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Toward Enabling Reproducibility for Data-Intensive Research using the Whole Tale Platform [article]

Kyle Chard, Niall Gaffney, Mihael Hategan, Kacper Kowalik, Bertram Ludaescher, Timothy McPhillips, Jarek Nabrzyski, Victoria Stodden, Ian Taylor, Thomas Thelen, Matthew J. Turk, Craig Willis
2020 pre-print
We describe opportunities, challenges, and solutions to facilitating reproducibility for data- and compute-intensive research, that we call "Tales at Scale," using the Whole Tale computing platform.  ...  Whole Tale http://wholetale.org is a web-based, open-source platform for reproducible research supporting the creation, sharing, execution, and verification of "Tales" for the scientific research community  ...  The goal of the Whole Tale project is to enable reproducibility for computation-and data-enabled research.  ... 
doi:10.3233/apc200107 arXiv:2005.06087v1 fatcat:2pjndo4y4bcxjnvx3onfqlozlq

Building a Vision for Reproducibility in the Cyberinfrastructure Ecosystem: Leveraging Community Efforts

2020 Supercomputing Frontiers and Innovations  
as those from simulations -are "reproducible", that is, the same results are obtained when one re-uses the same input data, methods, software and analysis conditions.  ...  The work also articulates avenues for future research at the intersection of transparency, reproducibility, and computational infrastructure that supports scientific discovery.  ...  This paper is distributed under the terms of the Creative Commons Attribution-Non Commercial 3.0 License which permits non-commercial use, reproduction and distribution of the work without further permission  ... 
doi:10.14529/jsfi200106 fatcat:65ngkgmfqjacbb2llj3exmpkei

Computing Environments for Reproducibility: Capturing the "Whole Tale" [article]

Adam Brinckman, Kyle Chard, Niall Gaffney, Mihael Hategan, Matthew B. Jones, Kacper Kowalik, Sivakumar Kulasekaran, Bertram Ludäscher, Bryce D. Mecum, Jarek Nabrzyski, Victoria Stodden, Ian J. Taylor (+1 others)
2018 arXiv   pre-print
The Whole Tale project aims to address these barriers by connecting computational, data-intensive research efforts with the larger research process--transforming the knowledge discovery and dissemination  ...  The Whole Tale focuses on the full spectrum of science, empowering users in the long tail of science, and power users with demands for access to big data and compute resources.  ...  Acknowledgments This research was supported by NSF grant 1541450: CC*DNI DIBBS: Merging Science and Cyberinfrastructure Pathways: The Whole Tale.  ... 
arXiv:1805.00400v1 fatcat:xluy3bo3xzav3eoyetu34a2egy

Computing environments for reproducibility: Capturing the "Whole Tale"

Adam Brinckman, Kyle Chard, Niall Gaffney, Mihael Hategan, Matthew B. Jones, Kacper Kowalik, Sivakumar Kulasekaran, Bertram Ludäscher, Bryce D. Mecum, Jarek Nabrzyski, Victoria Stodden, Ian J. Taylor (+2 others)
2018 Future generations computer systems  
Acknowledgments This research was supported by NSF, United States grant 1541450 (CC*DNI DIBBS: Merging Science and Cyberinfrastructure Pathways: The Whole Tale).  ...  In Section 3 we describe prior and current efforts toward enabling reproducible research.  ...  Using Whole Tale these researchers could streamline this process via access to a large and varied amount of data, a platform for conducting their analyses using containerized frontends, and the ability  ... 
doi:10.1016/j.future.2017.12.029 fatcat:quttkpfzkfamrlapqj4c7ykk64

