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references.bib
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@article{Alberts2015b,
abstract = {Improve incentives to support research integrity},
author = {Alberts, Bruce and Cicerone, Ralph J and Fienberg, Stephen E and Kamb, Alexander and McNutt, Marcia and Nerem, Robert M and Schekman, Randy and Shiffrin, Richard and Stodden, Victoria and Suresh, Subra and Zuber, Maria T and Pope, Barbara Kline and Jamieson, Kathleen Hall},
doi = {10.1126/science.aab3847},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Alberts et al. - 2015 - Self-correction in science at work(2).pdf:pdf},
isbn = {1095-9203 (Electronic)$\backslash$r0036-8075 (Linking)},
issn = {0036-8075},
journal = {Science},
keywords = {Reproducible Research,Research: correction,Research: ethics,Research: null results,Research: replication,Scientific integrity},
mendeley-tags = {Reproducible Research},
month = {jun},
number = {6242},
pages = {1420--1422},
pmid = {26113701},
title = {{Self-correction in science at work}},
url = {http://www.sciencemag.org/cgi/doi/10.1126/science.aab3847},
volume = {348},
year = {2015}
}
@article{Alonso2006,
author = {Alonso, B and Valladares, F},
journal = {Ecosistemas},
pages = {1--6},
title = {{Bases de datos y metadatos en ecolog{\'{i}}a: compartir para investigar en cambio global}},
volume = {15},
year = {2006}
}
@article{Anglim2012,
author = {Anglim, Jeromy},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Anglim - 2012 - Simple Reproducible Analysis with knitr, R Markdown, and RStudio.pdf:pdf},
keywords = {R,Reproducible Research},
mendeley-tags = {R,Reproducible Research},
number = {July},
title = {{Simple Reproducible Analysis with knitr, R Markdown, and RStudio}},
year = {2012}
}
@article{Bailey2014,
author = {Bailey, David H and Borwein, Jonathan M and Stodden, Victoria C},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Bailey, Borwein, Stodden - 2014 - Facilitating reproducibility in scientific computing Principles and practice.pdf:pdf},
keywords = {Reproducible Research},
mendeley-tags = {Reproducible Research},
pages = {1--29},
title = {{Facilitating reproducibility in scientific computing : Principles and practice}},
year = {2014}
}
@article{Barnes2010a,
abstract = {Nature - the world's best science and medicine on your desktop},
author = {Barnes, Nick},
doi = {10.1038/467753a},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Barnes - 2010 - Publish your computer code it is good enough.pdf:pdf},
isbn = {1476-4687 (Electronic)$\backslash$r0028-0836 (Linking)},
issn = {0028-0836},
journal = {Nature},
pages = {753},
pmid = {20944687},
title = {{Publish your computer code: it is good enough.}},
volume = {467},
year = {2010}
}
@incollection{Bass2008,
author = {Bass, B and Nixon, T},
booktitle = {Encyclopedia of Ecology},
editor = {Jorgensen, SE and Fath, B},
keywords = {programming},
mendeley-tags = {programming},
pages = {720--731},
title = {{Computer languages}},
year = {2008}
}
@article{Bray2014,
abstract = {Nolan and Temple Lang argue that "the ability to express statistical computations is an essential skill." A key related capacity is the ability to conduct and present data analysis in a way that another person can understand and replicate. The copy-and-paste workflow that is an artifact of antiquated user-interface design makes reproducibility of statistical analysis more difficult, especially as data become increasingly complex and statistical methods become increasingly sophisticated. R Markdown is a new technology that makes creating fully-reproducible statistical analysis simple and painless. It provides a solution suitable not only for cutting edge research, but also for use in an introductory statistics course. We present evidence that R Markdown can be used effectively in introductory statistics courses, and discuss its role in the rapidly-changing world of statistical computation.},
archivePrefix = {arXiv},
arxivId = {1402.1894},
author = {Baumer, Ben and Cetinkaya-Rundel, Mine and Bray, Andrew and Loi, Linda and Horton, Nicholas J},
eprint = {1402.1894},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop//Baumer et al. - 2014 - R Markdown Integrating A Reproducible Analysis Tool into Introductory Statistics.pdf:pdf},
keywords = {R,Reproducible Research,VIP,statistics},
mendeley-tags = {R,Reproducible Research,VIP,statistics},
month = {feb},
title = {{R Markdown: Integrating A Reproducible Analysis Tool into Introductory Statistics}},
url = {http://arxiv.org/abs/1402.1894},
year = {2014}
}
@misc{Beck2014a,
author = {Beck, Marcus W},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Beck - 2014 - The nuts and bolts of Sweave Knitr for reproducible research with LATEX.pdf:pdf},
keywords = {R,Reproducible Research},
mendeley-tags = {R,Reproducible Research},
title = {{The nuts and bolts of Sweave / Knitr for reproducible research with LATEX}},
year = {2014}
}
@article{Becker2015,
abstract = {Science depends on collaboration, result reproduction, and the development of supporting software tools. Each of these requires careful management of software versions. We present a unified model for installing, managing, and publishing software contexts in R. It introduces the package manifest as a central data structure for representing version specific, decentralized package cohorts. The manifest points to package sources on arbitrary hosts and in various forms, including tarballs and directories under version control. We provide a high-level interface for creating and switching between side-by-side package libraries derived from manifests. Finally, we extend package installation to support the retrieval of exact package versions as indicated by manifests, and to maintain provenance for installed packages. The provenance information enables the user to publish libraries or sessions as manifests, hence completing the loop between publication and deployment. We have implemented this model across two software packages, switchr and GRANbase, and have released the source code under the Artistic 2.0 license.},
archivePrefix = {arXiv},
arxivId = {1501.02284},
author = {Becker, Gabriel and Barr, Cory and Gentleman, Robert and Lawrence, Michael},
