Notebooks, terminals and Unix

Once you've logged in, the syzygy service will start a server for you, which is the computing service you are accessing. (If it doesn't start automatically, click on the "Start Server" button.) Once the server is running, you will be presented with a list of files and folders that exist in your account. This is called the Hub, and is a view like the Finder on a Mac, or the File Explorer on a Windows computer.

From this Hub, you can click on files and folders to open them, you can select them and take actions like renaming them, duplicating them, or removing them. Some of the files will have the suffix .ipynb, which stands for "iPython Notebook." Despite the name, the Notebook might have nothing to do with Python -- it is there for historical reasons.

Notebooks are files containing formatted text, math formulas, and computer code. Most of the time you will be creating and working with Notebooks in syzygy, Each Notebook has a collection of cells, which you create, edit and run.

So keep this as your focus for your work -- you will work in Notebooks, and you will create pieces of text, math, and code to use.

However, sometimes you need to know that in the background of the Jupyter Hub is a Unix machine that does all the work. In the PIMS case, this is running on hardware from Compute Canada, or Cybera.

To access the Unix shell, you can open a terminal from the Hub, and do all the usual Unix bash shell operations. You can't access superuser commands (sudo, etc.) but you can do just about everything else you like in Unix. If you are an experienced Unix user, feel free to open a terminal and browse around.

Personally, I try to avoid using the Unix shell, but there are times when it is a must. (For instance, to install certain packages, or to access files on Github or on remote machinces.) There are notes on how to do this later in this book.