#Topological features using cytoscape 3.2.1 software
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks.
Shannon P, Markiel A, Ozier O, Baliga NS, Wang J, Ramage D, Amin N, Schwikowski B, and Ideker T. CellDesigner: a process diagram editor for gene-regulatory and biochemical networks. Connections, 1998, 21:47–57.Īkira F, Mineo M, Hiroaki K, and Naoki T. PAJEK – Program for large network analysis. It also describes the development of a plugin used to investigate a particular research question in systems biology and walks through an example analysis using Cytoscape. This chapter discusses what Cytoscape does, why it was developed, and the extensions numerous groups have made available to the public. This community of users and developers has worked together since Cytoscape’s initial release to improve the basic project through contributions to the core code and public offerings of plugin modules. Plugins represent collections of community-contributed functionality and can be used to dynamically extend Cytoscape functionality. Cytoscape’s flexibility has encouraged many users to adopt it and adapt it to their own research by using the plugin framework offered to specialize data analysis, data integration, or visualization. Its development and use has been focused on the modeling requirements of systems biology, though it has been used in other fields. Cytoscape is a general network visualization, data integration, and analysis software package.
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