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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).  ...  We present here the design and current implementation of the Whole Tale environment (https://dashboard.wholetale.org).  ...  the Whole Tale environment.  ... 
doi:10.1016/j.future.2017.12.029 fatcat:quttkpfzkfamrlapqj4c7ykk64

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
We report here on the design, architecture, and implementation of the Whole Tale environment.  ...  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

The Whole Tale: Merging Science and Cyberinfrastructure Pathways

Craig Willis
2020 Zenodo  
Presentation of the Whole Tale project and platform given at the "Writing Reproducible & Executable Scientific Papers with R & Python: a Hands-On Workshop" held at the University of Washington eScience  ...  Lior Pachter, Stories from the Supplement, Simplifying Computational Reproducibility in Whole Tale • Researchers can easily package and share tales: ○ Data, Code, and Compute Environment ■ .. including  ...  Resolving Irreproducibility in Empirical and Computational Research. IMS Bulletin Why Whole Tale?  ... 
doi:10.5281/zenodo.3694085 fatcat:irpvilz2dfhazc24nm2dkhquzi

Application of BagIt-Serialized Research Object Bundles for Packaging and Re-execution of Computational Analyses

Kyle Chard, Niall Gaffney, Matthew B. Jones, Kacper Kowalik, Bertram Ludaescher, Jarek Nabrzyski, Victoria Stodden, Ian Taylor, Thomas Thelen, Matthew J. Turk, Craig Willis
2019 Zenodo  
In this paper we describe our experience adopting the Research Object Bundle (RO-Bundle) format with BagIt serialization (BagIt-RO) for the design and implementation of "tales" in the Whole Tale platform  ...  for review and computational reproducibility at the time of publication.  ...  Describing the Computing Environment Whole Tale uses a customized version of the Binder repo2docker package.  ... 
doi:10.5281/zenodo.3271763 fatcat:fy7s42fembgg5dafpvfyrw3qpe

Application of BagIt-Serialized Research Object Bundles for Packaging and Re-execution of Computational Analyses

Kyle Chard, Niall Gaffney, Matthew B. Jones, Kacper Kowalik, Bertram Ludaescher, Jarek Nabrzyski, Victoria Stodden, Ian Taylor, Thomas Thelen, Matthew J. Turk, Craig Willis
2019 Zenodo  
In this paper we describe our experience adopting the Research Object Bundle (RO-Bundle) format with BagIt serialization (BagIt-RO) for the design and implementation of "tales" in the Whole Tale platform  ...  for review and computational reproducibility at the time of publication.  ...  Describing the Computing Environment Whole Tale uses a customized version of the Binder repo2docker package.  ... 
doi:10.5281/zenodo.3268966 fatcat:hzc2qosshjcydb7z4fhigvuzke

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

2020 Supercomputing Frontiers and Innovations  
The scientific computing community has long taken a leadership role in understanding and assessing the relationship of reproducibility to cyberinfrastructure, ensuring that computational results -such  ...  in the tradition of community driven approaches to reproducibility and the acceleration of science and 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

Application of BagIt-Serialized Research Object Bundles for Packaging and Re-execution of Computational Analyses

Kyle Chard, Niall Gaffney, Matthew B. Jones, Kacper Kowalik, Bertram Ludaescher, Timothy McPhillips, Jarek Nabrzyski, Victoria Stodden, Ian Taylor, Thomas Thelen, Matthew J. Turk, Craig Willis
2019 Zenodo  
In this paper we describe our experience adopting the Research Object Bundle (RO-Bundle) format with BagIt serialization (BagIt-RO) for the design and implementation of "tales" in the Whole Tale platform  ...  for review and computational reproducibility at the time of publication.  ...  Describing the Computing Environment Whole Tale uses a customized version of the Binder repo2docker package.  ... 
doi:10.5281/zenodo.3381754 fatcat:fbhbghrruvhxlipbiwz5oqtete

Advancing computational reproducibility in the Dataverse data repository platform [article]

Ana Trisovic, Philip Durbin, Tania Schlatter, Gustavo Durand, Sonia Barbosa, Danny Brooke, Mercè Crosas
2020 arXiv   pre-print
This paper addresses the shortcomings of data repositories and reproducibility tools and how they could be overcome to improve the current lack of computational reproducibility in published and archived  ...  New specialized reproducibility tools provide cloud-based computational environments for code encapsulation, thus enabling research portability and reproducibility.  ...  ACKNOWLEDGMENTS Thank you to the Dataverse team for their help and support. This work is partially funded by the Sloan Foundation. Ana Trisovic is funded by the Sloan Foundation.  ... 
arXiv:2005.02985v2 fatcat:rfegdysbufc2jeb324slnmeqay