eprint = {1501.02284},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Becker et al. - 2015 - Enhancing reproducibility and collaboration via management of R package cohorts.pdf:pdf},
journal = {Arxiv},
keywords = {Collaboration,Package development,R package,Reproducibility,Reproducible Research,Software distribution},
mendeley-tags = {R package,Reproducible Research},
month = {jan},
pages = {http://arxiv.org/abs/1501.02284v2},
title = {{Enhancing reproducibility and collaboration via management of R package cohorts}},
url = {http://export.arxiv.org/abs/1501.02284 http://arxiv.org/abs/1501.02284},
year = {2015}
}
@misc{Berger2012,
author = {Berger, Jim},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Berger - 2012 - Reproducibility of Science P-values and Multiplicity.pdf:pdf},
keywords = {Bayesian,Reproducible Research,p-values,statistics},
mendeley-tags = {Bayesian,Reproducible Research,p-values,statistics},
pages = {1--44},
title = {{Reproducibility of Science : P-values and Multiplicity}},
year = {2012}
}
@article{Blischak2016,
author = {Blischak, John D. and Davenport, Emily R. and Wilson, Greg},
doi = {10.1371/journal.pcbi.1004668},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Blischak, Davenport, Wilson - 2016 - A Quick Introduction to Version Control with Git and GitHub.pdf:pdf},
issn = {1553-7358},
journal = {PLOS Computational Biology},
keywords = {Reproducible Research,programming,version control},
mendeley-tags = {Reproducible Research,programming,version control},
month = {jan},
number = {1},
pages = {e1004668},
pmid = {26785377},
title = {{A Quick Introduction to Version Control with Git and GitHub}},
url = {http://dx.plos.org/10.1371/journal.pcbi.1004668},
volume = {12},
year = {2016}
}
@article{Boettiger2015,
abstract = {As computational work becomes more and more integral to many aspects of scientific research, computational reproducibility has become an issue of increasing importance to computer systems researchers and domain scientists alike. Though computational reproducibility seems more straight forward than replicating physical experiments, the complex and rapidly changing nature of computer environments makes being able to reproduce and extend such work a serious challenge. In this paper, I explore common reasons that code developed for one research project cannot be successfully executed or extended by subsequent researchers. I review current approaches to these issues, including virtual machines and workflow systems, and their limitations. I then examine how the popular emerging technology Docker combines several areas from systems research - such as operating system virtualization, cross-platform portability, modular re-usable elements, versioning, and a `DevOps' philosophy, to address these challenges. I illustrate this with several examples of Docker use with a focus on the R statistical environment.},
archivePrefix = {arXiv},
arxivId = {arXiv:1410.0846v1},
author = {Boettiger, Carl},
doi = {10.1145/2723872.2723882},
eprint = {arXiv:1410.0846v1},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Boettiger - 2015 - An introduction to Docker for reproducible research.pdf:pdf},
issn = {01635980},
journal = {ACM SIGOPS Operating Systems Review},
keywords = {Reproducible Research},
mendeley-tags = {Reproducible Research},
month = {jan},
number = {1},
pages = {71--79},
title = {{An introduction to Docker for reproducible research}},
url = {http://dl.acm.org/citation.cfm?doid=2723872.2723882},
volume = {49},
year = {2015}
}
@misc{Bolker2013a,
author = {Bolker, B},
doi = {10.1016/j.csda.2012.01.026.http},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Bolker - 2013 - Generating HTML from knitr and Pandoc.pdf:pdf},
keywords = {R,Reproducible Research},
mendeley-tags = {R,Reproducible Research},
number = {8},
pages = {2012--2013},
title = {{Generating HTML from knitr and Pandoc}},
volume = {56},
year = {2013}
}
@misc{Bolker2013,
author = {Bolker, B},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Bolker - 2013 - Literate programming, version control, reproducible research, collaboration, and all that.pdf:pdf},
keywords = {R,Reproducible Research,version control},
mendeley-tags = {R,Reproducible Research,version control},
pages = {3153},
title = {{Literate programming, version control, reproducible research, collaboration, and all that}},
year = {2013}
}
@misc{Bond-Lamberty2014a,
author = {Bond-Lamberty, Ben},
keywords = {Reproducible Research},
mendeley-tags = {Reproducible Research},
title = {{Robust and reproducible research using R}},
url = {http://rstudio-pubs-static.s3.amazonaws.com/14911{\_}24ffedb113f74789b709cbd694dc255c.html{\#}/},
year = {2014}
}
@article{Bray2015,
author = {Bray, A},
doi = {10.1080/09332480.2014.965635},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Bray - 2015 - Your Students Should Be Learning to Analyze Data in the Reproducible Paradigm.pdf:pdf},
journal = {Chance},
keywords = {Reproducible Research,statistics,teaching},
mendeley-tags = {Reproducible Research,statistics,teaching},
number = {3},
pages = {37--41},
title = {{Your Students Should Be Learning to Analyze Data in the Reproducible Paradigm}},
volume = {27},
year = {2015}
}
@misc{Thompson2011c,
author = {Broman, K},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Broman - 2015 - Reproducible Research.pdf:pdf},
keywords = {PAT-Reference,Reproducible Research},
mendeley-tags = {Reproducible Research},
title = {{Reproducible Research}},
year = {2015}
}
@misc{Broman2014d,
author = {Broman, Karl},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Broman - 2014 - Big jobs simulations.pdf:pdf},
keywords = {R,Reproducible Research,programming},
mendeley-tags = {R,Reproducible Research,programming},
title = {{Big jobs / simulations}},
year = {2014}
}
@misc{Bromand,
author = {Broman, Karl},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Broman - Unknown - KnitR LATEX → paper.pdf:pdf},
keywords = {Reproducible Research},
mendeley-tags = {Reproducible Research},
title = {{KnitR + LATEX → paper}}
}
@article{Bromane,
author = {Broman, Karl},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Broman - Unknown - Licenses human subjects data.pdf:pdf},
keywords = {Reproducible Research,programming},
