GraphExplore is a stand-alone Java environment for dynamically displaying graphs of nodes and edges; it runs on any operating system that has a Java virtual machine installed. GraphExplore provides various displays of nodes/vertices of a graph with undirected or directed edges, and a number of additional features. Inputs are text files: a files with names/descriptors of the nodes of the graph, a file defining the edges/arrows between nodes, and an optional "cluster" file that identifies groups of nodes for colour coding.

GraphExplore is able to dynamically retrieve information about the objects in the network from the internet. You can either specify a relevant URL for each object or let GraphExplore query a relevant website with key words identifying objects of interest. The program creates displays using neato from AT&Ts GraphViz open source graph drawing software as well as modified versions of the layout libraries available from Java Universal Network/Graph Framework (JUNG). Once a project is loaded, you can modify and query the graph. The facilities include options to query "linking" nodes, defines weights/relevances on edges, move nodes around, and delete nodes. GraphExplore dynamically displays information about the neighbours and links of nodes, generates edge reports summarizing the information contained in an image, and save or print graphs.

In GraphExplore you can define various node colours and shapes and assign different features to nodes in clusters. GraphExplore has a range of other features to compare graphs, as well as a help file and tutorial.

Figure 1. A graph representing gene expression associations: nodes are genes and edges represent statistical associations in an analysis of gene expression data in breast cancer tissues. Target genes whose names were searched are shown in red, while linkers between these genes are green.