Preserving Reproducibility: Provenance And Executable Containers In Dataone Data Packages

Bryce Mecum, Matthew B. Jones, Dave Vieglais, Craig Willis
2018 Zenodo  
A short paper submission for the ResearchObject2018 Call for Papers: http://www.researchobject.org/ro2018/#call  ...  Like CodeOcean, Whole Tale provides a collaborative platform for the creation of reproducible computational research.  ...  Tales include descriptions of the computational environment, and the code, metadata, data objects (or references), and other inputs and outputs needed to fully reproduce a computational result [1] .  ... 
doi:10.5281/zenodo.1420531 fatcat:jpfnlb7mz5dcjiu5zmov6ttd54

Preserving Reproducibility: Provenance And Executable Containers In Dataone Data Packages

Bryce Mecum, Matthew B. Jones, Dave Vieglais, Craig Willis
2018 Zenodo  
A short paper submission for the ResearchObject2018 Call for Papers: http://www.researchobject.org/ro2018/#call  ...  Acknowledgements 7 Funding support for the work described in this paper was provided by National Science Foundation awards 1430508, 1541450, and 1262458.  ...  Additional support was provided by the National Center for Ecological Analysis and Synthesis, a Center funded by the University of California, Santa Barbara, and the State of California.  ... 
doi:10.5281/zenodo.1313218 fatcat:gey5myxzgfcynmmgjowiimobiy

Reproducibility by Other Means: Transparent Research Objects

Timothy McPhillips, Bertram Ludaescher
2019 Zenodo  
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  ...  Research Objects have the potential to significantly enhance the reproducibility and transparency of scientific research.  ...  For example, in the Whole Tale project [6, 29] we define a Reproducible Tale as one that includes sufficient information for the Tale to be re-executed for the review and verification of results.  ... 
doi:10.5281/zenodo.3270560 fatcat:fgtrffoqn5cezniocqyaoc3piq

Reproducibility by Other Means: Transparent Research Objects

Timothy McPhillips, Bertram Ludaescher
2019 Zenodo  
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  ...  Research Objects have the potential to significantly enhance the reproducibility and transparency of scientific research.  ...  For example, in the Whole Tale project [6, 29] we define a Reproducible Tale as one that includes sufficient information for the Tale to be re-executed for the review and verification of results.  ... 
doi:10.5281/zenodo.3270620 fatcat:g72jr3kk4zfwtogq5hm6fzdmbm

Reproducibility by Other Means: Transparent Research Objects

Timothy M McPhillips, Craig Willis, Michael R. Gryk, Santiago Nunez-Corrales, Bertram Ludaescher
2019 Zenodo  
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  ...  Research Objects have the potential to significantly enhance the reproducibility of scientific research.  ...  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

Publishing computational research - a review of infrastructures for reproducible and transparent scholarly communication

Markus Konkol, Daniel Nüst, Laura Goulier
2020 Research Integrity and Peer Review  
The trend toward open science increases the pressure on authors to provide access to the source code and data they used to compute the results reported in their scientific papers.  ...  All approaches provide features to assist readers in studying the materials, e.g., one-click reproducible results or tools for manipulating the analysis parameters.  ...  Acknowledgements We thank Timothy Errington and Mario Malicki for their reviews, Vicky Steeves for a helpful discussion on the article preprint [39] , and Celeste Brennecka for proofreading.  ... 
doi:10.1186/s41073-020-00095-y pmid:32685199 pmcid:PMC7359270 fatcat:clovjhifpnc2lpol7yr2mv4v5e

Publishing computational research – A review of infrastructures for reproducible and transparent scholarly communication [article]

Markus Konkol, Daniel Nüst, Laura Goulier
2020 arXiv   pre-print
This trend towards open science increases the pressure on authors to provide access to the source code and data underlying the computational results in their scientific papers.  ...  The key contribution of this paper is a review of applications addressing the issue of publishing executable computational research results.  ...  The authors of this paper are members of the o2r project that was also discussed in this paper (http://o2r. info/).  ... 
arXiv:2001.00484v1 fatcat:4nm6pmwzhvgptmcfhbkp7efvky
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