mendeley-tags = {Reproducible Research,programming},
title = {{Licenses ; human subjects data}}
}
@misc{Broman2014a,
author = {Broman, Karl},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Broman - 2014 - Organizing projects exploratory data analysis.pdf:pdf},
keywords = {R,Reproducible Research,advice,writing},
mendeley-tags = {R,Reproducible Research,advice,writing},
title = {{Organizing projects; exploratory data analysis}},
year = {2014}
}
@misc{Broman2014,
author = {Broman, Karl},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Broman - 2014 - Presentations and posters.pdf:pdf},
keywords = {Reproducible Research,advice,presenting},
mendeley-tags = {Reproducible Research,advice,presenting},
title = {{Presentations and posters}},
year = {2014}
}
@misc{Broman,
author = {Broman, Karl},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Broman - 2014 - Tools for Reproducible Research.pdf:pdf},
keywords = {R,Reproducible Research,VIP},
mendeley-tags = {R,Reproducible Research,VIP},
title = {{Tools for Reproducible Research}},
year = {2014}
}
@article{Buck2015,
author = {Buck, S},
doi = {10.1126/science.aac8041},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Buck - 2015 - Solving reproducibility.pdf:pdf},
issn = {0036-8075},
journal = {Science},
keywords = {Reproducible Research},
mendeley-tags = {Reproducible Research},
number = {6242},
pages = {6242},
pmid = {26113692},
title = {{Solving reproducibility}},
volume = {348},
year = {2015}
}
@article{Buckheit1995,
abstract = {Wavelab is a library of wavelet-packet analysis, cosine-packet analysis and matching pursuit. The library is available free of charge over the Internet. Versions are provided for Macintosh, UNIX and Windows machines. Wavelab makes available, in one package, all the code to reproduce all the figures in our published wavelet articles. The interested reader can inspect the source code to see exactly what algorithms were used, how parameters were set in producing our figures, and can then modify the source to produce variations on our results. WAVELAB has been developed, in part, because of exhortations by Jon Claerbout of Stanford that computational scientists should engage in “really reproducible” research.},
author = {Buckheit, Jb and Donoho, Dl},
doi = {10.1007/978-1-4612-2544-7},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Buckheit, Donoho - 1995 - WaveLab and Reproducible Research.pdf:pdf},
isbn = {978-0-387-94564-4},
journal = {Wavelets and Statistics},
keywords = {Reproducible Research},
mendeley-tags = {Reproducible Research},
pages = {55--81},
title = {{WaveLab and Reproducible Research}},
url = {http://link.springer.com/chapter/10.1007/978-1-4612-2544-7{\_}5$\backslash$nhttp://link.springer.com/10.1007/978-1-4612-2544-7},
volume = {103},
year = {1995}
}
@article{Cassey2006,
annote = {NOT IN FILE},
author = {CASSEY, PHILLIP and BLACKBURN, TIM M.},
doi = {10.1641/0006-3568(2006)56[958:RARIE]2.0.CO;2},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/CASSEY, BLACKBURN - 2006 - Reproducibility and Repeatability in Ecology.pdf:pdf},
issn = {0006-3568},
journal = {BioScience},
keywords = {Reproducible Research,ecology,repeatability},
mendeley-tags = {Reproducible Research},
number = {12},
pages = {958},
title = {{Reproducibility and Repeatability in Ecology}},
url = {http://dx.doi.org/10.1641/0006-3568(2006)56[958:RARIE]2.0.CO;2 http://bioscience.oxfordjournals.org/cgi/doi/10.1641/0006-3568(2006)56[958:RARIE]2.0.CO;2},
volume = {56},
year = {2006}
}
@misc{Cetinkaya-Rundel2013,
author = {Cetinkaya-Rundel, M},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Cetinkaya-Rundel - 2013 - Teaching data analysis in R through the lens of reproducibility.pdf:pdf},
keywords = {R,Reproducible Research},
mendeley-tags = {R,Reproducible Research},
title = {{Teaching data analysis in R through the lens of reproducibility}},
year = {2013}
}
@article{Cetinkaya-Rundel2014,
author = {{\c{C}}etinkaya-Rundel, Mine and Bray, Andrew},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/{\c{C}}etinkaya-Rundel, Bray - 2014 - Teaching data analysis in R through the lens of reproducibility.pdf:pdf},
keywords = {R,Reproducible Research},
mendeley-tags = {R,Reproducible Research},
pages = {2014},
title = {{Teaching data analysis in R through the lens of reproducibility}},
year = {2014}
}
@article{Chamberlain2014b,
abstract = {Reproducible research is a growing movement among scientists, but the tools for creating sustainable software to support the computational side of research are still in their infancy and are typically only being used by scientists with expertise in com- puter programming and system administration. Docker is a new platform developed for the DevOps community that enables the easy creation and management of consistent computational environments. This article describes how we have applied it to computational science and suggests that it could be a powerful tool for reproducible research.},
author = {Chamberlain, Ryan and Schommer, Jennifer},
doi = {http://dx.doi.org/10.6084/m9.figshare.1101910},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Chamberlain, Schommer - 2014 - Using Docker to support Reproducible Research (submission to WSSSPE2).pdf:pdf},
journal = {Figshare},
keywords = {Reproducible Research,code sharing,computational science,docker,open science,reproducible research,sustainable software,virtualization},
mendeley-tags = {Reproducible Research},
pages = {1--4},
title = {{Using Docker to support Reproducible Research (submission to WSSSPE2)}},
url = {http://figshare.com/articles/Using{\_}Docker{\_}to{\_}Support{\_}Reproducible{\_}Research/1101910},
year = {2014}
}
@article{Hayden2015,
abstract = {Nature Biotechnology asks peer reviewers to check accessibility of software used in computational studies.},
author = {{Check Hayden}, Erika},
doi = {10.1038/520276a},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Check Hayden - 2015 - Rule rewrite aims to clean up scientific software.pdf:pdf},
issn = {0028-0836},
journal = {Nature},
keywords = {Reproducibility,Reproducible Research},
mendeley-tags = {Reproducible Research},
month = {apr},
number = {7547},
pages = {276--277},
pmid = {25877185},
title = {{Rule rewrite aims to clean up scientific software}},
