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.

• Detachable Persistent Disks

  This document outlines the updated functionality of Jupyter Notebooks on Terra with the addition of a “persistent disk” to your cloud environment, as of September, 2020. Users are advised to save their data in the directory /home/jupyter-user/note...
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• Terra's Jupyter Notebooks environment Part I: Key components

  Terra provides infrastructure for running and writing interactive analyses with Jupyter Notebooks, which are files that contain analysis code and embedded documentation. This article is to help enhance your ability to do interactive analyses with ...
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• Terra's Jupyter Notebooks environment Part II: Key operations

  Terra uses a standard Jupyter Notebooks server implementation, so the interface and core capabilities are all basically the same as what you would see in any other setting. As a result, you can take advantage of the wealth of documentation and tut...
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• Terra's Jupyter Notebooks environment Part III: Best Practices

  This article outlines recommended practices when working with cloud-based Jupyter Notebooks in Terra. For more information about the capabilities of Terra-based notebooks, explore the Visualization and Statistics section of our support knowledge b...
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• Understanding and Customizing your Notebook Runtime

  Interactive applications - such as Jupyter notebooks - run on virtual machines or clusters of machines, called a "runtime." When running an interactive application in Terra, you can adjust the configuration of the your VM or cluster runtime to fit...
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• "Edit" and "Playground" Notebook Modes

  Attention: Notebook runtime environments created before August 1, 2019 are incompatible with the new "Edit" and "Playground" modes. Further action is required. Please keep reading for next steps. Otherwise, please skip ahead to the "What is a note...
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• Notebooks 101: How not to lose data stored or generated in a notebook runtime

  If you remember the days before Google docs, you know firsthand the pain of losing work you thought was safe: working for hours on a paper only to have it vanish if your computer shut down and you hadn't saved it. Notebooks are wonderful for inter...
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• Analyzing data from a workspace bucket in a notebook

  The virtual machine running a Jupyter notebook has its own storage, separate from the workspace bucket. To analyze data in your workspace bucket in a notebook, you will need to import the data to the virtual disk. Below are the two steps, and exac...
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• Using the Terminal and Interactive Analysis Shell in Terra

  With Terra's terminal interface you can execute UNIX command-line code quickly within the runtime that runs notebooks in a workspace. This allows you to perform actions like listing files, moving files to and from the notebook disk and a Google bu...
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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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• 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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• Changing data file directories

  UPDATE Oct 22, 2019: We were able to simplify how users need to change the file paths in notebooks that point to local data files. Therefore, the article below differs slightly from the email notification you may have received on October 18,2019. ...
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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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• Using the Bioconductor Docker image in Terra

  The Bioconductor Docker image is one of the current base images integrated into Terra. This guide will introduce you to the Terra Bioconductor image and how to use it with a Jupyter Notebook.  Contents Introduction to Bioconductor and the Terra B...
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• Preventing runaway costs with 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. Note that kernel activity will only prevent autopause ...
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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) you must send a PATCH command ...
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