], ucinet [], mapman [], patika [], medusa [], or osprey [] as well as 3d visualization tools such as arena3d [, ] and biolayout express [] already exist. each of them is designed to serve a different purpose. for example, ondex is implemented to gather and manage data from diverse and heterogeneous […]


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

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

[…] 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 […]


Visualizing time related data in biology, a review

PMCID: 4171679
PMID: 23585583
DOI: 10.1093/bib/bbt021

[…] and can be visualized using techniques described in the previous sections. one tool that goes further in the direction of simultaneously comparing different cellular states or different tissues is arena3d [, ] (c). tissues and their respective phenotypes can be visualized on different layers in 3d, highlighting the corresponding gene networks for each tissue and enabling comparison and linking […]


Using graph theory to analyze biological networks

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

[…] 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., protein-protein interaction (ppi) networks [] are very diverse and it is difficult to come to general conclusions […]


A survey of visualization tools for biological network analysis

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

[…] 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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