jupyter

Jupyter notebooks are a great way to organize and document analysis work flows.
A Jupyter notebooks is effectively an interactive shell/terminal that is rendered in html and displayed in a browser. Notebooks have individual cells, which can be in the kernel language (in this case, python), or in markdown (the language also used by GitHub).
A single cell can be run by hitting command-enter or shift-enter (the latter automatically advances to the next cell).
A cheat-sheet for Markdown syntax can be found here. Note that markdown cells support LaTeX equations.

Installing and starting jupyter

Users may install Jupyter notebooks in their accounts via the commands:

python -m pip install -U jupyter
jupyter notebook --generate-config

To start jupyter, type

jupyter notebook

on your command line. This will open a browser window, from which you can navigate to the notebook of choice.

To exit jupyter, hit ctrl-c twice in the terminal from which you started it. Not doing so will slow down the computer you're running on.

Tutorials

Jupyter notebook have many useful features to enhance the productivity. There exist many tutorials. A simple tutorial is by codeacademy.

Jupyter on uhura / the computing lab

On uhura, jupyter only works with chrome, so you need to start it with

jupyter notebook --browser="google-chrome"

Any other machine is configured to launch the default browser automatically.