url = {http://www.nature.com/doifinder/10.1038/520276a},
volume = {520},
year = {2015}
}
@inproceedings{Claerbout1992,
author = {Claerbout, J and Karrenbach, Martin},
booktitle = {Proceedings of the 62nd Annual International Meeting of the Society of Exploration Geophysics},
keywords = {Reproducible Research},
mendeley-tags = {Reproducible Research},
pages = {601--604},
title = {{Electronic documents give reproducible research a new meaning}},
year = {1992}
}
@misc{Hester2013,
author = {Collado, L},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Collado - 2013 - Creating awesome reports for multiple audiences using knitrBootstrap.pdf:pdf},
keywords = {R,R package,Reproducible Research},
mendeley-tags = {R,R package,Reproducible Research},
pages = {1--6},
title = {{Creating awesome reports for multiple audiences using knitrBootstrap}},
year = {2013}
}
@misc{Tools,
author = {Cranmer, K},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Cranmer - 2015 - New tools and trends in reproducible research {\&} open science.pdf:pdf},
keywords = {Reproducible Research},
mendeley-tags = {Reproducible Research},
title = {{New tools and trends in reproducible research {\&} open science}},
year = {2015}
}
@article{Donoho2010,
author = {Donoho, David L.},
doi = {10.1093/biostatistics/kxq028},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Donoho - 2010 - An invitation to reproducible computational research.pdf:pdf},
issn = {14654644},
journal = {Biostatistics},
keywords = {Reproducible Research},
mendeley-tags = {Reproducible Research},
number = {3},
pages = {385--388},
pmid = {20538873},
title = {{An invitation to reproducible computational research}},
volume = {11},
year = {2010}
}
@article{Drew2013,
author = {Drew, Bryan T and Gazis, Romina and Cabezas, Patricia and Swithers, Kristen S and Deng, Jiabin and Rodriguez, Roseana and Katz, Laura a and Crandall, Keith a and Hibbett, David S and Soltis, Douglas E},
doi = {10.1371/journal.pbio.1001636},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Drew et al. - 2013 - Lost Branches on the Tree of Life.pdf:pdf},
issn = {1545-7885},
journal = {PLoS Biology},
keywords = {Reproducible Research,phylogenetics},
mendeley-tags = {Reproducible Research,phylogenetics},
month = {sep},
number = {9},
pages = {e1001636},
pmid = {24019756},
title = {{Lost Branches on the Tree of Life}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3760775{\&}tool=pmcentrez{\&}rendertype=abstract http://dx.plos.org/10.1371/journal.pbio.1001636},
volume = {11},
year = {2013}
}
@manual{Eddelbuettel2015,
annote = {R package version 0.1.0},
author = {Eddelbuettel, Dirk},
keywords = {R,Reproducible Research},
mendeley-tags = {R,Reproducible Research},
title = {{drat: Drat R Archive Template}},
url = {https://cran.r-project.org/package=drat},
year = {2015}
}
@article{Fegraus2005,
author = {Fegraus, Eric H and Andelman, Sandy and Jones, Matthew B and Schildhauer, Mark},
doi = {10.1890/0012-9623(2005)86[158:MTVOED]2.0.CO;2},
issn = {2327-6096},
journal = {The Bulletin of the Ecological Society of America},
number = {3},
pages = {158--168},
publisher = {The Ecological Society of America},
title = {{Maximizing the Value of Ecological Data with Structured Metadata: An Introduction to Ecological Metadata Language (EML) and Principles for Metadata Creation}},
url = {http://dx.doi.org/10.1890/0012-9623(2005)86[158:MTVOED]2.0.CO;2},
volume = {86},
year = {2005}
}
@article{Feitelson2015,
author = {Feitelson, Dror G.},
doi = {10.1145/2723872.2723875},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Feitelson - 2015 - From repeatability to reproducibility and corroboration.pdf:pdf},
issn = {01635980},
journal = {ACM SIGOPS Operating Systems Review},
keywords = {Reproducible Research},
mendeley-tags = {Reproducible Research},
number = {1},
pages = {3--11},
title = {{From repeatability to reproducibility and corroboration}},
url = {http://dl.acm.org/citation.cfm?id=2723875},
volume = {49},
year = {2015}
}
@misc{Fitzjohn2014,
author = {Fitzjohn, Rich},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Fitzjohn - 2014 - Reproducible research.pdf:pdf},
keywords = {Reproducible Research,VIP},
mendeley-tags = {Reproducible Research,VIP},
title = {{Reproducible research}},
year = {2014}
}
@misc{FitzJohn2013f,
author = {FitzJohn, Richard G},
booktitle = {Nice R Code},
keywords = {R,Reproducible Research},
mendeley-tags = {R,Reproducible Research},
title = {{Designing projects}},
url = {http://nicercode.github.io/blog/2013-04-05-projects/},
year = {2013}
}
@article{FitzJohn2014,
author = {FitzJohn, Richard G. and Pennell, Matthew W and Zanne, Amy E and Stevens, Peter F and Tank, David C and Cornwell, William K},
doi = {10.1111/1365-2745.12260},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/FitzJohn et al. - 2014 - How much of the world is woody.pdf:pdf},
issn = {00220477},
journal = {Journal of Ecology},
keywords = {Reproducible Research,methods,plants,traits},
mendeley-tags = {Reproducible Research,methods,plants,traits},
month = {sep},
number = {5},
pages = {1266--1272},
title = {{How much of the world is woody?}},
url = {http://doi.wiley.com/10.1111/1365-2745.12260},
volume = {102},
year = {2014}
}
@article{Fomel2009,
abstract = {Reproducibility is a core principle of science. For computational experiments to become reproducible, one needs to develop a system for linking scientific publications with computational recipes. Articles in this special issue argue in favor of computational reproducibility and describe several practical approaches to reproducible research.},
author = {Fomel, Sergey and Claerbout, Jon F},
doi = {http://dx.doi.org/10.1109/MCSE.2009.14},
file = {::},
isbn = {1521-9615},
issn = {1521-9615},
journal = {Computing in Science {\&} Engineering},
pages = {5--7},
title = {{Reproducible Research}},
url = {http://cise.aip.org/dbt/dbt.jsp?KEY=CSENFA{\&}Volume=11{\&}Issue=1},
volume = {11},
year = {2009}
}
@misc{Gandrud,
author = {Gandrud, Christopher},
booktitle = {Reproducible Research with R and RStudio},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Gandrud - 2013 - Getting started with reproducible research(2).pdf:pdf},
keywords = {R,Reproducible Research},
