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Getting Started with Verily Workbench

The ASAP CRN Cloud serves as the central platform for discovering, accessing, and governing ASAP CRN data collections. Once access has been approved, analyses can be conducted in Verily Workbench, the preferred analysis environment for all ASAP-CRN datasets.

This guide walks you through the essentials of working in Verily Workbench, including how to access the ASAP CRN reference workspace, create and configure your own workspace, explore available resources, launch analysis apps, and connect external resources such as GitHub repositories.

New users are encouraged to start with the ASAP CRN reference workspace in Verily Workbench, which includes integrated data, documentation, and example analyses. Once familiar, you may choose to create a clean workspace and add references to approved ASAP CRN data collections for your own analyses.

1. Access

  1. Navigate to the Verily Workbench login page.
  2. Sign in using your institutional or approved credentials associated with ASAP CRN access.
  3. Once logged in, you will land on the Workbench dashboard, which lists your available pods and workspaces.

Pod required

You must belong to at least one billing pod in order to perform operations that incur costs, such as creating workspaces or running cloud apps. If you are unsure whether you have pod membership, contact your project administrator or Verily support before proceeding.

Workbench Dashboard Overview

2. Workspaces

Workspaces in Verily Workbench are collaborative environments where you can manage data, launch apps, and run notebooks. Each workspace serves as a container for your analyses, storing your data, compute environment, and version-controlled code together for easy collaboration and reproducibility.

Access the Learning Lab Workspace

The ASAP CRN Learning Lab workspace was created in conjunction with the ASAP CRN Learning Lab GitHub repository. It provides a pre-configured environment that mirrors the tutorials, scripts, and case studies included in this Learning Lab.

Open the workspace:
🔗 ASAP CRN Learning Lab

Note

The shared workspace is view-only. To run notebooks or make edits, you’ll need to duplicate it into your own project area.

Duplicating a Workspace

Duplicating the Learning Lab workspace creates your own editable copy while preserving the original as a reference. This is required for all users so you can freely explore, test, and save work without affecting the shared environment.

  1. Open the ASAP CRN Learning Lab workspace.

  2. Click the Workspace menu (⋮) in the upper-right corner.

    Duplicate Workspace Form

  3. Select Duplicate.

  4. Enter a clear name for your copy (for example, My-Learning-Lab-Sandbox).

  5. Complete the duplication dialog screens.

    Duplicate Workspace Form

  6. Click Duplicate on the final screen. It should take less than a minute for the system to duplicate the workspace and all associated resources. Your duplicated workspace will appear under the Workspaces tab in the left navigation panel.

Tip

Your duplicated workspace is fully independent. You can install packages, upload small test datasets, or modify notebooks without affecting the shared Learning Lab version.

3. Resources

The Resources tab in Verily Workbench lets you view, organize, and access data and documentation linked to your workspace. Each resource represents a connected Google Cloud Storage (GCS) bucket, dataset, or documentation file that you can browse and use in analyses.

Resources Tab Overview

Exploring and Navigating Resources

  1. From the top navigation bar, click Resources.
  2. Click Browse to open the folder tree and explore available datasets, curated tables, and metadata files.
  3. Select any file to open its details panel, where you can view size, modification date, and storage location.

Common folders in this workspace include:

  • Data – core datasets and metadata tables
  • Multi Cohort Curated Data – harmonized multi-cohort collections
  • Cohort Analysis – processed cohort-level outputs
  • Team Curated Data – data contributed by collaborating teams
  • ws_files – your personal workspace storage

Previewing and Downloading Files

Once you locate a file of interest, you can quickly view or download it without leaving the Resources tab.

  1. In the details panel, choose one of the following actions:
  2. Preview – opens a quick viewer for text, CSV, or JSON files.
  3. Download – click the ⋮ (three dots) menu next to the file name and select Download to save it locally.

Tip

To open the file in Google Cloud Platform (GCP), click Open in GCP in the upper-right corner above the details panel. This opens the linked Google Cloud Storage bucket in a new browser tab, where you can view the full directory and metadata.

5. GitHub Repositories

Your duplicated ASAP-CRN Learning Lab workspace should already have the Learning Lab GitHub repository connected. This ensures that all tutorial notebooks and example files are automatically available when you launch an App.

Note

GitHub repositories in Verily Workbench are automatically cloned to your apps to help you manage source code and stay synced with the latest materials.

Connecting a Repo

The ASAP-CRN Learning Lab is managed in GitHub and can be linked directly to your Verily Workbench workspace. You can either use the repository as-is or fork it if you plan to customize or contribute changes.

For full details on forking, reusing, and contributing with GitHub, see: 👉 Working with Github

Quick Start: Link the Learning Lab Repository If the Learning Lab repository is not already linked to your workspace (or if you want to add it manually):

  1. Open your workspace and navigate to the Apps tab.
  2. Click + Add Repository.
  3. In the Name field, enter asap-crn-learning-lab.
  4. In the Repository URL field, the repo URL:
    https://github.com/ASAP-CRN/asap-crn-learning-lab
  5. Click Add Repository to confirm and connect.

Once connected, the repository will be automatically cloned to your app environments, allowing you to access tutorial notebooks and scripts directly from within JupyterLab or RStudio.

When Should I Fork?

  • Fork the repository if you plan to modify notebooks, add content, or contribute improvements.
  • Link the upstream repository directly if you only need to explore or lightly edit notebooks without pushing changes.

(See the Working with GitHub page for details.)

6. Apps

Apps are cloud-based environments in Verily Workbench that let you run code, explore data, and manage analysis workflows. Each workspace can host multiple apps such as JupyterLab, RStudio, or Visual Studio Code, which are connected to your data and GitHub repositories.

Launching an App

  1. Open your duplicated ASAP-CRN Learning Lab workspace.
  2. In the top navigation bar, click the Apps tab.
  3. Select + New app instance.
    Create App Button
  4. In the setup dialog:
    • Name: Choose a clear name (e.g., learning-lab-python or learning-lab-rstudio).
    • App type: Select your preferred environment:
      • JupyterLab – recommended for Python-based analysis and tutorials. Can support Rstudio.
      • RStudio – for R and statistical workflows.
    • Machine type: Choose a standard configuration (e.g., n1-standard-4).
  5. Click Create App to launch.
    The app will initialize in a few minutes and appear under the Apps tab once ready.

Opening and Using Your App

Once your app is running:

  • Click your app name to launch the environment.
  • In JupyterLab, navigate to /repos/asap-crn-learning-lab/tutorials/ to open the Learning Lab notebooks.
  • Access workspace-mounted data from the ~/workspace/ directory, which mirrors the contents of the Resources tab.

Managing Your App

You can pause or delete apps from the Apps tab to manage costs or clean up environments.

  • Stop App - suspends compute billing while keeping data intact.
  • Delete App - permanently removes the app and any unsaved local changes.

Billing Reminder

Always stop your app when you’re finished working to avoid unnecessary compute costs.

For additional details, refer to the
📘 Verily Workbench Quickstart Guide – Create an App