Prototype requires a document object model so it only works in browsers that it supports.
Same with jQuery.
Someone got the Jasmine test running library working with UI Automation: https://github.com/shaune/jasmine-ios-acceptance-tests
You’re on your own though if they don’t work. UI Automation doesn’t have the same kind of robust debugging environment that you get with, say, the Chrome developer tools. I’ve found it better to use simpler libraries and move slow.