Terra's Jupyter Notebooks environment Part III: Best Practices

Anton Kovalsky
  • Updated

This article outlines recommended practices when working with cloud-based Jupyter Notebooks in Terra. For more information about the capabilities of Terra-based notebooks, see the Jupyter Notebooks section of our support knowledge base. 

Content for this article was contributed by Matt Bookman from Verily Life Sciences based on work done in Terra for AMP PD, a public/private partnership collaborating toward biomarker discovery to advance the development of Parkinson’s Disease therapies.

1. Save output to workspace storage (Google Bucket)

There are several instances where you will want or need to save output generated in an interactive analysis to the workspace bucket.

Sharing data with colleagues

The Persistent Disk associated with your workspace Cloud Environment is unique to you. To share generated data with colleagues, even colleagues who are working in the same workspace and the same notebook, you need to copy it to your workspace bucket. 

Using generated data as workflow input

Because the PD is inaccessible from outside your Cloud Environment, you need to copy any data generated in an interactive analysis to the workspace bucket to use as input for a workflow. 

Deleting the Persistent Disk

When you delete or recreate your Cloud Environment, you have the option of keeping or deleting the associated Persistent Disk. If you choose to delete the PD, ensure that any data you want to keep is copied to the workspace bucket. 

A note of caution when deleting your Cloud Environment Persistent Disk!If the current outputs are important, you should save them to your workspace bucket before re-creating your Cloud Environment Persistent Disk. To learn more, see How to transfer data between your Cloud Environment PD and workspace storage.

If you are not worried about how the outputs will change after updating your Cloud Environment, you can rerun the notebook as soon as your Cloud Environment and Persistent Disk has been re-created.

2. Re-create your cluster regularly

We recommend deleting and re-creating Cloud Environments every month or two to stay updated.

To keep track of how old your Cloud Environments are, you can navigate to the Cloud Environments section of your Terra profile.

Screenshot of profile under the main navigation menu with an arrow pointing to the Cloud Environments link under the name

Why do you need to update?

To maintain the highest standards of OS security, and to add new features, we regularly update the implementation of the Cloud Environment. Frequent updates mean you may run into trouble if a software update affects the type of environment you have set up for notebooks. To mitigate potential problems, we recommend deleting and then re-creating cloud environments every other month.

Deleting and re-creating a Cloud Environment is quick and simple! Just click on the "Cloud Environment" button in the right sidebar to open the configuration tab, and click "Delete Environment Options". 

Screenshot of Cloud Environment configuration pane with option to delete the cloud environment at the bottom left

You have the option of keeping your Persistent Disk. 

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