Get Started with Data Apps-Latest

	Abbreviations Key
AIFI	Allen Institute for Immunology
CLI	command line interface
dbGaP	Database of Genotypes and Phenotypes (NIH database)
DOI	digital object identifier
EMR	electronic medical record
GCP	Google Cloud Platform
HISE	Human Immune System Explorer
IDE	integrated development environment
NIH	National Institutes of Health
PHI	private health information
UI	user interface

At a Glance

Data Apps is a dynamic platform that showcases the data and computational resources in HISE, helps scientists explore AIFI experimental data and analyses in context, validates research with certificates of reproducibility, and packages assets in a custom-designed UI. This tutorial focuses on how to build and manage a Data App after you understand what Data Apps are and what content they contain. For details, see Explore Data Apps.

Description

Data Apps are built in the Collaboration Space in AIFI, and they move to the Explore portal when they're published. Presenting your work in the Explore portal lets you showcase your work in an Allen Institute–affiliated space. A Data App is a—known as a Data App—that better represents your work and enables other scientists to explore it. All Data Apps include publications, then, but not all publications are Data Apps. For details about the Data Apps content and UI, see Explore Data Apps.

Manage Accounts

Any visitor who browses Data Apps in the Explore portal can delve into AIFI research, visualizations, or data sets. Visitors who want to re-execute portions of another scientist's certificate of reproducibility (CertPro), however, must either be HISE users or establish a Data Apps workspace guest account.

HISE Accounts

HISE users work with their respective account administrators to track costs and stay within the established For details, see Manage HISE Accounts.

Track Your Cloud Compute Spend

View Your Personal IDE Billing

Data Apps Workspaces

If you're not a HISE user, you can establish a Data Apps guest workspace account tied to your Google Cloud Platform (GCP) billing ID. For details, see Manage Data Apps Workspaces (Tutorial).

Step 1: Set Up Your GCP Billing ID

Step 2: Sign In with Google

Step 3: Agree to Terms and Authorize Billing

Step 4: Associate Your GCP Billing ID with HISE

Data Privacy

Masking metadata is part of AIFI's obligation to earn the trust of study participants who supply samples and the IRB boards tasked with protecting their confidentiality and well-being. The data trace in your Data App's CertPro can be partially masked to protect PHI:

Metadata can be masked
Raw data accessed through NIH gateways, such as dbGaP, can be masked

For details, see Use Deidentified Data.

Attribution

Proper attribution is a core principle of Open Science. Each Data App has a Study Overview that includes a Contributors section. A Data App credits authorship of data releases at all levels, including scientific insight, back-end infrastructure development, insights, datasets, and community support efforts. Data apps use DOIs to track document provenance and versioning. These unique identifiers are registered in a central database () and include metadata, such as a title and author, that helps That information can be used to create a citation recognized in the system.

Manage Assets

In the simplest terms, Data Apps consist of content wrapped in a Django UI.

File sets

A file set is a selected file collection that users want to use again or share with others. For details, see .

Notebooks

Jupyter notebook is an open-source web app that lets you create and share documents and code. For details, see the following documents:

Use Jupyter Notebooks

Work with IDE Instances

Schedule a Notebook Job

Get Jupyter Notebook Tips

Visualizations

A visualization can be a metadata visualization saved from an advanced search in HISE or a custom visualization generated by an analyst in the IDE. For details, see the following documents:

Create a Visualilzation

Build and Save Visualizations

Create Visualization Templates (Abstractions)

Certificates of Reproducibility

A certificate of reproducibility (CertPro) is a detailed record of your scientific research generated in real time to foster reliable reproducibility of study results. This step-by-step trace includes your data, scientific algorithms, computational environment, tools stack, and results.

Certificates are awarded for file sets, visualizations, and notebooks. Reports and GitHub repositories are not eligible for certification. For details, see the following documents:

Understand Certificates of Reproducibility

Explore Your HISE Certificate of Reproducibility

Style Your Data App

A Data App can contain a large number of web pages. The look and feel of those pages depends on the nature of the data and the various insights you want to highlight. The Data Apps environment offers a web content management system (CMS) for custom styling of your Data Apps components.

Use custom templates

To help you create a uniform look and feel for your Data Apps site, we offer preconfigured templates that give you a head start on styling your content.

Perform Other Functions

Search

Advanced Search lets you specify the samples, subjects, file types, or studies you want to find. For details, see the following topics:

Open Advanced Search

Find Data Files and Reports

Create or Build a Query

Use Search Results

Preview

As you build your Data App, you can click Preview any time to see how your publication will look after publication on the public Explore portal. Navigate to Collaboration Space > Publications, and find the publication you want to preview. On the publication tile, in the lower-left corner, click Preview Publication.

Location of Refresh Function	Component Updated
Update Publication page	To update report format or content, click Refresh.
Update File Sets page	To update file sets, click Refresh Files.

Refresh

Starting a publication captures the associated report and files in their current state. Use the Refresh function to apply changes after you initiate publication, as shown in the accompanying table.

Check Status

The accompanying table shows the status indicators within each publication.

Status Indicator	Component	Description
Visibility indicator	Publication	On the Update Publication page, the visibility indicator appears twice: 1. Near the lower-left corner, a radio button toggles from Unlisted (not explicitly listed and accessible only to visitors who know the DOI or full URL) to Public (listed on the public website). 2. In the info box in the right margin, the visibility indicator appears as a tag in the Visibility field.
Publication status tag	Publication	On the Update Publication page, in the info box in the right margin, the Publication Status field shows one of the following tags: In Progress (default) – Being prepared or in review Published – Publicly available Retracted – Withdrawn
Publication progress bar	Publication	Navigate to Collabortation Space > Publications, and choose the publication you want to work with. The home page for that publication opens, and a progress bar appears across the top of the screen. It's divided into thirds as follows: In Progress (default) – Being prepared or in review Under Review – Awaiting peer feedback Published – Publicly available Retracted publications return
Visualizations status	Visualizations	Navigate to Visualizations > All Visualizations. On the Tags page, each visualization is marked either DRAFT (default) or FINAL.

Upload

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat.