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William J.R. Longabaugh (Institute for Systems Biology, Seattle, WA USA)
BioTapestry and BioFabric are two open-source network visualization tools being developed at the Institute for Systems Biology. BioTapestry is a well-established tool for building, visualizing, and sharing models of gene regulatory networks (GRNs), with particular emphasis on the GRNs that drive development. Work on BioTapestry is ongoing: a major feature of Version 6.0 allows the user to lay out a high-level block diagram of the network, and the software handles the detailed layout. BioTapestry has also served as the inspiration for a new network visualization tool released in late 2012 called BioFabric. BioTapestry uses "link trees" (orthogonal directed hyperedges) of contrasting colors to maximize clarity and organization of the GRN. BioTapestry's approach has morphed into a novel technique that can be used in very large, general, undirected graphs: the new BioFabric tool depicts nodes in a network as horizontal lines, one per row. Edges are then presented as vertical lines, each arranged in a unique column. This technique allows edges to be organized in a meaningful way that can provide much greater insight into network structure than the traditional node-link diagram.