Boutiques/Boutiques: Release 0.5.4

Glatard, Tristan; Kiar, Greg; Benderoff, Erin; Fong, Darrin; Thiel, Stuart; Tristan, A A; Charrière, Jérôme; Zhou, Joey Tianyi; friesenA,; Dugré, Mathieu; ValHayot,; Beck, Natacha; simon-dube,; Jeyachandra, Jerry; Thiels,; Brown, Shawn T.; shawntbrown,; MontrealSergiy,; Silva, Rafael Ferreira da; Lecours, Xavier; gabiherman,; Rioux, Pierre; Nadeau, P.Eng. Nicholas; Rousseau, M.; Doyle, Andrew; Pinzón, Alfredo

doi:10.5281/zenodo.1098558

Cited by 3 publications

(4 citation statements)

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“…Neurodesk is not the first platform to address the limited accessibility and reproducibility available for many neuroimaging data analysis tools. Indeed, software distribution mechanisms like NeuroDebian 2 have made great progress in making neuroimaging software more accessible, while projects such as OpenNeuro 37 , Brainlife 38 , Flywheel 39 , XNAT 42 , Code-Ocean 110 , Boutiques 40,41 and Qmenta 43 have greatly improved the accessibility and reproducibility of neuroimaging analyses. However, all current existing solutions have lacked portability and flexibility.…”

Section: Discussionmentioning

confidence: 99%

“…However, despite the benefits of containerization, only a small number of integrated neuroscience-specific or adaptable workflow systems support containerized distributed computing 6,34–36 . Although projects such as OpenNeuro 37 , Brainlife 38 , Flywheel 39 , Boutiques 40,41 , XNAT 42 and Qmenta 43 have improved the accessibility and reproducibility of neuroimaging analyses, these projects still lack portability. At this stage, no solution exists that universally addresses the issues of Accessibility , Flexibility , Portability, and Reproducibility .…”

Section: Introductionmentioning

confidence: 99%

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Neurodesk: An accessible, flexible, and portable data analysis environment for reproducible neuroimaging

Renton

Dao

Abbott

et al. 2022

Preprint

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Neuroimaging data analysis often requires purpose-built software, which can be difficult to install and may produce different results across computing environments. Beyond being a roadblock to neuroscientists, these issues of accessibility and portability can hamper the reproducibility of neuroimaging data analysis pipelines. Here, we introduce the Neurodesk platform, which offers a sustainable, flexible solution; harnessing software containers to support a comprehensive and growing suite of neuroimaging software (https://www.neurodesk.org/). Neurodesk includes both a browser-accessible virtual desktop environment and a command line interface, mediating access to containerised neuroimaging software libraries from multiple systems; including personal computers, cloud computing, high-performance computers, and Jupyter notebooks. This community-driven, open-source platform represents a paradigm shift for neuroimaging data analysis, allowing for accessible, fully reproducible and portable data analysis pipelines, which can be redeployed in perpetuity, in any computing environment, with ease.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Neurodesk: An accessible, flexible, and portable data analysis environment for reproducible neuroimaging

Renton

Dao

Abbott

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

Section: Understanding Inter-system Differences In Image Registration...mentioning

confidence: 99%

“…However, despite the benefits of containerization, only a small number of integrated neuroscience-specific or adaptable workflow systems support containerized distributed computing 6,[34][35][36] . Although projects such as OpenNeuro 37 , Neurodesk: An accessible platform for reproducible neuroimaging Brainlife 38 , Flywheel 39 , Boutiques 40,41 , XNAT 42 and Qmenta 43 have improved the accessibility and reproducibility of neuroimaging analyses, these projects still lack portability. At this stage, no solution exists that universally addresses the issues of Accessibility, Flexibility, Portability, and Reproducibility.…”

Section: Introductionmentioning

confidence: 99%

Neurodesk: an accessible, flexible and portable data analysis environment for reproducible neuroimaging

Renton,

Dao,

Johnstone

et al. 2024

Nat Methods

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Neuroimaging data analysis often requires purpose-built software, which can be challenging to install and may produce different results across computing environments. Beyond being a roadblock to neuroscientists, these issues of accessibility and portability can hamper the reproducibility of neuroimaging data analysis pipelines. Here, we introduce the Neurodesk platform, which harnesses software containers to support a comprehensive and growing suite of neuroimaging software (https://www.neurodesk.org/). Neurodesk includes a browseraccessible virtual desktop environment and a command line interface, mediating access to containerized neuroimaging software libraries on various computing platforms, including personal and high-performance computers, cloud computing and Jupyter Notebooks. This community-oriented, open-source platform enables a paradigm shift for neuroimaging data analysis, allowing for accessible, flexible, fully reproducible, and portable data analysis pipelines.

show abstract

Neurodesk: An accessible, flexible, and portable data analysis environment for reproducible neuroimaging

Bollmann

Renton²,

Dao

et al. 2023

Preprint

View full text Add to dashboard Cite

Neuroimaging data analysis often requires purpose-built software, which can be challenging to install and may produce different results across computing environments. Beyond being a roadblock to neuroscientists, these issues of accessibility and portability can hamper the reproducibility of neuroimaging data analysis pipelines. Here, we introduce the Neurodesk platform, which harnesses software containers to support a comprehensive and growing suite of neuroimaging software (https://www.neurodesk.org/). Neurodesk includes a browser-accessible virtual desktop environment and a command line interface, mediating access to containerized neuroimaging software libraries on various computing platforms, including personal and high-performance computers, cloud computing and Jupyter Notebooks. This community-oriented, open-source platform enables a paradigm shift for neuroimaging data analysis, allowing for accessible, flexible, fully reproducible, and portable data analysis pipelines.

show abstract

Boutiques/Boutiques: Release 0.5.4

Cited by 3 publications

References 0 publications

Neurodesk: An accessible, flexible, and portable data analysis environment for reproducible neuroimaging

Neurodesk: An accessible, flexible, and portable data analysis environment for reproducible neuroimaging

Neurodesk: an accessible, flexible and portable data analysis environment for reproducible neuroimaging

Neurodesk: An accessible, flexible, and portable data analysis environment for reproducible neuroimaging

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