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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  ...  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

Dr. Ana Trisovic, Dr. Merce Crosas
2020 Zenodo  
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

Ana Trisovic, Katherine Mika, Ceilyn Boyd, Sebastian Feger, Mercè Crosas
2021 Data  
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

Vyacheslav Tykhonov
2021 Zenodo  
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]

Anthony Mammoliti, Petr Smirnov, Zhaleh Safikhani, Wail Ba-Alawi, Benjamin Haibe-Kains
2019 bioRxiv   pre-print
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

Latanya Sweeney, Merce Crosas
2013 Social Science Research Network  
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

Bill McKinney, Peter A. Meyer, Mercè Crosas, Piotr Sliz
2016 Annals of the New York Academy of Sciences  
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

Nadica Miljković
2021 Zenodo  
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

Hua Nie, Pengcheng Luo, Ping Fu
2021 Data Intelligence  
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

Patrick Mair
2016 Frontiers in Psychology  
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

Mercè Crosas, Gary King, James Honaker, Latanya Sweeney, Dhavan V. Shah, Joseph N. Cappella, W. Russell Neuman
2015 The Annals of the American Academy of Political and Social Science  
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

Anthony Mammoliti, Petr Smirnov, Zhaleh Safikhani, Wail Ba-Alawi, Benjamin Haibe-Kains
2019 Scientific Data  
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

Mercè Crosas
2014 IASSIST Quarterly  
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]

Anirudh Prabhu, Peter Fox
2020 arXiv   pre-print
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

Limor Peer, Ann Green, Elizabeth Stephenson
2014 International Journal of Digital Curation  
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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