You can use the standard PeriodicalExecuter#stop /
http://api.prototypejs.org/language/periodicalexecuter.html#stop-instance_method
/ method for stopping.

And one undocumented method PeriodicalExecuter#registerCallback /
http://github.com/sstephenson/prototype/blob/master/src/lang/periodical_executer.js#L31
/ start it again. It's strange why this method isn't documented at
all. ( You could fire a ticket for that )

One thing to know though is that registerCallback don't check if the
timer was started ( and I don't like registerCallback as method name,
I always forget it :) So you could do:

<code>
PeriodicalExecuter.addMethods({
  start: function(){
    if (!this.timer) this.registerCallback();
  }
});
</code>

and have PeriodicalExecuter#start method :)

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