While working on jQuery Mobile Framework project, I had already used Prototype library for some features in the application. But jQuery and Prototype refused to play ball and application broke.
The issue was shortcut or both jQuery and Prototype and both use $.
Luckily, jQuery foresaw such scenario and already planned for library conflicts and has easy solution. The no-conflict mode allows you to define your own shortcut, and of course it worked. I did not need to touch Prototype at all.
You can rename the $ shorcut by a new name easily like this:
//place this code anywhere in your code inside scripts tags
var myJQ = jQuery.noConflict();
//so you will use it like this
Hope that helps.