Reproducibility by Other Means: Transparent Research Objects

Timothy M McPhillips, Craig Willis, Michael R. Gryk, Santiago Nunez-Corrales, Bertram Ludaescher
2019 Zenodo  
We show how support for science-oriented queries can enable researchers to assess the reproducibility of Research Objects and the individual methods and results they encapsulate.  ...  One important way Research Objects can do this is by encapsulating the means for re-executing the computational components of studies, thus supporting the new form of reproducibility enabled by digital  ...  ACKNOWLEDGMENTS The authors would like to thank Victoria Stodden, Matthew B. Jones, Kacper Kowalik, Ana Trisovic, and members of the Whole Tale team for useful discussion.  ... 
doi:10.5281/zenodo.3382423 fatcat:igyxmzaudfekvikik26juoaema

Reproducibility by Other Means: Transparent Research Objects

Timothy McPhillips, Bertram Ludaescher
2019 Zenodo  
We show how support for science-oriented queries can enable researchers to assess the reproducibility of Research Objects and the individual methods and results they encapsulate.  ...  One important way Research Objects can do this is by encapsulating the means for re-executing the computational components of studies, thus supporting the new form of reproducibility enabled by digital  ...  Consequently, we view the Whole Tale project-as currently chartered and funded-as just a step towards the kind of platforms, infrastructure, and standards needed to enable researchers using computing technology  ... 
doi:10.5281/zenodo.3270560 fatcat:fgtrffoqn5cezniocqyaoc3piq

Reproducibility by Other Means: Transparent Research Objects

Timothy McPhillips, Bertram Ludaescher
2019 Zenodo  
We show how support for science-oriented queries can enable researchers to assess the reproducibility of Research Objects and the individual methods and results they encapsulate.  ...  One important way Research Objects can do this is by encapsulating the means for re-executing the computational components of studies, thus supporting the new form of reproducibility enabled by digital  ...  Consequently, we view the Whole Tale project-as currently chartered and funded-as just a step towards the kind of platforms, infrastructure, and standards needed to enable researchers using computing technology  ... 
doi:10.5281/zenodo.3270620 fatcat:g72jr3kk4zfwtogq5hm6fzdmbm

The Rockerverse: Packages and Applications for Containerization with R [article]

Daniel Nüst, Dirk Eddelbuettel, Dom Bennett, Robrecht Cannoodt, Dav Clark, Gergely Daroczi, Mark Edmondson, Colin Fay, Ellis Hughes, Lars Kjeldgaard, Sean Lopp, Ben Marwick (+13 others)
2020 arXiv   pre-print
These use cases cover diverse topics such as package development, reproducible research, collaborative work, cloud-based data processing, and production deployment of services.  ...  The Rocker Project provides widely used Docker images for R across different application scenarios.  ...  Acknowledgements DN is supported by the project Opening Reproducible Research (o2r) funded by the German Research Foundation (DFG) under project number PE 1632/17-1.  ... 
arXiv:2001.10641v4 fatcat:sbbpn3xs6jbsboslowxabtbx4u

The Rockerverse: Packages and Applications for Containerisation with R

Daniel Nüst, Dirk Eddelbuettel, Dom Bennett, Robrecht Cannoodt, Dav Clark, Gergely Daróczi, Mark Edmondson, Colin Fay, Ellis Hughes, Lars Kjeldgaard, Sean Lopp, Ben Marwick (+13 others)
2020 The R Journal  
These use cases cover diverse topics such as package development, reproducible research, collaborative work, cloud-based data processing, and production deployment of services.  ...  The Rocker Project provides widely used Docker images for R across different application scenarios.  ...  CW is supported by the Whole Tale project (https://wholetale.org) funded by the US National Science Foundation (NSF) under award OAC-1541450.  ... 
doi:10.32614/rj-2020-007 fatcat:kkwisxzkmfcpzdeujhnvw6nmji

Traceability for Trustworthy AI: A Review of Models and Tools

Marçal Mora-Cantallops, Salvador Sánchez-Alonso, Elena García-Barriocanal, Miguel-Angel Sicilia
2021 Big Data and Cognitive Computing  
reproducibility of the research trusted to them.  ...  of their efforts in making data analytic processes reproducible or repeatable.  ...  Data Availability Statement: Data available in a publicly accessible repository. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/bdcc5020020 fatcat:qnlnfdbxabc7nldvrs3hsowfya

