While I was writing a WordPress plugin for a client, it came to a situation where I need to use both jquery.min.js & prototype.js and this result in a conflict. After googling around I found this page citing the same problem. Still no luck after trying the suggested solution (jQuery.noConflict();).

It is the link in the comment from Ahsan Shahzad which save my day. Thanks!

Since both script use $()-function, I just need to be more specific on my jquery lines by adding adding the jQuery(function($){ bla; }); portion.