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Getting Started with Quark TRE

Overview

A Trusted Research Environment (TRE) on Quark is a digitally secure environment that rigorously controls the flow of data at all times. TREs add a layer of security that enables fine-grained access control over data assets, ensuring that patient data remains confidential while remaining Findable, Accessible, Interoperable, and Reusable for research — in accordance with FAIR data principles.

Data cannot leave the TRE without explicit permission from an administrator. Additionally, TREs enable full remote access to data without compromising data security and protection standards.

Quark's TRE provides researchers with a comprehensive space for data discovery, cohort building, dataset analysis, and controlled result downloads — all within a governed, audit-ready environment.

Key Capabilities

Quark's Trusted Research Environment supports the following capabilities:

  • Data Discovery: Browse and explore a catalog of clinicogenomic data assets available on the platform. Review aggregate statistics and visualisations before requesting access.
  • Cohort Building: Define subsets of data that match your study's phenotypic and genotypic criteria using an intuitive Query Builder — no coding or database expertise required.
  • Data Access Governance: Submit access requests for entire datasets or custom-built cohorts. All requests are reviewed and approved by the Data Access Committee (DAC) before access is granted.
  • Secure Workstations: Request and connect to cloud-based workstations equipped with the operating systems and analytical tools required for your research, including JupyterLab and RStudio.
  • Pipeline Execution: Discover and launch pre-configured bioinformatics pipelines from the Launchpad, or run custom analysis workflows within your workstation.
  • Controlled Result Downloads: Request the download of result files generated within the TRE. All download requests are reviewed and approved by the Project Administrator to ensure data governance.

Logging In

  1. Open your organisation's Quark TRE URL in a web browser.
  2. Click on the TRE icon on the main page.
  3. Enter your registered username (your email address) and password when prompted.
  4. Upon successful authentication, you will be directed to the TRE home screen.

Once logged in, the TRE interface provides a Navigation Menu on the left-hand side. The primary navigation items include:

Menu Item Description
Datasets Browse the data catalog, view dataset summaries, create cohorts, and submit access requests.
Workstations Request, launch, and connect to secure cloud-based workstations for data analysis.
My Requests Track the status of all your access requests, including dataset access, workstation provisioning, file uploads, and file downloads.

Typical Researcher Workflow

The following outlines the typical end-to-end workflow for a researcher using Quark's TRE:

  1. Discover Data — Browse the Data Catalog to explore available datasets and review their aggregate summaries.
  2. Build a Cohort — Use the Query Builder to define a subset of data that meets your study criteria, or request access to an entire dataset.
  3. Request Data Access — Submit an access request for your cohort or dataset. The Data Access Committee will review and approve (or reject) your request.
  4. Explore Approved Data — Once approved, browse your cohort's dashboards, including the Cohort Summary, Person Dashboard, and Specimen Dashboard.
  5. Set Up a Workstation — Request a cloud-based workstation pre-configured with the tools you need for analysis.
  6. Analyse Data — Connect to your workstation and run your analysis scripts (e.g., in JupyterLab) or launch pipelines from the Launchpad.
  7. Download Results — Request the download of your output files. The Project Administrator will review and approve each download request.

What's Next