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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, Quark TRE enables full remote access to data without compromising data security and protection standards.

Quark 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 TRE 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 your project's administrators 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.
  • Pipeline Execution: Discover and launch pre-configured bioinformatics pipelines, 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 an administrator to ensure data governance.

Logging In

  1. Open the Quark TRE URL in a web browser.
  2. Enter your registered username and password when prompted.
  3. Upon successful authentication, you will be directed to your personalised home screen.

Once logged in, Quark TRE 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, request data access, and explore approved cohort dashboards.
Workstations Request, launch, and connect to secure cloud-based workstations for data analysis. Manage workstation files and monitor resources.
Pipelines Discover, configure, and launch pre-configured bioinformatics pipelines. Monitor pipeline runs and view results.
My Files Upload data files to workstations and download approved result files from the TRE.
My Requests Track the status of all your access requests, including dataset access, workstation provisioning, file uploads, and file downloads.

Administrators see additional navigation items not covered in this guide. See the Administrator Guide for details on monitoring workstations, managing datasets and cohort access, reviewing requests, and platform configuration.

What's Next