Adding slide up and slide down effect

In the css file of a custom theme I added some rules for positioning the message box at the bottom of the page. I am trying now is to implement the effect of slide up and the slide down. The slide up is working fine, but when the OK button is clicked, the message box disappears. Do I have to change something on the module php code(make a patch) or work only with the javascript file?
Thanks in advance!