mendeley-tags = {R,Reproducible Research},
title = {{Getting started with reproducible research}},
year = {2013}
}
@incollection{Gandruda,
author = {Gandrud, Christopher},
booktitle = {Reproducible Research with R and RStudio},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Gandrud - 2013 - Showing results with tables.pdf:pdf},
keywords = {R,Reproducible Research},
mendeley-tags = {R,Reproducible Research},
title = {{Showing results with tables}},
year = {2013}
}
@article{Garijo2013,
abstract = {How easy is it to reproduce the results found in a typical computational biology paper? Either through experience or intuition the reader will already know that the answer is with difficulty or not at all. In this paper we attempt to quantify this difficulty by reproducing a previously published paper for different classes of users (ranging from users with little expertise to domain experts) and suggest ways in which the situation might be improved. Quantification is achieved by estimating the time required to reproduce each of the steps in the method described in the original paper and make them part of an explicit workflow that reproduces the original results. Reproducing the method took several months of effort, and required using new versions and new software that posed challenges to reconstructing and validating the results. The quantification leads to "reproducibility maps" that reveal that novice researchers would only be able to reproduce a few of the steps in the method, and that only expert researchers with advance knowledge of the domain would be able to reproduce the method in its entirety. The workflow itself is published as an online resource together with supporting software and data. The paper concludes with a brief discussion of the complexities of requiring reproducibility in terms of cost versus benefit, and a desiderata with our observations and guidelines for improving reproducibility. This has implications not only in reproducing the work of others from published papers, but reproducing work from one's own laboratory.},
author = {Garijo, Daniel and Kinnings, Sarah and Xie, Li and Xie, Lei and Zhang, Yinliang and Bourne, Philip E. and Gil, Yolanda},
doi = {10.1371/journal.pone.0080278},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Garijo et al. - 2013 - Quantifying Reproducibility in Computational Biology The Case of the Tuberculosis Drugome.pdf:pdf},
isbn = {10.1371/journal.pone.0080278},
issn = {1932-6203},
journal = {PLoS ONE},
keywords = {Reproducible Research},
mendeley-tags = {Reproducible Research},
month = {nov},
number = {11},
pages = {e80278},
pmid = {24312207},
title = {{Quantifying Reproducibility in Computational Biology: The Case of the Tuberculosis Drugome}},
url = {http://dx.plos.org/10.1371/journal.pone.0080278},
volume = {8},
year = {2013}
}
@article{Gelmanb,
author = {Gelman, Andrew},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Gelman - 2014 - The AAA Tranche of Subprime Science.pdf:pdf},
journal = {Chance},
keywords = {NHST,Reproducible Research,statistics},
mendeley-tags = {NHST,Reproducible Research,statistics},
pages = {51--56},
title = {{The AAA Tranche of Subprime Science}},
year = {2014}
}
@article{Sangil2010,
author = {Gil, Inigo San and Hutchison, Vivian and Frame, Mike and Palanisamy, Giri},
doi = {10.1080/19386389.2010.506389},
journal = {Journal of Library Metadata},
number = {2-3},
pages = {99--118},
title = {{Metadata Activities in Biology}},
volume = {10},
year = {2010}
}
@article{Goodman2014,
author = {Goodman, Alyssa and Pepe, Alberto and Blocker, Alexander W and Borgman, Christine L and Cranmer, Kyle and Crosas, Merce and {Di Stefano}, Rosanne and Gil, Yolanda and Groth, Paul and Hedstrom, Margaret and Hogg, David W and Kashyap, Vinay and Mahabal, Ashish and Siemiginowska, Aneta and Slavkovic, Aleksandra},
doi = {10.1371/journal.pcbi.1003542},
editor = {Bourne, Philip E.},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Goodman et al. - 2014 - Ten Simple Rules for the Care and Feeding of Scientific Data.pdf:pdf},
issn = {1553-7358},
journal = {PLoS Computational Biology},
keywords = {Reproducible Research,VIP,advice,data,statistics},
mendeley-tags = {Reproducible Research,VIP,advice,data,statistics},
month = {apr},
number = {4},
pages = {e1003542},
pmid = {24763340},
title = {{Ten Simple Rules for the Care and Feeding of Scientific Data}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/24763340 http://dx.plos.org/10.1371/journal.pcbi.1003542},
volume = {10},
year = {2014}
}
@misc{Goring2013b,
author = {Goring, Simon J},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Goring - 2013 - Reproducibility and R.pdf:pdf},
keywords = {R,Reproducible Research,version control},
mendeley-tags = {R,Reproducible Research,version control},
number = {November},
title = {{Reproducibility and R}},
year = {2013}
}
@article{Goring2013c,
author = {Goring, Simon and Lacourse, Terri and Pellatt, Marlow G. and Mathewes, Rolf W.},
doi = {10.1111/1365-2745.12135},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Goring et al. - 2013 - Pollen assemblage richness does not reflect regional plant species richness a cautionary tale.pdf:pdf},
issn = {00220477},
journal = {Journal of Ecology},
keywords = {fossils,palaeo,pollen,species richness,uncertainty},
mendeley-tags = {fossils,palaeo,pollen,species richness,uncertainty},
month = {sep},
number = {5},
pages = {1137--1145},
title = {{Pollen assemblage richness does not reflect regional plant species richness: a cautionary tale}},
url = {http://doi.wiley.com/10.1111/1365-2745.12135},
volume = {101},
year = {2013}
}
@article{Haddaway2015,
author = {Haddaway, Neal R. and Verhoeven, Jos T.a.},
doi = {10.1002/ece3.1722},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Haddaway, Verhoeven - 2015 - Poor methodological detail precludes experimental repeatability and hampers synthesis in ecology.pdf:pdf},
issn = {20457758},
journal = {Ecology and Evolution},
keywords = {Reproducible Research,evidence synthesis,experimental design,meta-analysis,reliability,research legacy,susceptibility to bias,systematic review},
mendeley-tags = {Reproducible Research},
month = {oct},
number = {19},
pages = {4451--4454},
