ABSTRACT
VisANT is a free, online software platform used for integrative visualization, modeling, and analysis of biological networks. VisANT was developed in an effort to model the cell as an interconnected information network, with molecular components linked with one another in topologies that can encode and represent many features of cellular function. This networked view of biology brings the potential for systematic understanding of living molecular systems (Hu, Mellor, and DeLisi 2004; Hu et al. 2004, 2005, 2007b). Important features that VisANT offers to the research community are (1) exploratory navigation of integrated database-driven interaction and association networks; (2) multi-scale visualization, manipulation, and storage of known and/or user-defined networks with integrated hierarchical knowledge; (3) the ability to perform data mining and basic graph operations on arbitrary networks and subnetworks, including loop detection, degree distribution (the distribution of edges per node), and exhaustive shortest path identification between various component genes or proteins; and (4) expression visualization and analysis in the network context. Unlike other network visualization tools, VisANT provides fundamental data integration services driven by the Predictome database (Mellor et al. 2002), such as name resolution, which greatly lessens the burden of integrating data from various sources (Hu et al. 2008). For example, expression data can automatically be mapped to the appropriate nodes in a network once the Name Resolution function has been applied to its nodes, regardless of the different naming conventions used in expression and network data, respectively.
