V-1. Download example dataset and notebooks

On your computer (with anaconda/ipython installed), download day3_plotting_data.tar.gz into a new directory (e.g., day3_plotting/ ) and unpack it
```
mkdir day3_plotting

cd day3_plotting
```
download the read count dataset and notebook
```
tar zxvf day3_plotting_data.tar.gz

ipython notebook
```
- Navigate to http://localhost:8888 and make a new notebook

Or, if you’d like to run ipython notebook on flux:

mkdir day3_plotting

cd day3_plotting

copy the read count dataset and notebook


cp /scratch/biobootcamp_fluxod/kitzmanj/biobootcamp/day3_plotting_data.tar.gz ./

tar zxvf day3_plotting_data.tar.gz

Start a notebook server Notes:
1. you need to know which host you’re on. The command line prompt will show this (e.g., flux-login3)
2. you need to know which port your instance of ipython listens to. The first few lines of output from ipython notebook will list this for you.

kitzmanj@flux-login3:/scratch/biobootcamp_fluxod/kitzmanj/biobootcamp$ ipython notebook --ip=flux-login3 --no-browser

[I 13:26:18.660 NotebookApp] Using MathJax from CDN: https://cdn.mathjax.org/mathjax/latest/MathJax.js
[I 13:26:19.220 NotebookApp] The port 8888 is already in use, trying another random port.
[I 13:26:19.473 NotebookApp] Serving notebooks from local directory: /scratch/biobootcamp_fluxod/kitzmanj
[I 13:26:19.473 NotebookApp] 0 active kernels
[I 13:26:19.473 NotebookApp] The IPython Notebook is running at: http://flux-login3:8889/
[I 13:26:19.473 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).

A word of warning: in general, running on the head node of the flux cluster is not a good practice, because the head node controls the job queue for the entire cluster. Instead you would want to enter the queue, login to a compute node, and do your work there.
Now, your own ipython server is running on flux. But you will need to open a tunnel to get there. The below command will securely connect port 8889 on the computer flux-login3 to port 9000 on my computer.

 ssh -L localhost:9000:flux-login3:8889 YOURNAME@flux-login.engin.umich.edu

Navigate to http://localhost:9000 and make a new notebook

Ipython notebook reminders:
- Green box - marks active cell. You are in EDIT mode.
- Hit escape to exit mode mode and go to COMMAND mode.
- In command mode:
  - A : insert new cell above
  - B : insert new cell below
  - Enter : edit the currently selected cell
  - up/down arrow : navigate up or down
- In either:
  - Shift-Enter : run the current cell
- Remember, you can run commands out of order in the notebook.