Key steps for visualizing a large-scale biological network using Cytoscape 3.0. (A) Loading the network data from a tab-delimited text file. (B) Creating a preliminary view of the network. (C) Organizing the network using the edge-weighted spring-embedded layout. (D) Adjusting the visual appearance of the network by changing color, shape, size, and transparency of nodes and edges. (E) Loading customized functional annotations as node attributes. (F) Adjusting node appearance based on node attributes.