First, you will need to have a correct python environment to use the notebook. If you don’t have an ipython 0.13 environment installed, you need to setup for whatever computer you are using. I use a Mac or a Linux VM for most of my personal work. (Linux VM/Linux/Windows for my day time job.) Here is my instruction on how I set it up on my own computer: pythonbrew_ipython.rst
Once you get the pythonbrew environment installed. Start with a clean shell. Activate the environment by
$ source "$HOME/.pythonbrew/etc/bashrc"
Now go to a clean working directory. Let’s call it “workdir”.
$ cd workdir
You will need to install “networkx” for the de Brujin group example to work.
$ pip install networkx
Then, you can clone my github repository and start IPython Notebook in a correct directory
$ git clone https://github.com/cschin/ipython_d3_mashup.git
$ cd ipython_d3_mashup/ipython_13_vis_example/
$ ipython notebook --pylab=inline
If you have a Mac OS X.8 and you don’t block any local host port, you should get your Safari browser pop up.
Click the link pointing to the “De_Bruijn_VIS” notebook. It should open the notebook. Shift-Enter to execute each cell.
The notebook does use some IPython extension mechanism to download some extra code from the github python_d3_mashup repository. Sometimes, you might need to run the notebook twice to make sure some of the extension is working.
I could put up a video instruction later if I have time. And if you damage on your computer by following these instructions, you are on your own.