Boutiques: a flexible framework to integrate command-line applications in computing platforms

We present Boutiques, a system to automatically publish, integrate, and execute command-line applications across computational platforms. Boutiques applications are installed through software containers described in a rich and flexible JSON language. A set of core tools facilitates the construction,...

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Vydáno v:Gigascience Ročník 7; číslo 5
Hlavní autoři: Glatard, Tristan, Kiar, Gregory, Aumentado-Armstrong, Tristan, Beck, Natacha, Bellec, Pierre, Bernard, Rémi, Bonnet, Axel, Brown, Shawn T, Camarasu-Pop, Sorina, Cervenansky, Frédéric, Das, Samir, Ferreira da Silva, Rafael, Flandin, Guillaume, Girard, Pascal, Gorgolewski, Krzysztof J, Guttmann, Charles R G, Hayot-Sasson, Valérie, Quirion, Pierre-Olivier, Rioux, Pierre, Rousseau, Marc-Étienne, Evans, Alan C
Médium: Journal Article
Jazyk:angličtina
Vydáno: United States Oxford University Press 01.05.2018
Témata:
Applications programs
Bioinformatics
Computer science
Operating systems
Redundancy
Reproducibility
Software engineering
Technical Note
ISSN:2047-217X, 2047-217X
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Abstract We present Boutiques, a system to automatically publish, integrate, and execute command-line applications across computational platforms. Boutiques applications are installed through software containers described in a rich and flexible JSON language. A set of core tools facilitates the construction, validation, import, execution, and publishing of applications. Boutiques is currently supported by several distinct virtual research platforms, and it has been used to describe dozens of applications in the neuroinformatics domain. We expect Boutiques to improve the quality of application integration in computational platforms, to reduce redundancy of effort, to contribute to computational reproducibility, and to foster Open Science.
AbstractList We present Boutiques, a system to automatically publish, integrate, and execute command-line applications across computational platforms. Boutiques applications are installed through software containers described in a rich and flexible JSON language. A set of core tools facilitates the construction, validation, import, execution, and publishing of applications. Boutiques is currently supported by several distinct virtual research platforms, and it has been used to describe dozens of applications in the neuroinformatics domain. We expect Boutiques to improve the quality of application integration in computational platforms, to reduce redundancy of effort, to contribute to computational reproducibility, and to foster Open Science.
We present Boutiques, a system to automatically publish, integrate, and execute command-line applications across computational platforms. Boutiques applications are installed through software containers described in a rich and flexible JSON language. A set of core tools facilitates the construction, validation, import, execution, and publishing of applications. Boutiques is currently supported by several distinct virtual research platforms, and it has been used to describe dozens of applications in the neuroinformatics domain. We expect Boutiques to improve the quality of application integration in computational platforms, to reduce redundancy of effort, to contribute to computational reproducibility, and to foster Open Science.We present Boutiques, a system to automatically publish, integrate, and execute command-line applications across computational platforms. Boutiques applications are installed through software containers described in a rich and flexible JSON language. A set of core tools facilitates the construction, validation, import, execution, and publishing of applications. Boutiques is currently supported by several distinct virtual research platforms, and it has been used to describe dozens of applications in the neuroinformatics domain. We expect Boutiques to improve the quality of application integration in computational platforms, to reduce redundancy of effort, to contribute to computational reproducibility, and to foster Open Science.
Author Kiar, Gregory
Cervenansky, Frédéric
Ferreira da Silva, Rafael
Bonnet, Axel
Camarasu-Pop, Sorina
Evans, Alan C
Rousseau, Marc-Étienne
Aumentado-Armstrong, Tristan
Rioux, Pierre
Brown, Shawn T
Hayot-Sasson, Valérie
Bernard, Rémi
Glatard, Tristan
Gorgolewski, Krzysztof J
Flandin, Guillaume
Beck, Natacha
Guttmann, Charles R G
Girard, Pascal
Bellec, Pierre
Das, Samir
Quirion, Pierre-Olivier
AuthorAffiliation 2 McGill University, Montreal, Canada
3 Montreal Neurological Institute, Montreal, Canada
1 Department of Computer Science and Software Engineering, Concordia University, Montreal, Canada
7 Wellcome Trust Centre for Neuroimaging, London, UK
8 Department of Psychology, Stanford University, Stanford, California, USA
5 University of Lyon, CNRS, INSERM, CREATIS, Villeurbanne, France
6 University of Southern California, Information Sciences Institute, Marina del Rey, CA, USA
9 Center for Neurological Imaging, Department of Radiology, Brigham and Women's Hospital,, Boston, Massachusetts, USA
10 Compute Canada, 155 University Ave, Suite 302, Toronto, ON M5H 3B7, Canada
4 Centre de Recherche de l’Institut de Gériatrie de Montréal CRIUGM, Montréal, QC, Canada
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SubjectTerms Applications programs
Bioinformatics
Computer science
Operating systems
Redundancy
Reproducibility
Software engineering
Technical Note
Title Boutiques: a flexible framework to integrate command-line applications in computing platforms
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