• About this Book
    • Skills Level
    • AnVIL Collection
  • 1 Introduction
    • 1.0.1 What Is AnVIL?
    • 1.0.2 Does AnVIL Cost Money?
    • 1.0.3 Where Can I Get Help?
    • 1.0.4 How to Use This Book
    • 1.0.5 Activate scroll_highlight Feature
  • Account Setup
  • 2 PIs and Lab Managers
    • 2.1 Account Setup Overview
      • 2.1.1 Goals for This Guide
      • 2.1.2 Design Philosophy
      • 2.1.3 Before You Start
      • 2.1.4 Starting Setup
      • 2.1.5 Lab Management Roles
    • 2.2 Step 1: Create a Google Account
    • 2.3 Step 2: Set Up Google Billing
      • 2.3.1 Create a Google Billing Account
      • 2.3.2 Add Users or Viewers (optional)
    • 2.4 Step 3: Add Terra to Google Billing Account
    • 2.5 Step 4: Create Terra Billing Projects
      • 2.5.1 Create a Billing Project
    • 2.6 Step 5: Set Budgets and Alerts
      • 2.6.1 Set Alerts
      • 2.6.2 View spend
      • 2.6.3 Export Cost Data to BigQuery
    • 2.7 Step 6: Add Users and Workspaces
      • 2.7.1 Create a New Workspace
      • 2.7.2 Add Members to Workspaces
      • 2.7.3 Request Quota Increase
    • 2.8 Wrap-Up
  • 3 Data Analysts
    • 3.1 Account Setup Overview
      • 3.1.1 Goals for This Guide
      • 3.1.2 Starting Setup
    • 3.2 Step 1: Create a Google Account
    • 3.3 Step 2: Set Up Terra
    • 3.4 Step 3: Link External Accounts (optional)
    • 3.5 Wrap-Up
  • 4 Consortia
    • 4.1 Account Setup Overview
      • 4.1.1 Goals for This Guide
      • 4.1.2 Choosing a Role
      • 4.1.3 Consortia Responsibilities
    • 4.2 Consortium Data Managers
      • 4.2.1 Managing Security and Privacy Policies
      • 4.2.2 Account Setup
      • 4.2.3 Two Factor Authentication
      • 4.2.4 Set Up Terra Authorization Domains
      • 4.2.5 Granting Access
      • 4.2.6 Revoking Access
    • 4.3 Consortium PIs and Lab Managers
      • 4.3.1 Be Aware of Security Policies
      • 4.3.2 Account Setup
      • 4.3.3 Two Factor Authentication
    • 4.4 Consortium Data Analysts and Researchers
      • 4.4.1 Be Aware of Security Policies
      • 4.4.2 Account Setup
      • 4.4.3 Two Factor Authentication
    • 4.5 Consortium Data Submitters
      • 4.5.1 Be Aware of Security Policies
      • 4.5.2 Account Setup
      • 4.5.3 Two Factor Authentication
    • 4.6 Wrap-Up
  • Working on AnVIL
  • 5 Workspaces
    • 5.1 Access Your Workspaces
    • 5.2 Clone an Existing Workspace
    • 5.3 Create a New Workspace
    • 5.4 Add Members to Workspace
  • 6 Jupyter Notebook
    • 6.1 Jupyter Notebook: Video tutorial
      • 6.1.1 Objectives
      • 6.1.2 Slides
  • 7 Galaxy
    • 7.1 Galaxy: Video tutorial
      • 7.1.1 Objectives
      • 7.1.2 Slides
    • 7.2 Galaxy: Step-by-step guide
      • 7.2.1 Starting Galaxy
      • 7.2.2 Navigating Galaxy
      • 7.2.3 Deleting Galaxy environment
  • 8 RStudio
    • 8.1 RStudio: Video tutorial
      • 8.1.1 Objectives
      • 8.1.2 Slides
    • 8.2 RStudio: Step-by-step guide
      • 8.2.1 Launch RStudio Cloud Environment
      • 8.2.2 Tour RStudio
      • 8.2.3 Pause RStudio
      • 8.2.4 Delete RStudio Cloud Environment
  • 9 Data
    • 9.1 Bring Your Own Data
      • 9.1.1 Overview
      • 9.1.2 Browser: Upload Single Files
      • 9.1.3 Browser: Upload Folders
      • 9.1.4 gsutil: Local to Cloud
    • 9.2 Analyze Existing Data
      • 9.2.1 AnVIL Data Library
      • 9.2.2 AnVIL Dataset Catalog
      • 9.2.3 Gen3 Data Explorer
  • 10 Workflows
    • 10.0.1 Pre-configured Workflow
    • 10.0.2 Create a Custom Workflow
  • Appendix
  • A FAQs
    • A.0.1 What is AnVIL?
    • A.0.2 How Do I Get Started?
    • A.0.3 What Data Is Available?
    • A.0.4 How Do I Perform an Analysis?
    • A.0.5 Where Can I Get Help?
  • B Troubleshooting
    • B.0.1 Create Terra Billing Project
  • C Authorization Domains
  • D Budget Templates
    • D.0.1 Types of Costs
    • D.0.2 Usage of Budget Templates
  • E IRB Templates
    • E.0.1 General Information
    • E.0.2 Description of AnVIL
    • E.0.3 Data Storage
    • E.0.4 Privacy and Confidentiality
    • E.0.5 Security
    • E.0.6 Example Language for Informed Consent
    • E.0.7 Additional Resources
  • F Overview Videos
  • G Give us Feedback
  • About the Authors
  • This content was published with bookdown by:

    The Johns Hopkins Data Science Lab

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Getting Started on AnVIL

3.4 Step 3: Link External Accounts (optional)

AnVIL provides access to a wide selection of datasets, including controlled-access data. Linking your accounts will enable you to import these data into Terra.

The following links will take you to the Terra documentation for setting up and linking external accounts.

  • Set up a Gen3 account - allows you to use the Gen3 data explorer to create artificial cohorts over AnVIL datasets that have been indexed by Gen3.
  • Link Gen3 and Terra accounts - allows you to analyze Gen3 data on Terra.
  • Link Terra and eRA Commons ID - To use controlled-access data on Terra, you will need to link your Terra user ID to your authorization account (such as a dbGaP account). Linking to external servers will allow Terra to automatically determine if you can access controlled datasets hosted in Terra (ex. TCGA, TOPMed, etc.) based on your approved dbGaP applications.

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