Arena3D 2.0 – Visualization of Biological Networks in 3D

Arena3D 2.0


Arena3D is a new visualization tool, which introduces a new concept of staggered layers in 3D space. Related data–such as proteins, chemicals, or pathways–can be grouped onto separate layers and arranged via layout algorithms, such as Fruchterman-Reingold, distance geometry, and a novel hierarchical layout. Data on a layer can be clustered via k-means, affinity propagation, Markov clustering, neighbor joining, tree clustering, or UPGMA (‘unweighted pair-group method with arithmetic mean’). A simple input format defines the name and URL for each node, and defines connections or similarity scores between pairs of nodes.


Schneider (Reinhard) Group



  • Windows / Linux /MacOsX
  • Java
  • Java 3D





Maria Secrier, Georgios A. Pavlopoulos, Jan Aerts, and Reinhard Schneider.
Arena3D: visualizing time-driven phenotypic differences in biological systems.
BMC Bioinformatics 2012, 13:45.

Georgios A. Pavlopoulos, Sean I. O’Donoghue, Venkata P. Satagopam, Theodoros Soldatos, Evangelos Pafilis, and Reinhard Schneider.
Arena3D: visualization of biological networks in 3D.
BMC Systems Biology 2008, 2:104.