Arena3D: visualization of biological networks in 3D

Abstract

BackgroundComplexity is a key problem when visualizing biological networks; as the number of entities increases, most graphical views become incomprehensible. Our goal is to enable many thousands of entities to be visualized meaningfully and with high performance.ResultsWe present a new visualization tool, Arena3D, 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. The use of Arena3D is illustrated with datasets related to Huntington's disease.ConclusionArena3D is a user friendly visualization tool that is able to visualize biological or any other network in 3D space. It is free for academic use and runs on any platform. It can be downloaded or lunched directly from . Java3D library and Java 1.5 need to be pre-installed for the software to run.

On Different Aspects of Network Analysis in Systems Biology

“…Among public network management tools that currently exist to visually explore and analyse biological networks (see review in [60]) such as Arena3D [61], GEPHI [62], igraph [63] and VisANT [64] (Table 6.2), Cytoscape [65], CellDesigner [66] and Copasi [67] are the most powerful and widely used. Cytoscape (449,030 downloads as on September 2012) is the most popular software for the visualization and analysis of interaction networks.…”

Computational Tools for the Interactive Exploration of Proteomic and Structural Data

“…The most commonly used tool is certainly Cytoscape (6,7), but others such as VisANT (8), Osprey (9), BioLayout Express3D (10), Arena3D (11), and PATIKA (12) are also cited. In the commercial space, Pathway Studio is commonly used (13).…”

APCluster: an R package for affinity propagation clustering

“…AP clustering has been used successfully for clustering microarray/gene expression data (Frey and Dueck, 2007;Kiddle et al, 2010;Leone et al, 2007;Liu et al, 2010;Tang et al, 2010), in structural biology (North et al, 2011;Pandit and Skolnick, 2010;Wang et al, 2010), biological network analysis (Pavlopoulos et al, 2008;Vasblom and Wodak, 2009;Woźniak et al, 2010) and sequence analysis (Yang et al, 2010).…”