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.

• Customizing your interactive analysis application compute

    When running an interactive application - such as a Jupyter notebook - in Terra, you can adjust the configuration of your virtual "application compute" to fit your computational needs. Customizing allows you to balance cost and functionality, a...
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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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• 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

  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. Content for this article was contributed...
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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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• "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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• 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

  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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• 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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• 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 for up to 24 hours when there is no web browser or kernel activity for 30 minutes. This article explains how auto-paus...
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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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