gistfile1.js

var timer;
var sections = [] // array of sections, could just be a jQuery selector
var i = 0;
var cycle = function (sections, i) {
	if (i < sections.length) {
		timer = setTimeout(function () {
			//animate section
			cycle(i+=1, sections)
		}, 3000)
	} else { // start again
		cycle(0, sections);
	}
}
cycle(0 , sections);

$('.bubble').click(function () {
	clearTimeout(timer);
	//animate section
});