You may be running out of memory. Java applications run in a Java virtual machine which needs to have its memory size fixed at start time. This becomes a problem if later you need more than what was initially allocated. For cytoscape 3, see this note in the user manual.

Greetings,

centiscape is usually really reliable, so I'm surprised you are having problems on such a small network. There are two things you can try:

1. You could look at plotting the values using Cytoscape's built-in plotting package (under the Tools menu)
2. You could try running Cytoscape from the console to see if you are getting some kind of error report from either Cytoscape or centiscape. Often errors aren't properly carried through to the user interface.

Hope this helps!

-- scooter