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Git can facilitate greater reproducibility and increased transparency in science

Karthik Ram
2013 Source Code for Biology and Medicine  
In this paper I provide an overview of Git along with use-cases that highlight how this tool can be leveraged to make science more reproducible and transparent, foster new collaborations, and support novel  ...  Despite this increase in transparency, it is still difficult to reproduce or build upon the findings of most scientific publications without access to a more complete workflow.  ...  an increasing burden to be more transparent in order to maintain their credibility [6] .  ... 
doi:10.1186/1751-0473-8-7 pmid:23448176 pmcid:PMC3639880 fatcat:hkumjkt2urcllhqj6l5zhkmryy

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

Néhémie Strupler, Toby C. Wilkinson
2017 Open Archaeology  
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  ...  But new digital technology now offers field practitioners a set of tools that can at least increase the transparency of the data-collection process as well as bring other benefits of an Open Science approach  ...  In the spirit of archaeological collaboration, Anja Slawisch (DAI) and Ben Marwick (Washington) offered invaluable advice and suggestions to early drafts of this article, which considerably improved to  ... 
doi:10.1515/opar-2017-0019 fatcat:kezebiak6zawjbzm5ertoov42e

r-cubed: Guiding the overwhelmed scientist from random wrangling to Reproducible Research in R

Luke Johnston, Helene Juel, Bettina Lengger, Daniel Witte, Hannah Chatwin, Malene Christiansen, Anders Isaksen
2021 Journal of Open Source Education  
Along with the open science movement on the rise, methods and analytic processes are also increasingly expected to be open and transparent and for scientific studies to be reproducible (Watson, 2015) .  ...  The computational learning module we have developed and described below aims to introduce and improve skills in R, reproducibility, and open science for researchers in the biomedical field, with a focus  ...  ., (2021) . r-cubed: Guiding the overwhelmed scientist from random wrangling to Reproducible Research in R. Journal of Open Source Education, 4(44), 122.  ... 
doi:10.21105/jose.00122 fatcat:c2rlbbxssbfx7gcs4crv7zsmzm

Moving forward: Transparency, Openness, and Reproducibility in Our Lab - Handout for Workshop Activity

Bram Zandbelt
2018 Figshare  
of transparency, openness, and reproducibility in science and what various stakeholders are doing to address this (available here:  ...  The presentation was followed by a breakout session centered on the question: what can we, as a team, do to becomemore transparent, open, and reproducible?  ...  Git can facilitate greater reproducibility and increased transparency in science. Source Code for Biology and Medicine, 8(1), 1-8.  ... 
doi:10.6084/m9.figshare.5822766.v1 fatcat:hcp5as5fzvbsrfasdff7hffaiq

Running an open experiment: transparency and reproducibility in soil and ecosystem science

Ben Bond-Lamberty, A Peyton Smith, Vanessa Bailey
2016 Environmental Research Letters  
Researchers in soil and ecosystem science, and almost every other field, are being pushed-by funders, journals, governments, and their peers-to increase transparency and reproducibility of their work.  ...  Nonetheless, we encourage the communities in our respective fields to consider its advantages, and to lead rather than follow with respect to scientific reproducibility, transparency, and data availability  ...  Acknowledgments This research was supported by the Office of Science of the US Department of Energy as part of the Terrestrial Ecosystem Sciences Program.  ... 
doi:10.1088/1748-9326/11/8/084004 fatcat:fbgepaurljgndijjmfu4xokewm

Our path to better science in less time using open data science tools

Julia S. Stewart Lowndes, Benjamin D. Best, Courtney Scarborough, Jamie C. Afflerbach, Melanie R. Frazier, Casey C. O'Hara, Ning Jiang, Benjamin S. Halpern
2017 Nature Ecology & Evolution  
See as an example of a website built with RMarkdown and the RStudio-GitHub workflow, and for links and resources referenced in the paper.  ...  Pacheco and L. Mosher who are our partners at Conservation International. We thank all past contributors and funders that have supported the Ocean Health Index, including B. Wrigley and H.  ...  Now, with available tools, the benefits of openness can be a byproduct of time saving efficiencies, because tools that reduce data headaches also result in science that is more transparent, reproducible  ... 
doi:10.1038/s41559-017-0160 pmid:28812630 fatcat:p4fyln5njnbj5olpyjlcvqyl5u

Striving for transparent and credible research: practical guidelines for behavioral ecologists

Malika Ihle, Isabel S. Winney, Anna Krystalli, Michael Croucher
2017 Behavioral Ecology  
Finally, we suggest that all journals in our field, such as Behavioral Ecology, give additional weight to transparent studies and therefore provide greater incentives to align our scientific practices  ...  same finding (lack of reproducibility), will result in a low probability of independent studies reaching the same outcome (lack of replicability).  ...  The authors thank all speakers and attendees of the post ISBE 2016 conference symposium "Challenge for our generation: Open, reproducible, and reliable science," as well as Wolfgang Forstmeier, Shinichi  ... 
doi:10.1093/beheco/arx003 pmid:29622916 pmcid:PMC5873838 fatcat:j5fk27qu5zf3lnwiw5qmrquzcy

