GUIdock: Using Docker Containers with a Common Graphics User Interface to Address the Reproducibility of Research.
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 environm...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2016-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC4821530?pdf=render |
| _version_ | 1819048374868901888 |
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| author | Ling-Hong Hung Daniel Kristiyanto Sung Bong Lee Ka Yee Yeung |
| author_facet | Ling-Hong Hung Daniel Kristiyanto Sung Bong Lee Ka Yee Yeung |
| author_sort | Ling-Hong Hung |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-21T11:15:15Z |
| format | Article |
| id | doaj.art-fba3cef507364e7e812f4195b7b1bbc3 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-21T11:15:15Z |
| publishDate | 2016-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-fba3cef507364e7e812f4195b7b1bbc32022-12-21T19:05:57ZengPublic Library of Science (PLoS)PLoS ONE1932-62032016-01-01114e015268610.1371/journal.pone.0152686GUIdock: Using Docker Containers with a Common Graphics User Interface to Address the Reproducibility of Research.Ling-Hong HungDaniel KristiyantoSung Bong LeeKa Yee YeungReproducibility 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.http://europepmc.org/articles/PMC4821530?pdf=render |
| spellingShingle | Ling-Hong Hung Daniel Kristiyanto Sung Bong Lee Ka Yee Yeung GUIdock: Using Docker Containers with a Common Graphics User Interface to Address the Reproducibility of Research. PLoS ONE |
| title | GUIdock: Using Docker Containers with a Common Graphics User Interface to Address the Reproducibility of Research. |
| title_full | GUIdock: Using Docker Containers with a Common Graphics User Interface to Address the Reproducibility of Research. |
| title_fullStr | GUIdock: Using Docker Containers with a Common Graphics User Interface to Address the Reproducibility of Research. |
| title_full_unstemmed | GUIdock: Using Docker Containers with a Common Graphics User Interface to Address the Reproducibility of Research. |
| title_short | GUIdock: Using Docker Containers with a Common Graphics User Interface to Address the Reproducibility of Research. |
| title_sort | guidock using docker containers with a common graphics user interface to address the reproducibility of research |
| url | http://europepmc.org/articles/PMC4821530?pdf=render |
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