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Neurodesk: An accessible, flexible, and portable data analysis environment for reproducible neuroimaging
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 neuroima...
| Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Formato: | Online Artículo Texto |
| Lenguaje: | English |
| Publicado: |
American Journal Experts
2023
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| Materias: | |
| Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10055538/ https://www.ncbi.nlm.nih.gov/pubmed/36993557 http://dx.doi.org/10.21203/rs.3.rs-2649734/v1 |
| _version_ | 1785015895571038208 |
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| author | Renton, Angela I. Dao, Thuy T. Johnstone, Tom Civier, Oren Sullivan, Ryan P. White, David J. Lyons, Paris Slade, Benjamin M. Abbott, David F. Amos, Toluwani J. Bollmann, Saskia Botting, Andy Campbell, Megan E. J. Chang, Jeryn Close, Thomas G. Eckstein, Korbinian Egan, Gary F. Evas, Stefanie Flandin, Guillaume Garner, Kelly G. Garrido, Marta I. Ghosh, Satrajit S. Grignard, Martin Hannan, Anthony J. Huber, Renzo Kaczmarzyk, Jakub R. Kasper, Lars Kuhlmann, Levin Lou, Kexin Mantilla-Ramos, Yorguin-Jose Mattingley, Jason B. Morris, Jo Narayanan, Akshaiy Pestilli, Franco Puce, Aina Ribeiro, Fernanda L. Rogasch, Nigel C. Rorden, Chris Schira, Mark Shaw, Thomas B. Sowman, Paul F. Spitz, Gershon Stewart, Ashley Ye, Xincheng Zhu, Judy D. Hughes, Matthew E. Narayanan, Aswin Bollmann, Steffen |
| author_facet | Renton, Angela I. Dao, Thuy T. Johnstone, Tom Civier, Oren Sullivan, Ryan P. White, David J. Lyons, Paris Slade, Benjamin M. Abbott, David F. Amos, Toluwani J. Bollmann, Saskia Botting, Andy Campbell, Megan E. J. Chang, Jeryn Close, Thomas G. Eckstein, Korbinian Egan, Gary F. Evas, Stefanie Flandin, Guillaume Garner, Kelly G. Garrido, Marta I. Ghosh, Satrajit S. Grignard, Martin Hannan, Anthony J. Huber, Renzo Kaczmarzyk, Jakub R. Kasper, Lars Kuhlmann, Levin Lou, Kexin Mantilla-Ramos, Yorguin-Jose Mattingley, Jason B. Morris, Jo Narayanan, Akshaiy Pestilli, Franco Puce, Aina Ribeiro, Fernanda L. Rogasch, Nigel C. Rorden, Chris Schira, Mark Shaw, Thomas B. Sowman, Paul F. Spitz, Gershon Stewart, Ashley Ye, Xincheng Zhu, Judy D. Hughes, Matthew E. Narayanan, Aswin Bollmann, Steffen |
| author_sort | Renton, Angela I. |
| collection | PubMed |
| description | 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. |
| format | Online Article Text |
| id | pubmed-10055538 |
| institution | National Center for Biotechnology Information |
| language | English |
| publishDate | 2023 |
| publisher | American Journal Experts |
| record_format | MEDLINE/PubMed |
| spelling | pubmed-100555382023-03-30 Neurodesk: An accessible, flexible, and portable data analysis environment for reproducible neuroimaging Renton, Angela I. Dao, Thuy T. Johnstone, Tom Civier, Oren Sullivan, Ryan P. White, David J. Lyons, Paris Slade, Benjamin M. Abbott, David F. Amos, Toluwani J. Bollmann, Saskia Botting, Andy Campbell, Megan E. J. Chang, Jeryn Close, Thomas G. Eckstein, Korbinian Egan, Gary F. Evas, Stefanie Flandin, Guillaume Garner, Kelly G. Garrido, Marta I. Ghosh, Satrajit S. Grignard, Martin Hannan, Anthony J. Huber, Renzo Kaczmarzyk, Jakub R. Kasper, Lars Kuhlmann, Levin Lou, Kexin Mantilla-Ramos, Yorguin-Jose Mattingley, Jason B. Morris, Jo Narayanan, Akshaiy Pestilli, Franco Puce, Aina Ribeiro, Fernanda L. Rogasch, Nigel C. Rorden, Chris Schira, Mark Shaw, Thomas B. Sowman, Paul F. Spitz, Gershon Stewart, Ashley Ye, Xincheng Zhu, Judy D. Hughes, Matthew E. Narayanan, Aswin Bollmann, Steffen Res Sq Article 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. American Journal Experts 2023-03-13 /pmc/articles/PMC10055538/ /pubmed/36993557 http://dx.doi.org/10.21203/rs.3.rs-2649734/v1 Text en https://creativecommons.org/licenses/by/4.0/This work is licensed under a Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/) , which allows reusers to distribute, remix, adapt, and build upon the material in any medium or format, so long as attribution is given to the creator. The license allows for commercial use. |
| spellingShingle | Article Renton, Angela I. Dao, Thuy T. Johnstone, Tom Civier, Oren Sullivan, Ryan P. White, David J. Lyons, Paris Slade, Benjamin M. Abbott, David F. Amos, Toluwani J. Bollmann, Saskia Botting, Andy Campbell, Megan E. J. Chang, Jeryn Close, Thomas G. Eckstein, Korbinian Egan, Gary F. Evas, Stefanie Flandin, Guillaume Garner, Kelly G. Garrido, Marta I. Ghosh, Satrajit S. Grignard, Martin Hannan, Anthony J. Huber, Renzo Kaczmarzyk, Jakub R. Kasper, Lars Kuhlmann, Levin Lou, Kexin Mantilla-Ramos, Yorguin-Jose Mattingley, Jason B. Morris, Jo Narayanan, Akshaiy Pestilli, Franco Puce, Aina Ribeiro, Fernanda L. Rogasch, Nigel C. Rorden, Chris Schira, Mark Shaw, Thomas B. Sowman, Paul F. Spitz, Gershon Stewart, Ashley Ye, Xincheng Zhu, Judy D. Hughes, Matthew E. Narayanan, Aswin Bollmann, Steffen Neurodesk: An accessible, flexible, and portable data analysis environment for reproducible neuroimaging |
| title | Neurodesk: An accessible, flexible, and portable data analysis environment for reproducible neuroimaging |
| title_full | Neurodesk: An accessible, flexible, and portable data analysis environment for reproducible neuroimaging |
| title_fullStr | Neurodesk: An accessible, flexible, and portable data analysis environment for reproducible neuroimaging |
| title_full_unstemmed | Neurodesk: An accessible, flexible, and portable data analysis environment for reproducible neuroimaging |
| title_short | Neurodesk: An accessible, flexible, and portable data analysis environment for reproducible neuroimaging |
| title_sort | neurodesk: an accessible, flexible, and portable data analysis environment for reproducible neuroimaging |
| topic | Article |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10055538/ https://www.ncbi.nlm.nih.gov/pubmed/36993557 http://dx.doi.org/10.21203/rs.3.rs-2649734/v1 |
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