Visualization and Statistics (notebooks)

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A Jupyter Notebook is an open-source web application that allows you to create and share documents that contain live code, equations, visualizations and narrative text. Uses include: data cleaning and transformation, numerical simulation, statistical modeling, data visualization, and machine learning. Terra supports notebooks with R and Python kernels.

• Terra's Jupyter Notebooks environment Part I - Key components

  This article is to help enhance your ability to do interactive analyses - with a deeper understanding of key components (i.e. Billing Projects) in Terra's notebooks environment. A second article addresses key operations and how they impact your wo...
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• Terra's Jupyter Notebooks environment Part II: Key operations

  This article walks through what happens when you perform key operations with your notebooks. Understanding what is happening behind the curtain can help your process to be more efficient and avoid pitfalls (such as overwriting collaborator's work ...
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• "Edit" and "Playground" Notebook Modes

  Attention: If using a Notebook Runtime Environment created before August 1, 2019, the new "Edit" and "Playground" modes are incompatible and further action is required. Please keep reading for next steps. Otherwise, please skip ahead to the "What ...
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• Protecting data from an old notebook runtime (cluster)

  1. Identify notebooks in old clusters To see what notebook VMs you created under each billing project, and when you created them, go to https://app.terra.bio/#clustersSee a virtual machine or cluster created before August 1st? Note the Billing Pro...
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• Copying notebook output to a Google bucket

  Data generated by running an analysis in a Jupyter notebook is saved to the disk associated with the virtual notebook runtime. When the runtime is deleted, the data are as well. To transfer data generated within a notebook to more permanent storag...
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• Notebooks 101: How not to lose data output files or collaborator edits

  If you remember the days before Google docs, when you could work for hours on a paper only to have it vanish if your computer shut down and you hadn't saved it, you know firsthand the pain of losing work you thought was safe. Notebooks are wonderf...
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• Changing data file directories

  To help collaborators avoid overwriting each other's work in a notebook, we’re releasing new functionality that locks a notebook when it is in use by another user. At the same time, we’re adding a 'playground mode' that lets users run and explore ...
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• Viewing IGV tracks of BAM files in your workspace data

  This article explains three ways you can use the Integrative Genomics Viewer (IGV) to examine tracks from BAM (.bam) files in Terra. From the workspace Data tab By adding a startup script to a notebook runtime creation From the IGV web app   1...
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• What you need to know about notebook auto-pause

  To prevent runaway charges when no computational work is being done in a notebook, runtime environments will automatically pause when there is no web browser or kernel activity for 30 minutes . This article explains how auto-pause on Terra works b...
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• Manually setting auto-pause for notebooks using gsutil

  Occasionally, users may want to manually adjust the default auto-pause time (30 minutes). To do this without restarting the runtime environment (simultaneously losing outputs and any newly loaded programs), you can send a PATCH command on a curren...
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• Adjusting autopause for notebooks using Swagger

  Occasionally, users may need to extend the default autopause time (30 minutes) to accommodate long-running jobs. To do this without restarting the cluster (simultaneously losing outputs and any newly loaded programs) is to send a PATCH command on ...
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