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Advancing computational reproducibility in the Dataverse data repository platform
[article]
2020
arXiv
pre-print
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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 ...
One of their conclusions was that the way data repositories store research data and code cannot fully facilitate reproducibility due to the absence of a runtime environment needed for the code execution ...
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
Improving FAIRness with containers
2020
Zenodo
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This talk will present insights from community discussions on improving FAIRness with encapsulation in the context of the Dataverse data repository platform. ...
We evaluate each of these approaches against established FAIR principles in the context of dissemination in data repositories. ...
This talk will present insights from community discussions on improving FAIRness with encapsulation in the context of the Dataverse data repository platform. ...
doi:10.5281/zenodo.4430831
fatcat:zq5eqlcqavhrjjlzlspvrfxdai
Repository Approaches to Improving Quality of Shared Data and Code
2021
Data
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The findings of these studies are sorted into three approaches that can be valuable to data repositories, archives, and other research dissemination platforms. ...
This paper presents a combination of original and secondary data analysis studies focusing on computational reproducibility, data curation, and gamified design elements that can be employed to indicate ...
The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results. ...
doi:10.3390/data6020015
fatcat:puufemmjkfelbijf2q65jjkb2i
5 years of Dataverse evolution
2021
Zenodo
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DANS seminar on the innovations in the development of Dataverse data repository both on the national and international levels. ...
ability of computer systems to transmit data with unambiguous, shared meaning. ...
Points (FDP) in Dataverse • ODISSEI -using Dataverse as a data registry One metadata field can be linked to many ontologies Language switch in Dataverse will change the language of suggested terms! ...
doi:10.5281/zenodo.5831945
fatcat:pckhp5pybbdknbpp4r4khjp5hy
Creating reproducible pharmacogenomic analysis pipelines
[article]
2019
bioRxiv
pre-print
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To address this issue, we developed pharmacogenomic workflows in the Common Workflow Language to process two breast cancer datasets in a reproducible and transparent manner. ...
to access and share our data with the community. ...
INTRODUCTION With the advances of high-throughput technologies in biomedicine, the volume of data has drastically increased in the last decade across scientific disciplines 1 . ...
doi:10.1101/614560
fatcat:bkwwawj62nh2zbuq4rbabtxz4m
An Open Science Platform for the Next Generation of Data
2013
Social Science Research Network
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Imagine an online work environment where researchers have direct and immediate access to myriad data sources and tools and data management resources, useful throughout the research lifecycle. ...
Other data repositories can expand their data sharing. Publishers gain a framework for citing data and reproducing results. ...
will store data in the repository and at least 50K of them will share some data with research. ...
doi:10.2139/ssrn.2302084
fatcat:jom2o6zwsjcsjiopazg7n55ye4
Extension of research data repository system to support direct compute access to biomedical datasets: enhancing Dataverse to support large datasets
2016
Annals of the New York Academy of Sciences
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In this paper, we describe one such extension-functionality supporting preservation of filesystem structure within Dataverse-which is essential for both in-place computation and supporting non-http data ...
(dataverse.org) open-source data repository system to structural biology datasets. ...
In summary, we have presented recent advances of the SBDG, particularly in the area of an ongoing transition to the Dataverse research data repository system. ...
doi:10.1111/nyas.13272
pmid:27862010
pmcid:PMC5546227
fatcat:zbcxvm465zecrbyei5p7musare
FAIR principi za istraživačke podatke i za softver
2021
Zenodo
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management practices" held on March 9, 2021 as part of the Co-creation activity Boosting EOSC readiness: Creating a scalable model for capacity [...] ...
Institucionalna infrastruktura i podrška upravljanju istraživačkim podacima" održana 9. marta 2021. kao deo Co-creation projekta Boosting EOSC readiness: Creating a scalable model for capacity building in ...
Dataverse repozitorijumom za podatke (ili sa Zenodom) ispunjeni su i FAIR principi.• Više u Trisovic, Ana, et al. "Advancing computational reproducibility in the Dataverse data repository platform." ...
doi:10.5281/zenodo.4593828
fatcat:ndb2x7afhfdqljgiz2cxvqdumy
Research Data Management Implementation at Peking University Library: Foster and Promote Open Science and Open Data
2021
Data Intelligence
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Using the Peking University Open Research Data Repository (PKU-ORDR) project as an example, this paper will review a library-based university-wide open research data repository project and related RDM ...