WORCS: A workflow for open reproducible code in science

Caspar J. Van Lissa, Andreas M. Brandmaier, Loek Brinkman, Anna-Lena Lamprecht, Aaron Peikert, Marijn E. Struiksma, Barbara M.I. Vreede, Tobias Kuhn
2021 Data Science  
This paper introduces the Workflow for Open Reproducible Code in Science (WORCS): A step-by-step procedure that researchers can follow to make a research project open and reproducible.  ...  Adopting open science principles can be challenging, requiring conceptual education and training in the use of new tools.  ...  We acknowledge Jeroen Ooms for offering feedback and suggesting the use of the R package gert.  ... 
doi:10.3233/ds-210031 fatcat:buhljyyembakdobcdrlleoj5ie

Administrative social science data: The challenge of reproducible research

Christopher J Playford, Vernon Gayle, Roxanne Connelly, Alasdair JG Gray
2016 Big Data & Society  
We would also like to thank Professor Chris Dibben (University of Edinburgh) and colleagues at the Administrative Data Research Centre -Scotland.  ...  Professor Philip Stark (UC Berkeley), Kellie Ottoboni (UC Berkeley), Dr Nicole Janz (University of Cambridge), Dr Alasdair Rutherford (University of Stirling), Dr Iain Atherton (Edinburgh Napier University), and  ...  Sharing can be automated within the Git environment through global repositories such as GitHub and BitBucket and this enhances transparency, maintainability, and ultimately reproducibility.  ... 
doi:10.1177/2053951716684143 fatcat:rwducs6vhrgwlhbz7bsmj6acgu

GESIS Open Science Strategy

2020 EUROLAB annual report  
Open Methodology in the Social Sciences Open Methodology refers to the transparent documentation of data collection, processing and analysis, and means of reproducing these steps.  ...  Only once data and methodology are open, can results be reproduced. Additionally, Open Data can be re-used and help to address new research questions.  ... 
doi:10.21241/ssoar.68697 fatcat:ve7hka7mmnasjbxtjymyt3ntky

Seven Reasons Why: A User's Guide to Transparency and Reproducibility

Dalson Figueiredo Filho, Rodrigo Lins, Amanda Domingos, Nicole Janz, Lucas Silva
2019 Brazilian Political Science Review  
Despite a widespread agreement on the importance of transparency in science, a growing body of evidence suggests that both the natural and the social sciences are facing a reproducibility crisis.  ...  In addition, we review the most recent computational tools to work reproducibly. With this paper, we hope to foster transparency within the political science scholarly community.  ...  ) Council approved the changes to the Ethics Guide to facilitate data access and increase research transparency (LUPIA and ELMAN, 2014).  ... 
doi:10.1590/1981-3821201900020001 fatcat:v7i46mzolvhy3h3dzltit5lnai

The Tao of open science for ecology

Stephanie E. Hampton, Sean S. Anderson, Sarah C. Bagby, Corinna Gries, Xueying Han, Edmund M. Hart, Matthew B. Jones, W. Christopher Lenhardt, Andrew MacDonald, William K. Michener, Joe Mudge, Afshin Pourmokhtarian (+3 others)
2015 Ecosphere  
We present an overview of tools and best practices that can enable these shifts in mindset at each stage of the research process, including tools to support data management planning and reproducible analyses  ...  The concept of transparency at all stages of the research process, coupled with free and open access to data, code, and papers, constitutes "open science."  ...  Both data sources show an increase in the number of publications about open science, and an increase in annual citations of those papers.  ... 
doi:10.1890/es14-00402.1 fatcat:hoitnkpzczhl5nj2l3bqqhrr3u

Reproducible Research in R: A Tutorial on How to Do the Same Thing More Than Once

Aaron Peikert, Caspar J. van Lissa, Andreas M. Brandmaier
2021 Psych  
It is a building block for transparent and cumulative science because it enables the originator and other researchers, on other computers and later in time, to reproduce and thus understand how results  ...  In this tutorial, we demonstrate how the R package repro supports researchers in creating fully computationally reproducible research projects with tools from the software engineering community.  ...  We are grateful to Julia Delius for her helpful assistance in language and style editing.  ... 
doi:10.3390/psych3040053 fatcat:2rwhjoeksnerteyw4vbaktc5y4

Enabling Reproducibility for Small and Large Scale Research Data Sets

Stefan Pröll, Andreas Rauber
2017 D-Lib Magazine  
Git can facilitate greater reproducibility and increased transparency in science. Source code for biology and medicine 8.1 (2013): 1.  ...  Git [11].  ... 
doi:10.1045/january2017-proell fatcat:vhtxuslylndqrjotvla4lkjh5m

The importance of open science for biological assessment of aquatic environments

Marcus W. Beck, Casey O'Hara, Julia S. Stewart Lowndes, Raphael D. Mazor, Susanna Theroux, David J. Gillett, Belize Lane, Gregory Gearheart
2020 PeerJ  
At the core of this philosophy is the concept that research should be reproducible and transparent, in addition to having long-term value through effective data preservation and sharing.  ...  In this article, we review core open science concepts that have recently been adopted in the ecological sciences and emphasize how adoption can benefit the field of bioassessment for both prescriptive  ...  ADDITIONAL INFORMATION AND DECLARATIONS Funding The authors received no funding for this work. Competing Interests The authors declare there are no competing interests.  ... 
doi:10.7717/peerj.9539 pmid:32742805 pmcid:PMC7377246 fatcat:ewzf3zevifgx5hyqseb6zvponq
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