Hi Alvin,
The samples are currently configured to be run against the latest development sources (version 3.1.0-SNAPSHOT). To run them without modification, you should be using app-developer from the develop branch:
Just run mvn clean install, and it'll create a development distribution of Cytoscape 3.1.0-SNAPSHOT in the "target" directory.
If you want to run the samples against 3.0.1, change your dependencies to use version "3.0.1". You'd normally do this by changing the <cytoscape.api.version> property at the top of pom.xml.
Hope this helps,
Jason