If you have recent IPython, for example v3.0.0 or higher, and you see only sporadic success of this method, you need to connect to the RequireJS dependency loader and put it in your common.js :
require(['jquery'], function($) { $('#header-container').hide(); });
common.js loads at the bottom of the page, so there is no need to wait for the DOM ready event, i.e. $(function() { ... }) .
For further discussion, see my answer in Disable automatic closing brackets in ipython and its comments.
chbrown
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