Development of an integrated network visualisation and graph analysis tool for biological networks

There has been a 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 organisation and structure of the massive and complex biological networks formed by the interacting molecules. To that end, this paper presents a newly developed plugin for integrated network visualisation and graph analysis within the Cytoscape framework. The plugin is capable of computing and visualising a comprehensive set of node and graph level statistics. 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 customisable application that expects no prior knowledge in graph theory from users.