Analyzing your data in Jupyter Notebooks

All data analyses using the All of Us dataset occur in the Researcher Workbench within notebooks. When you are ready to start analyzing your dataset, you can export it to a notebook. For additional help with analyzing your data within Jupyter Notebooks, see How to Get Started with Registered Tier Data.

 

Saving a Dataset → Exporting to Notebook

  1. Name your dataset.
  2. "Export to notebook" is selected by default. Exporting to a notebook will load this dataset into a notebook within your workspace.
  3. Select which notebook to use. You can insert the dataset into an existing notebook by selecting it from the drop-down or you can create a new one.
  4. Select which programming language you would like to use. You can “See Code Preview” to examine the differences between R and Python.
  5. Click on “Save and Analyze.”

 

If you choose to "Export to Notebook," the screen below will load. Note: It may take a few minutes depending on the size of your dataset.

 

This is your notebook. The code used to create your dataset is pre-loaded. Select "EDIT" to begin analyzing in the new code boxes below. Note: If you export multiple concept sets in a dataset to a notebook, you will still need to join the resulting data frames.

 

Opening a Notebook from the Analysis Tab

After exporting your dataset to a notebook, you will need to go to the "ANALYSIS" tab to find and open it.

Alternatively, you can create a new notebook by clicking on the  under "Create a New Notebook."

Rename, Duplicate, Delete, or Copy a Notebook

Click on the snowman to see options for your notebook. You can rename, duplicate or delete the notebook. You can also copy it to another workspace.

View, Edit, or Run a Notebook

When you first open a notebook, you will see it in read-only mode. To make changes to the notebook, select the "EDIT" option. To run the notebook, but not make any alterations, choose “playground mode.”

Note that opening a notebook can take up to 10 minutes. The Researcher Workbench platform works behind the scenes to spin up a new instance of Jupyter Notebooks.

Notebook Edit Mode

This is your Jupyter Notebook in EDIT mode.

Cells form the body of the notebook.

 Code cell
• Contains code to be executed in the kernel and displays its output below

Cells have labels on the left
• In [ ]
• In [*]
• In [1]

Markdown cell
• Contains text formatted using Markdown and displays its output in-place when it is run.

 

For additional information about Jupyter Notebooks, see our article Jupyter Notebooks and programming and also our Featured Workspace How to Backup Notebooks and Intermediate Results for information how to backup your notebooks and access earlier saved versions. You can also find more information in the following video:

 

 

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