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.
- 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
- Open the Quark URL in a web browser.
- Enter your registered username and password when prompted.
- Upon successful authentication, you will be directed to your personalised home screen.
Navigating the TRE Interface
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, 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 from the Launchpad. 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. |
What's Next
- Datasets — Browse the data catalog, build cohorts, and request data access.
- Workstations — Request, launch, and use secure cloud-based workstations.
- Pipelines — Discover and run bioinformatics analysis pipelines.
- My Files — Upload files and download approved results.
- My Requests — Track all your pending and completed requests.