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GUIdock: Using Docker Containers with a Common Graphics User Interface to Address
the Reproducibility of Research
#MMPMID27045593
Hung LH
; Kristiyanto D
; Lee SB
; Yeung KY
PLoS One
2016[]; 11
(4
): e0152686
PMID27045593
show ga
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.
free
free
free
