#Use kitematic to link containers full#
Kristiyanto gratefully acknowledges sponsorship from the Fulbright scholarship 2014–2016 and from the University of Washington in the form of full tuition waivers. Microsoft Azure for Research Award provided computational resources for all authors. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.ĭata Availability: All relevant data are within the paper and its Supporting Information files.įunding: Yeung and Hung are supported by National Institutes of Health U54 HL127624. Received: SeptemAccepted: MaPublished: April 5, 2016Ĭopyright: © 2016 Hung et al. 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.Ĭitation: Hung L-H, Kristiyanto D, Lee SB, Yeung KY (2016) GUIdock: Using Docker Containers with a Common Graphics User Interface to Address the Reproducibility of Research. 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.
#Use kitematic to link containers software#
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. Complex graphics based workflows, ubiquitous in systems biology, can now be easily exported and reproduced on many different platforms. GUIdock allows for the facile distribution of a systems biology application along with its graphics environment. 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.
Virtual machines, and container software such as Docker, make it possible to reproduce the exact environment regardless of the underlying hardware and operating system. For complex computational methods, it is often necessary, not just to recreate the code, but also the software and hardware environment to reproduce results.