Through the review, some issues revealed during the stages of the implementation process are also discussed and addressed in the paper such as awareness of research data, demands from data providers and ...
Luo (luopc@ lib.pku.edu.cn) mainly contributed to the RDM Implementation especially with a focus on "The Establishment of the Open Research Data Repository" and "Usage, Data Curation, Skills Training and ...
doi:10.1162/dint_a_00088
fatcat:33nj4vedanattjufdppbvbydfm
Thou Shalt Be Reproducible! A Technology Perspective
2016
Frontiers in Psychology
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Second, R is advocated as the data-analytic lingua franca in psychology for achieving reproducible statistical analysis. ...
First, data archiving platforms that make datasets publicly available are presented. ...
Dataverse Project Let us briefly review the "three pillars of data publishing" (Crosas and King, 2015) in order to make data in open repositories accessible and reusable: 1. ...
doi:10.3389/fpsyg.2016.01079
pmid:27471486
pmcid:PMC4943952
fatcat:ixyyrib2tbd4vdhlknr4ksnkzu
Automating Open Science for Big Data
2015
The Annals of the American Academy of Political and Social Science
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Progressive, expansive scientific advance rests on access to data accompanied by sufficient information for reproducible results (King 1995) , a scientific ethic to maximize the utility of data to the ...
Data repositories, such as the Harvard Dataverse, ODuM Dataverse, IcPSr, and roper, as well as other general-purpose repositories, such as Dryad and figshare, have played an important role in making small-and ...
doi:10.1177/0002716215570847
fatcat:kn2qrwd3e5hwpp225kenjyqpya
Creating reproducible pharmacogenomic analysis pipelines
2019
Scientific Data
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To address this issue, we developed pharmacogenomic workflows in the Common Workflow Language to process two breast cancer datasets in a reproducible and transparent manner. ...
to access and share our data with the community. ...
Introduction With the advances of high-throughput technologies in biomedicine, the volume of data has drastically increased in the last decade across scientific disciplines 1 . ...
doi:10.1038/s41597-019-0174-7
pmid:31481707
pmcid:PMC6722117
fatcat:jznstbylxje33chef2llnqkwdq
The Evolution of Data Citation: From Principles to Implementation
2014
IASSIST Quarterly
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The Evolution of Data Citation: From Principles to Implementation ...
Acknowledgments We would like to thank the members of the Data Citation Synthesis Task Group and of the Co-Data Data Citation Working Group for commentary on this paper and on the ideas leading into it ...
The publisher or data repository element in the citation is automatically populated as the repository name, in this case, the Harvard Dataverse. ...
doi:10.29173/iq504
fatcat:e3iogfi3jfgkvitf4dbgdv5syu
Reproducible Workflow
[article]
2020
arXiv
pre-print
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We also describe the role of reproducibility (and other R's) in scientific workflows. ...
In this encyclopedia article, we explore the different definitions used in scientific literature (specifically pertaining to computational research), whether there is a need for a single standardized definition ...
The datasets used in the experiment/study should be included along with the publication in many ways, such as: • Releasing to data repositories like Zenodo, Dryad, Dataverse, Figshare etc. ...
arXiv:2012.13427v1
fatcat:ay7yx6pw65epbhzjdqyisf4csm
Committing to Data Quality Review
2014
International Journal of Digital Curation
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We explore a selection of other data repositories in the research data ecosystem, as well as the roles of researchers, academic libraries, and scholarly journals in regard to their application of data ...
And who should be responsible for data quality? We believe an essential measure of data quality is the ability to engage in informed reuse, which requires that data are independently understandable. ...
We also recognize the members of the International Association of Social Science Information Services and Technology (IASSIST), upon the 40th anniversary of the organization, for their dedication to data ...
doi:10.2218/ijdc.v9i1.317
fatcat:5364qjctujcw7jbifgfkf5u6oa
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