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Navigating Quark V3

This page explains how to access and get started with Quark V3.

Logging In

Steps:

  1. Access the Quark URL (provided by your administrator)
  2. Click Quark V3
  3. Authenticate using your corporate credentials
  4. On successful login, you will land on the Quark home screen

Once logged in, the main Quark interface consists of the following areas:

The Navigator pane is the primary way to move between Quark's modules. Key sections include:

Section Description
Pipelines Access the Dashboard, Runs, Launchpad, and My Pipelines
Dashboard Access a user curated dashboard for Workspaces and Pipelines
Workspaces Create, define and customise different workspaces for your projects
Projects View, create and add members to your organisational projects
My Files Upload, organise, and manage your data files
Apps Add and customise visualisation apps (such as Mol*) for your pipeline runs

Quark Screen

Pipelines

The primary module for discovering and executing scientific workflows. It contains four sections:

  • Dashboard — a status summary of all pipeline runs for the current calendar month
  • Runs — full run history, searchable and filterable by name, status, and time
  • Launchpad — a curated catalogue of ready-to-run pipelines across ten scientific categories (see below)
  • My Pipelines — where bioinformaticians import, build, version, and publish their own pipelines

Dashboard

The home Dashboard provides a personalised overview of the platform — displaying user-curated pipelines and workspaces for quick access to frequently used resources.

V3 Dashboard

HealthOmics Pipelines

Quark V3 integrates natively with AWS HealthOmics, offering two workflow types:

  • AWS HealthOmics Private Workflow — run your organisation's own private workflows within a secure HealthOmics environment
  • AWS HealthOmics Ready2Run Workflow — launch pre-validated, production-ready genomics workflows directly from AWS

V3 HealthOmics

Workspaces

Workspaces give bioinformaticians a fully configurable compute environment with an IDE purpose-built for writing, testing, and running analysis code directly within Quark.

Workspaces eliminate the need to configure local environments or manage compute infrastructure manually.

V3 Workspaces

Projects

Projects are the organisational unit for grouping pipelines, workspaces, data, and team members in Quark V3.

V3 Projects

Apps

The Apps module allows users to add and customise visualisation applications for interpreting pipeline outputs.

V3 Apps

My Files

My Files is the central file management area, organised into three tabs:

  • Data — input files and datasets available for pipeline runs
  • Results — outputs and artefacts from completed pipeline runs
  • Activity — a log of file-level actions and events

V3 Files