You can use a virtualenv for your IPython notebook. Follow these steps:
Install the ipython kernel module into your virtualenv:
workon my-virtualenv-name # activate your virtualenv, if you haven't already pip install tornado==4.5.3 pip install ipykernel==4.8.2
You should now be able to see your kernel in the IPython notebook menu:
Kernel -> Change kerneland be able to switch to it (you may need to refresh the page before it appears in the list). IPython will remember which kernel to use for that notebook from then on.