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

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Název: GUIdock: Using Docker Containers with a Common Graphics User Interface to Address the Reproducibility of Research.
Autoři: Hung LH; Institute of Technology, University of Washington, Tacoma, WA 98402, United States of America., Kristiyanto D; Institute of Technology, University of Washington, Tacoma, WA 98402, United States of America., Lee SB; Institute of Technology, University of Washington, Tacoma, WA 98402, United States of America., Yeung KY; Institute of Technology, University of Washington, Tacoma, WA 98402, United States of America.
Zdroj: PloS one [PLoS One] 2016 Apr 05; Vol. 11 (4), pp. e0152686. Date of Electronic Publication: 2016 Apr 05 (Print Publication: 2016).
Způsob vydávání: Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
Jazyk: English
Informace o časopise: Publisher: Public Library of Science Country of Publication: United States NLM ID: 101285081 Publication Model: eCollection Cited Medium: Internet ISSN: 1932-6203 (Electronic) Linking ISSN: 19326203 NLM ISO Abbreviation: PLoS One Subsets: MEDLINE
Imprint Name(s): Original Publication: San Francisco, CA : Public Library of Science
Výrazy ze slovníku MeSH: Programming Languages* , Software Design* , User-Computer Interface*
Abstrakt: 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.
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Grant Information: U54 HL127624 United States HL NHLBI NIH HHS
Entry Date(s): Date Created: 20160406 Date Completed: 20160812 Latest Revision: 20190219
Update Code: 20250114
PubMed Central ID: PMC4821530
DOI: 10.1371/journal.pone.0152686
PMID: 27045593
Databáze: MEDLINE
Popis
Abstrakt: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.
ISSN:1932-6203
DOI:10.1371/journal.pone.0152686