title = {{Poor methodological detail precludes experimental repeatability and hampers synthesis in ecology}},
url = {http://doi.wiley.com/10.1002/ece3.1722},
volume = {5},
year = {2015}
}
@article{Hampton2015a,
abstract = {The field of ecology is poised to take advantage of emerging technologies that facilitate the gathering, analyzing, and sharing of data, methods, and results. 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.” Despite the many benefits of an open approach to science, a number of barriers to entry exist that may prevent researchers from embracing openness in their own work. Here we describe several key shifts in mindset that underpin the transition to more open science. These shifts in mindset include thinking about data stewardship rather than data ownership, embracing transparency throughout the data life-cycle and project duration, and accepting critique in public. Though foreign and perhaps frightening at first, these changes in thinking stand to benefit the field of ecology by fostering collegiality and broadening access to data and findings. We present an overview of tools and best practices that ...},
author = {Hampton, Stephanie E. and Anderson, Sean S. and Bagby, Sarah C. and Gries, Corinna and Han, Xueying and Hart, Edmund M. and Jones, Matthew B. and Lenhardt, W. Christopher and MacDonald, Andrew and Michener, William K. and Mudge, Joe and Pourmokhtarian, Afshin and Schildhauer, Mark P. and Woo, Kara H. and Zimmerman, Naupaka},
doi = {10.1890/ES14-00402.1},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Hampton et al. - 2015 - The Tao of open science for ecology.pdf:pdf},
issn = {2150-8925},
journal = {Ecosphere},
keywords = {Reproducible Research,accepted 18 march 2015,al,article distributed under the,collins,commons,copyright,corresponding,data management,ecology,editor,l,open access,open science,published 23 july 2015,received 21 october 2014,reproducible research,revised 7 march 2015,s,terms of the creative,this is an open-access,{\'{o}} 2015 hampton et},
mendeley-tags = {Reproducible Research,open science},
month = {jul},
number = {7},
pages = {art120},
title = {{The Tao of open science for ecology}},
url = {http://www.esajournals.org/doi/10.1890/ES14-00402.1 http://doi.wiley.com/10.1890/ES14-00402.1},
volume = {6},
year = {2015}
}
@article{Hart2016,
author = {Hart, Edmund and Barmby, P and LeBauer, D and Michonneau, F and Mount, S and Mulrooney, P and Poisot, T and Woo, KH and Zimmerman, N and Hollister, JW},
doi = {10.7287/peerj.preprints.1448v2},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Hart - 2015 - Ten simple rules for digital data storage.pdf:pdf},
issn = {2167-9843},
journal = {PeerJ preprints},
keywords = {Reproducible Research},
mendeley-tags = {Reproducible Research},
pages = {e1448v2},
title = {{Ten simple rules for digital data storage}},
volume = {4},
year = {2016}
}
@article{Hey2015a,
author = {Hey, Tony and Payne, Mike C.},
doi = {10.1038/nphys3313},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Hey, Payne - 2015 - Open science decoded.pdf:pdf},
issn = {1745-2473},
journal = {Nature Physics},
keywords = {Reproducible Research},
mendeley-tags = {Reproducible Research},
month = {apr},
number = {5},
pages = {367--369},
publisher = {Nature Publishing Group},
title = {{Open science decoded}},
url = {http://www.nature.com/doifinder/10.1038/nphys3313},
volume = {11},
year = {2015}
}
@article{Horton2014,
author = {Horton, NJ and Baumer, BS and Wickham, H},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Horton, Baumer, Wickham - 2014 - Teaching precursors to data science in introductory and second courses in statistics.pdf:pdf},
journal = {arXiv preprint arXiv:1401.3269},
keywords = {R,Reproducible Research},
mendeley-tags = {R,Reproducible Research},
title = {{Teaching precursors to data science in introductory and second courses in statistics}},
url = {http://arxiv.org/abs/1401.3269},
year = {2014}
}
@article{Huang2014,
author = {Huang, Xiaolei},
file = {::},
journal = {Science},
number = {6215},
pages = {1307},
title = {{Reproducibility in ecological research}},
volume = {346},
year = {2014}
}
@article{Humburg2014,
author = {Humburg, Peter},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Humburg - 2014 - Using knitr and pandoc to create reproducible scientific reports.pdf:pdf},
keywords = {R,Reproducible Research,VIP},
mendeley-tags = {R,Reproducible Research,VIP},
title = {{Using knitr and pandoc to create reproducible scientific reports}},
year = {2014}
}
@article{Ince2012,
author = {Ince, Darrel C. and Hatton, Leslie and Graham-Cumming, John},
doi = {10.1038/nature10836},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Ince, Hatton, Graham-Cumming - 2012 - The case for open computer programs.pdf:pdf},
issn = {0028-0836},
journal = {Nature},
keywords = {Reproducible Research,VIP,programming},
mendeley-tags = {Reproducible Research,VIP,programming},
month = {feb},
number = {7386},
pages = {485--488},
publisher = {Nature Publishing Group},
title = {{The case for open computer programs}},
url = {http://www.nature.com/doifinder/10.1038/nature10836},
volume = {482},
year = {2012}
}
@article{Johnston2015,
author = {Johnston, Susan},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Johnston - 2015 - Introduction to Reproducible Research in R and R Studio . What is Reproducible Research.pdf:pdf},
keywords = {Reproducible Research},
mendeley-tags = {Reproducible Research},
title = {{Introduction to Reproducible Research in R and R Studio . What is Reproducible Research ?}},
year = {2015}
}
@misc{Jones2015a,
author = {Jones, MB and Jones, C and Walker, L},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Jones, Jones, Walker - 2015 - Reproducible science via semantics and provenance for ecological data.pdf:pdf},
isbn = {0012-9658},
issn = {0012-9658},
keywords = {Reproducible Research},
mendeley-tags = {Reproducible Research},
title = {{Reproducible science via semantics and provenance for ecological data}},
url = {{\textless}Go to ISI{\textgreater}://000272700800001},
year = {2015}
}
@misc{Jones2013f,
author = {Jones, ZM},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Jones - 2013 - GNU Make for reproducible data analysis.pdf:pdf},
keywords = {Reproducible Research,programming},
