GUIdock: Using Docker Containers with a Common Graphics User Interface to Address the Reproducibility of Research

Abstract

Reproducibility is vital in science. For complex computational methods, it is often necessary, not just to recreate the code, but also the software and hardware environment to reproduce results. Virtual machines, and container software such as Docker, make it possible to reproduce the exact environment regardless of the underlying hardware and operating system. However, workflows that use Graphical User Interfaces (GUIs) remain difficult to replicate on different host systems as there is no high level graphical software layer common to all platforms. GUIdock allows for the facile distribution of a systems biology application along with its graphics environment. Complex graphics based workflows, ubiquitous in systems biology, can now be easily exported and reproduced on many different platforms. GUIdock uses Docker, an open source project that provides a container with only the absolutely necessary software dependencies and configures a common X Windows (X11) graphic interface on Linux, Macintosh and Windows platforms. As proof of concept, we present a Docker package that contains a Bioconductor application written in R and C++ called networkBMA for gene network inference. Our package also includes Cytoscape, a java-based platform with a graphical user interface for visualizing and analyzing gene networks, and the CyNetworkBMA app, a Cytoscape app that allows the use of networkBMA via the user-friendly Cytoscape interface.

Approaches for containerized scientific workflows in cloud environments with applications in life science

“…There are also initiatives for standardizing containers in the life sciences such as BioContainers [11] . Containers have seen an increasing uptake in the life sciences, both for delivering software tools and for facilitating data analysis in various ways [12][13][14][15][16] .…”

GeNNet: an integrated platform for unifying scientific workflows and graph databases for transcriptome data analysis

“…Many traditional software and tools are available on Docker Hub and it is widely used with around five billion software containers downloaded from the repository up to August, 2016 (https://blog.docker.com/2016/08/docker-hub-hits-5-billion-pulls/). In Bioinformatics, there are already tools that are available as Docker software containers and explore features such as reproducibility (Hung et al, 2016; Belmann et al, 2015) or applications areas such as transcriptomics (Zichen et al, 2016). Di Tommaso et al (2015) showed that containers have a negligible impact on the performance of bioinformatics applications.…”

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

“…We have previously described and implemented GUIdock-X11 [3], an X11-based methodology for portably supporting GUI applications in containers on different platforms. While the X11-based display method can be conveniently deployed in the local environment by exposing a file socket from a container, deploying the image on a cloud and accessing it remotely is non-trivial.…”

“…Our previous work, GUIdock-X11 [3], is one of the solutions in bridging the graphical information from user and Docker containers by using the X11 common graphic interface. GUIdock-X11 passes the container X11 commands to a host X11 client, which renders the GUI.…”