Cytoscape

Cytoscape is an application used for the integration, visualization, and data analysis in networks. With this application, users can easily give a form to and visualize complex networks and integrate these with other attribute data. Apps or plugins can be used in conjunction with this application to add functionality to networks. This application is primarily used in systems biology, proteomics, molecular biology, and genomics, but it may also be utilized in other fields dealing with networks, such as the social sciences.

Molecular biologists can use this program to load genetic and molecular interaction data sets in standard annotation and network file formats such as SIF, GraphML, OBO, GML, and BioPAX, among others. This tool enables users to perform advanced analysis as well as modeling through the Apps, and establish visual maps across their data. Social scientists can also use this program to visualize and analyze data pertaining to large social networks. The data can be assembled from tables containing the networks of interpersonal relationships.

Cytoscape has an easily navigable interface. The toolbar contains the command buttons. At the upper right portion of the window is the Main Network View window where users can see the network data. The left portion displays the Control Panel, which contains tabs. Users can see the list of available networks from the Network tab in this panel.