Cytoscape to D3.js Exporter What is this for? This is a Cytoscape 3 App for exporting network and its data table to D3.js compatible JSON. D3.js is a general data visualization JavaScript library, and some of its presets support network/tree style data. This App directly creates JSON file for those presets from Cytoscape network and data tables. Currently, this App supports: Network JSON for force layout (example) Tree JSON (example) How to Use Build, and install the JAR file from Cytoscape's App manager. You can export your network and its data table as JSON from File-->Export-->Network. For Tree data, you need to select root node manually (simply click the root node before exporting).