A Web service for executable research compendia enables reproducible publications and transparent reviews in geospatial sciences

Daniel Nüst
2021 Zenodo  
The executable research compendium (ERC) is a concept for packaging data, code, text, and user interface configurations in a single unit to increase transparency, reproducibility, and reusability of computational  ...  We critically discuss both the project set-up and features of ERC and ERS, and we examine them in the light of various classifications for reproducible research.  ...  This work is supported by the project Opening Reproducible Research (o2r, o2r.info) funded by the German Research Foundation (DFG) under project numbers PE 1632/10-1, KR 3930/3-1 and TR 864/6-1 for phase  ... 
doi:10.5281/zenodo.5108218 fatcat:mcamxfyx7zhdnaox25y2jjh6be

Streamlining Data-Intensive Biology With Workflow Systems [article]

Taylor Reiter, Phillip T. Brooks, Luiz Irber, Shannon E.K. Joslin, Charles M. Reid, Camille Scott, C. Titus Brown, N. Tessa Pierce
2020 bioRxiv   pre-print
As the scale of biological data generation has increased, the bottleneck of research has shifted from data generation to analysis.  ...  , and empowering researchers to conduct reproducible analyses at scale.  ...  Acknowledgements Thank you to all the members and a liates of the Lab for Data-Intensive Biology at UC Davis for providing valuable feedback on earlier versions of this manuscript and growing these practices  ... 
doi:10.1101/2020.06.30.178673 fatcat:up6eozdxyjhlxmkllqa4deewfm

A Web service for executable research compendia enables reproducible publications and transparent reviews in geospatial sciences

Daniel Nüst
2021 Zenodo  
The Executable Research Compendium (ERC) is a concept for packaging data, code, text, and user interface configurations in a single package to increase transparency, reproducibility, and reusability of  ...  We critically discuss both the project set-up and features of ERC and ERS, and examine them in the light of various classifications for reproducible research.  ...  This work is supported by the project Opening Reproducible Research (o2r, o2r.info) funded by the German Research Foundation (DFG) under project numbers PE 1632/10-1, KR 3930/3-1 and TR 864/6-1 for phase  ... 
doi:10.5281/zenodo.4818120 fatcat:t55narivpnhubdk2ec66fzjski

Recent trends in smartphone-based detection for biomedical applications: a review

Soumyabrata Banik, Sindhoora Kaniyala Melanthota, Arbaaz, Joel Markus Vaz, Vishak Madhwaraj Kadambalithaya, Iftak Hussain, Sibasish Dutta, Nirmal Mazumder
2021 Analytical and Bioanalytical Chemistry  
Depending on the application and imaging capability required, the optical arrangement of the SID varies which enables them to be used in multiple setups like bright-field, fluorescence, dark-field, and  ...  With the increasing demand for high-quality medical services, technological interventions such as portable devices that can be used in remote and resource-less conditions and have an impact on quantity  ...  platform showing the attachments for intraoral imaging and whole cavity imaging.  ... 
doi:10.1007/s00216-021-03184-z pmid:33586007 fatcat:y6r4xhkw3nae5nabjjg5t7rska

Reproducibility in the Field: Transparency, Version Control and Collaboration on the Project Panormos Survey

Néhémie Strupler, Toby C. Wilkinson
2017 Open Archaeology  
project in western Turkey, and highlights the potential consequences of Open Science approaches for archaeology as a whole.  ...  This article shares our perspectives, choices and experiences of piloting a set of tools (namely: ODK, Git, GitLab CE and R) which can address reproducibility of fieldwork in the form of an intensive survey  ...  Acknowledgements: Thanks to: Anja Slawisch (DAI), Hasibe Akat (Milet Müzesi), as directors of the Project Panormos field projects from 2012 to 2015; Sebastian Weber (DAI) for technical help; the whole  ... 
doi:10.1515/opar-2017-0019 fatcat:kezebiak6zawjbzm5ertoov42e
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