If you want to use JQuery in your rails application but still want prototype working as well there is a simple way to make sure they play nice and work side by side. All you have to do after you include your JQuery includes code is have the following

  <script>
   var $j = jQuery.noConflict();
  </script>

Now all you have to do to use jquery is use "$j" instead of just "$" and your good to go. To use just the standard prototype library is still just "$". Simple isn't it