What does Cytoscape Web do?
Cytoscape Web is a network visualisation library that you can use to embed networks onto a webpage. It is not a stand alone application for users; it is a tool for developers to display networks on the web.
What are the minimum system requirements for end users?
End users need a modern browser with the Flash plugin installed. Cytoscape Web is tested on the latest versions of Chrome (OS X, Windows, Ubuntu), Firefox (OS X, Windows, Ubuntu), Safari (OS X), and Internet Explorer (Windows).
What is the license of Cytoscape Web?
Cytoscape Web is an open source project under the LGPL.
How do I reference Cytoscape Web?
What development skills should I have to use Cytoscape Web?
What technologies is Cytoscape Web made from?
Do I need to be a Flash developer to use Cytoscape Web?
I tried to open the Cytoscape Web SWF file. Why doesn't it work?
I copied the example from the tutorial and it doesn't work! Why?
Set your Flash security settings properly, or deploy the HTML file to a webserver, like Apache.
What network formats does Cytoscape Web support?
My favourite network format isn't supported? What can I do?
You can either write some code that translates your networks into a supported format on-the-fly, or you could add it to Cytoscape Web itself. Cytoscape Web is an open source project, so feel free to check out the source and try things out!
Yes, see the API reference for more information.
Can I modify the network programmatically?
Can I load a network from a URL?
Interacting with Cytoscape Web
I added a listener, changed the data schema, filtered, or called some function on Cytoscape Web. Why isn't it working?
You need to call new, ready, and draw in that order with interactions with Cytoscape Web within the ready callback. All interaction with Cytoscape Web has to occur within the callback function passed to the ready function. See the tutorial for an example.
What formats can I export the network to?
How do I make a node edge link to somewhere?
You can perform any action you want on mouse click of a node or edge. See the documentation for more information
Customizing visual styles
What options do I have to change the visual style?
See the API reference.
Can I change the visual style after the network has been drawn?
Yes, use visualStyle.
How do I set the visual style to be dependent on the network data?
Use a mapper.
Can I set the edge length to be dependent on an attribute?
Not precisely. You can use an edge weighted layout, but the lengths will only be approximate based on the weight attribute.
Can I load images into Cytoscape Web?
Yes, but only for nodes. See the VisualStyle object for more.
Modifying network data
How do I change node or edge attribute values after the graph is drawn?
How can I add a new node or edge attribute to an existing network?
How can I delete a node or edge attribute?
How can I add nodes and edges to an existing network?
How can I delete nodes and edges from a network?
What layouts does Cytoscape Web support?
See the API for details.
Can I customize the layout parameters?
Yes, see the API for details.
Why is the force-directed layout not animated?
It's computationally expensive such that large networks become unresponsive even on modern computers.
Does the force-directed layout support an edge-weighted option?
weightAttr in the API.
Can I use my own custom layout algorithm?