Table 1.
A summary of the criteria that would define a general genomics workbench environment, and suggested implications on technical requirements.
Table 2.
Summary of specific technical solutions used to meet the design requirements of the GVL.
Fig 1.
The GVL launch process for starting self-launched instances of the GVL workbench.
(a) A user initiates the launch process via the launch service (launch.genome.edu.au) by providing their cloud credentials to the launcher application and (b) within a few minutes is able to access the management interface (CloudMan) on the deployed instance of the workbench. (c) After workbench services have started, the researcher can use the applications as desired (e.g., Galaxy).
Fig 2.
A screenshot of the GVL Dashboard.
The GVL Dashboard is a portal running on every GVL instance. It lists all of the available services, their status, and offers a direct link to access those.
Fig 3.
An evolution of the data analysis solutions for genomics.
Initially, standalone and purpose-specific tools were most prevalent. As the complexity of analyses grew, new platforms formed that aggregate many standalone tools and support different types of computational infrastructures to offer more versatile functionality. The GVL represents another step in this evolution where it aggregates a large number of the best-of-breed software and technologies available today.
Fig 4.
Three basic architectural layers composing the GVL workbench.
The GVL leverages cloud resource and is compatible with multiple cloud technologies. Through a set of cloud resource management tools, the details of cloud resources are hidden enabling non-cloud aware applications to readily execute in this environment.
Fig 5.
Architectural components of the GVL’s management layer.
Each GVL instance is, at runtime, composed of a number of components that the GVL provides: a virtual machine image, a volume snapshot or an archive of the tools file system, and a snapshot or a hosted instance of the indices file system. Combined at runtime by CloudMan into a virtual cluster, the components enable a flexible and feature-full bioinformatics workbench.