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What Are Jupyter Notebooks?


Launching Jupyter on Sagehen HPC


Figure 1

Pomona College single sign-on login page showing username and password fields
Pomona College sign-in page for OnDemand access

Figure 2

Pomona College OnDemand dashboard showing Interactive Apps sidebar with pinned applications
OnDemand dashboard showing pinned apps and navigation menu

Figure 3

OnDemand Interactive Apps dropdown menu with Jupyter Notebook highlighted among other applications
Interactive Apps dropdown showing Jupyter Notebook option

Figure 4

OnDemand Jupyter Notebook launch form with fields for partition, Jupyter version, number of hours, CPU cores, and memory
Jupyter Notebook launch form showing resource request options

Notebook Interface Basics


Figure 1

OnDemand session card showing Jupyter Notebook job in Starting state with session details and time remaining
Session starting with status card showing job details

Figure 2

OnDemand session card showing Jupyter Notebook job in Running state with green Connect to Jupyter button
Session running with Connect to Jupyter button

Figure 3

JupyterLab interface showing file browser on the left and Launcher tab with Notebook, Console, and Other sections including Python 3, ipyrad, and Python Data Visualization kernels
JupyterLab interface showing the Launcher with notebook, console, and other options

Figure 4

OnDemand session card showing Jupyter Notebook session in Completed state with message that the card will be retained for 7 more days
OnDemand session card showing completed status

Working with Cells


Figure 1

A JupyterLab notebook. The upper cell holds markdown source with a heading, Methods and Results sections and a bullet list. Below it the same cell is shown rendered as formatted text, with Analysis of Temperature Data as a heading, a short paragraph, and bulleted mean, maximum and minimum values.
A markdown cell before and after running it: the source on top, the formatted result below.

Figure 2

JupyterLab interface with the file browser on the left showing home directory folders and the Launcher on the right with Python 3 ipykernel notebook option
JupyterLab interface showing file browser and notebook area

Figure 3

JupyterLab toolbar cell type dropdown menu expanded showing dash, Code, Markdown, and Raw cell type options
Cell type dropdown showing Code, Markdown, and Raw options

Figure 4

JupyterLab Run menu expanded showing options including Run Selected Cell, Run All Cells, and Restart Kernel and Run All Cells with keyboard shortcuts
Run menu showing cell execution options and keyboard shortcuts

Figure 5

JupyterLab notebook showing three code cells with execution numbers: cell 1 sets x equals 5, cell 2 prints x showing output 5, cell 3 sets x equals 10
Code cells showing execution numbers In[1], In[2], In[3] with variable assignments and print output

Python Fundamentals in Notebooks


Data Analysis in Notebooks


Visualization in Notebooks


Figure 1

JupyterLab notebook with Python code importing numpy and matplotlib, creating a sine wave plot that displays inline below the code cell
Notebook showing Python code with matplotlib and a rendered sine wave plot

Managing Kernels and Environments


Figure 1

JupyterLab Restart Kernel dialog asking Do you want to restart the kernel of Untitled.ipynb with Cancel and red Restart buttons
Restart Kernel confirmation dialog

Figure 2

JupyterLab Select Kernel dialog showing available kernels including ipyrad, Python Data Visualization, and Python 3 ipykernel under Start python Kernel section
Select Kernel dialog showing available Python kernels

Figure 3

JupyterLab Launcher showing three notebook kernel options: Python 3 ipykernel, ipyrad, and Python Data Visualization
JupyterLab Launcher showing available notebook kernels

Sharing and Exporting Notebooks


Figure 1

JupyterLab File menu expanded showing Save and Export Notebook As submenu with options including HTML, PDF, Executable Script, and more
File menu showing Save and Export Notebook As with format options

Best Practices