mendeley-tags = {Reproducible Research,programming},
pages = {1--3},
title = {{GNU Make for reproducible data analysis}},
year = {2013}
}
@article{Kaiser2012,
abstract = {A nonprofit's effort to replicate 50 top cancer papers is shaking up labs},
author = {Kaiser, Jocelyn},
doi = {10.1126/science.348.6242.1411},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Kaiser - 2012 - The cancer test.pdf:pdf},
issn = {1099274X},
journal = {Science},
keywords = {Reproducible Research,Research: correction,Research: ethics,Research: replication,Scientific integrity},
mendeley-tags = {Reproducible Research},
number = {6242},
pages = {44--47},
title = {{The cancer test}},
volume = {348},
year = {2012}
}
@article{Kenall2015,
author = {Kenall, Amye and Edmunds, Scott and Goodman, Laurie and Bal, Liz and Flintoft, Louisa and Shanahan, Daniel R and Shipley, Tim},
doi = {10.1186/s12868-015-0177-z},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Kenall et al. - 2015 - Better reporting for better research a checklist for reproducibility.pdf:pdf},
issn = {1471-2202},
journal = {BMC Neuroscience},
keywords = {Reproducible Research},
mendeley-tags = {Reproducible Research},
month = {dec},
number = {1},
pages = {44},
publisher = {BioMed Central},
title = {{Better reporting for better research: a checklist for reproducibility}},
url = {http://www.biomedcentral.com/1471-2202/16/44},
volume = {16},
year = {2015}
}
@article{Kitzes2015,
author = {Kitzes, Justin and Wilber, Mark},
doi = {10.1111/oik.02629},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Kitzes, Wilber - 2015 - macroeco Reproducible ecological pattern analysis in Pyhon.pdf:pdf},
journal = {Ecography},
keywords = {Reproducible Research},
mendeley-tags = {Reproducible Research},
number = {November 2015},
pages = {1--7},
title = {{macroeco: Reproducible ecological pattern analysis in Pyhon}},
year = {2015}
}
@article{Leek2015,
author = {Leek, Jeffrey T and Peng, Roger D},
doi = {10.1073/pnas.1421412111},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Leek, Peng - 2015 - Opinion Reproducible research can still be wrong Adopting a prevention approach Fig. 1.pdf:pdf},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences},
keywords = {Reproducible Research},
mendeley-tags = {Reproducible Research},
month = {feb},
number = {6},
pages = {1645--1646},
title = {{Opinion: Reproducible research can still be wrong: Adopting a prevention approach}},
url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1421412111},
volume = {112},
year = {2015}
}
@article{Leeper2014a,
author = {Leeper, Thomas J},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Leeper - 2014 - Archiving Reproducible Research with R and Dataverse.pdf:pdf},
journal = {The R journal},
keywords = {R package,Reproducible Research,data},
mendeley-tags = {R package,Reproducible Research,data},
pages = {151--158},
title = {{Archiving Reproducible Research with R and Dataverse}},
volume = {6},
year = {2014}
}
@article{LeVeque2012a,
abstract = {This article considers the obstacles involved in creating reproducible computational research as well as some efforts and approaches to overcome them.},
author = {LeVeque, Randall J and Mitchell, Ian M and Stodden, Victoria},
doi = {10.1109/MCSE.2012.38},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/LeVeque, Mitchell, Stodden - 2012 - Reproducible research for scientific computing Tools and strategies for changing the culture.pdf:pdf},
isbn = {1521-9615},
issn = {1521-9615},
journal = {Computing in Science {\&} Engineering},
keywords = {Reproducible Research},
mendeley-tags = {Reproducible Research},
month = {jul},
number = {4},
pages = {13--17},
pmid = {4125329905357828556},
title = {{Reproducible research for scientific computing: Tools and strategies for changing the culture}},
url = {http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=6171147},
volume = {14},
year = {2012}
}
@article{Lim2014a,
author = {Lim, Eric and Murrell, Paul and Thompson, Finlay},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Lim, Murrell, Thompson - 2014 - Invertible Reproducible Documents.pdf:pdf},
keywords = {R,Reproducible Research,VIP},
mendeley-tags = {R,Reproducible Research,VIP},
title = {{Invertible Reproducible Documents}},
year = {2014}
}
@article{Liu2014b,
abstract = {BACKGROUND: It is scientifically and ethically imperative that the results of statistical analysis of biomedical research data be computationally reproducible in the sense that the reported results can be easily recapitulated from the study data. Some statistical analyses are computationally a function of many data files, program files, and other details that are updated or corrected over time. In many applications, it is infeasible to manually maintain an accurate and complete record of all these details about a particular analysis. RESULTS: Therefore, we developed the rctrack package that automatically collects and archives read only copies of program files, data files, and other details needed to computationally reproduce an analysis. CONCLUSIONS: The rctrack package uses the trace function to temporarily embed detail collection procedures into functions that read files, write files, or generate random numbers so that no special modifications of the primary R program are necessary. At the conclusion of the analysis, rctrack uses these details to automatically generate a read only archive of data files, program files, result files, and other details needed to recapitulate the analysis results. Information about this archive may be included as an appendix of a report generated by Sweave or knitR. Here, we describe the usage, implementation, and other features of the rctrack package. The rctrack package is freely available from http://www.stjuderesearch.org/site/depts/biostats/rctrack under the GPL license.},
author = {Liu, Zhifa and Pounds, Stan},
doi = {10.1186/1471-2105-15-138},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Liu, Pounds - 2014 - An R package that automatically collects and archives details for reproducible computing.pdf:pdf},
issn = {1471-2105},
journal = {BMC Bioinformatics},
keywords = {R package,Reproducible Research},
mendeley-tags = {R package,Reproducible Research},
month = {jan},
