This showcase gives a description of Cytoscape Web and how you can use it in your webapp.
Inspired by Cytoscape's VizMapper, Cytoscape Web supports complex visual styles based on programmatic mappers. You can use continuous mappers and discrete mappers as in Cytoscape, and you can even create your own functional, custom mappers.
Cytoscape Web has many built-in layouts. You can also compute your own layout and apply it to the network. Here, you see the built-in force-directed layout.
Cytoscape Web supports XGMML, GraphML, SIF, and JSON.