Cytoscape is the worldwide standard open-source platform for network visualization and data integration. This project, which we started at the Institute for Systems Biology in Seattle, provides a universal, customizable tool for the network-based visualization and analysis of large-scale datasets. The Cytoscape core software is now co-developed in the United States, Canada, and Europe, and is regarded as an innovative model for scientific collaboration. As part of the NIH-funded National Resource for Network Biology, we currently extend Cytoscape towards the learning of networks from omics data. Our Cyni network inference toolbox for Cytoscape 3 provides an infrastructure for the inference of networks from global measurements, such as transcriptomics.