Fix various documentation issues

[olgabot]

• Example ipython notebooks were missing due to IPython upgrading to v3.0
• Separate downloading and reformatting shalek data to two different notebooks: getting started and recreating papers
• Add notebooks for downloading and correcting for batch effects using combat for Brainspan data
• Is it mergable?
• Did it pass the tests?
• If it introduces new functionality in is it tested?
  Check for code coverage. To run code coverage on only the file you changed,
  for example flotilla/compute/splicing.py, use this command:
  py.test --cov flotilla/compute/splicing.py --cov-report term-missing flotilla/test/compute/test_splicing.py
  which will show you which lines aren't covered by the tests.
• Do the new functions have descriptive
  numpydoc
  style docstrings?
• If it adds a new feature, is it documented as an IPython Notebook in
  examples/, and is that notebook added to doc/tutorial.rst?
• If it adds a new plot, is it documented in the gallery, as a .py file
  in examples/?
• Is it well formatted? Look at make pep8 and make lint output
• Is it documented in the doc/releases/?
• Was a spellchecker run on the source code and documentation after
  changes were made?