GUIdock-VNC: Using a graphical desktop sharing system to provide a browser-based interface for containerized software

Abstract

Background: Software container technology such as Docker can be used to package and distribute bioinformatics workflows consisting of multiple software implementations and dependencies. However, Docker is a command line–based tool, and many bioinformatics pipelines consist of components that require a graphical user interface. Results: We present a container tool called GUIdock-VNC that uses a graphical desktop sharing system to provide a browser-based interface for containerized software. GUIdock-VNC uses the Virtual Network Computing protocol to render the graphics within most commonly used browsers. We also present a minimal image builder that can add our proposed graphical desktop sharing system to any Docker packages, with the end result that any Docker packages can be run using a graphical desktop within a browser. In addition, GUIdock-VNC uses the Oauth2 authentication protocols when deployed on the cloud. Conclusions: As a proof-of-concept, we demonstrated the utility of GUIdock-noVNC in gene network inference. We benchmarked our container implementation on various operating systems and showed that our solution creates minimal overhead.

Building Containerized Workflows Using the BioDepot-Workflow-Builder

“…Jupyter notebooks (Kluyver et al, 2016) can also be used to interactively execute, visualize, and document part of the pipeline while remaining within the Bwb sandbox. This functionality is achieved using methodologies derived from our GUIdock-X11 (Hung et al, 2016) and GUIdock-VNC (Mittal et al, 2017) to directly export graphics created by a module to the browser window.…”

Cloud-enabled Fiji for reproducible, integrated and modular image processing

“…The major technical challenge to porting desktop based image analyses applications to the cloud is to support the same graphical interface and display on the cloud that one would see on a laptop or desktop. Bwb supports two methodologies for accomplishing this using software containers [6, 7]. We combine both methods in Bwb to allow the user to export graphics from a container that functions both on a local laptop and on a remote cloud server.…”

“…This requires software on the client to process these commands and draw the screen. The other approach is to draw the screen and then export the resulting frames using a VNC protocol (Mittal et al, 2017). This also requires VNC viewer software on the client to manage the transfer and buffering of the frame data.…”

Building containerized workflows using the BioDepot-workflow-builder (Bwb)

“…A graphical interface is provided through the use of our GUIdock-VNC [24] technology. Bwb is itself a container which is accessed through a browser.…”