Development of an Integrated Network Visualization and Graph Analysis Tool for Biological Networks

There has been steady increase in the amount of molecular data generated by experiments and computational methods performed on biological networks.  There is a growing need to obtain an insight into the organization and structure of the massive and complex biological networks formed by the interacting molecules. To that end, this paper presents a development of the integrated network visualization and graph analysis plugin within the Cytoscape framework. The plugin is capable of computing and visualizing a comprehensive set of node and graph level statistics, which includes the shortest path, critical path, all paths, and max flow between two nodes, mean shortest path, degree distribution, average number of interaction partners, clustering coefficient, topological coefficient, diameter of a graph and centrality. The evaluation of the plugin on a range of biological networks and its memory performance is conducted. The plugin, proven to be scalable, is an interactive and highly customizable application that expects no prior knowledge in graph theory from the user.

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