number = {1},
pages = {138},
pmid = {24886202},
title = {{An R package that automatically collects and archives details for reproducible computing}},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4026591{\&}tool=pmcentrez{\&}rendertype=abstract http://www.biomedcentral.com/1471-2105/15/138},
volume = {15},
year = {2014}
}
@article{Markowetz2015a,
abstract = {And so, my fellow scientists: ask not what you can do for reproducibility; ask what reproducibility can do for you! Here, I present five reasons why working reproducibly pays off in the long run and is in the self-interest of every ambitious, career-oriented scientist.},
author = {Markowetz, Florian},
doi = {10.1186/s13059-015-0850-7},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Markowetz - 2015 - Five selfish reasons to work reproducibly.pdf:pdf},
issn = {1465-6906},
journal = {Genome Biol},
keywords = {Reproducibility,Scientific career,Reproducible Research,a black board,a complex equation on,a short,an,equations,even more complex equation,here a miracle oc-,on the right half,reproducibility,scientific career,sentence links the two,the left half of},
mendeley-tags = {Reproducible Research},
number = {1},
pages = {274},
publisher = {Genome Biology},
title = {{Five selfish reasons to work reproducibly}},
url = {http://genomebiology.com/2015/16/1/274},
volume = {16},
year = {2015}
}
@article{Marwick2016,
author = {Marwick, Ben},
doi = {10.1007/s10816-015-9272-9},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Marwick - 2016 - Computational Reproducibility in Archaeological Research Basic Principles and a Case Study of Their Implementation.pdf:pdf},
issn = {1072-5369},
journal = {Journal of Archaeological Method and Theory},
keywords = {Australian archaeology,Computer programming,Open science,Reproducible Research,Reproducible research,Software engineering,VIP,australian archaeology,computer programming,open science,reproducible research,software engineering},
mendeley-tags = {Reproducible Research,VIP},
month = {jan},
pages = {en prensa},
publisher = {Journal of Archaeological Method and Theory},
title = {{Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation}},
url = {http://link.springer.com/10.1007/s10816-015-9272-9},
year = {2016}
}
@misc{Marwick2015,
author = {Marwick, Ben},
booktitle = {The conversation},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Marwick - 2015 - How Computers Broke Science — and What We Can Do to Fix It.pdf:pdf},
keywords = {Reproducible Research},
mendeley-tags = {Reproducible Research},
title = {{How Computers Broke Science — and What We Can Do to Fix It}},
url = {http://theconversation.com/how-computers-broke-science-and-what-we-can-do-to-fix-it-49938},
year = {2015}
}
@article{McCafferty2010,
author = {McCafferty, Dennis},
doi = {10.1145/1831407.1831415},
file = {::},
journal = {Communications of the ACM},
number = {10},
pages = {16--17},
title = {{Should Code be Released?}},
url = {http://cacm.acm.org/magazines/2010/10/99494-should-code-be-released/fulltext},
volume = {53},
year = {2010}
}
@article{Merali2010,
author = {Merali, Zeeya},
doi = {doi:10.1038/467775a},
file = {::},
journal = {Nature},
pages = {775--777},
title = {{Computational science: ...Error}},
volume = {467},
year = {2010}
}
@article{Michener2015,
abstract = {In this article, the author offers suggestions on improving data management during research. Topics discussed include creating data management plan (DMP) by identifying the data to be collected, understanding the organization of the data collected, improving the quality of products by taking adequate measures for quality control, and development of a data storage strategy with reference to accessibility and preservation.},
author = {Michener, William K.},
doi = {10.1371/journal.pcbi.1004525},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Michener - 2015 - Ten Simple Rules for Creating a Good Data Management Plan.pdf:pdf},
isbn = {10.1371/journal.pcbi.1004525},
issn = {15537358},
journal = {PLoS Computational Biology},
keywords = {Reproducible Research},
mendeley-tags = {Reproducible Research},
number = {10},
pages = {1--9},
pmid = {26492633},
title = {{Ten Simple Rules for Creating a Good Data Management Plan}},
volume = {11},
year = {2015}
}
@article{Michener2012,
author = {Michener, William K. and Jones, Matthew B.},
doi = {10.1016/j.tree.2011.11.016},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Michener, Jones - 2012 - Ecoinformatics supporting ecology as a data-intensive science.pdf:pdf},
issn = {01695347},
journal = {Trends in Ecology and Evolution},
keywords = {Reproducible Research,methods,review},
mendeley-tags = {Reproducible Research,methods,review},
month = {jan},
number = {2},
pages = {85--93},
publisher = {Elsevier Ltd},
title = {{Ecoinformatics: supporting ecology as a data-intensive science}},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0169534711003399},
volume = {27},
year = {2012}
}
@article{Michener1997,
author = {Michener, William K and Brunt, James W and Helly, John J and Kirchner, Thomas B and Stafford, Susan G},
doi = {10.1890/1051-0761(1997)007[0330:NMFTES]2.0.CO;2},
issn = {1939-5582},
journal = {Ecological Applications},
keywords = {data archive,data lineage,data management,information science,metadata,quality assurance},
number = {1},
pages = {330--342},
publisher = {Ecological Society of America},
title = {{Nongeospatial metadata for the ecological sciences}},
url = {http://dx.doi.org/10.1890/1051-0761(1997)007[0330:NMFTES]2.0.CO;2},
volume = {7},
year = {1997}
}
@article{Morin2012a,
abstract = {The publication and open exchange of knowledge and material form the backbone of scientifi c progress and reproducibility and are obligatory for publicly funded research. Despite increasing reliance on computing in every domain of scientific endeavor, the computer source code critical to understanding and evaluating computer programs is commonly withheld, effectively rendering these programs “black boxes” in the research work flow. Exempting from basic publication and disclosure standards such a ubiquitous category of research tool carries substantial negative consequences. Eliminating this disparity will require concerted policy action by funding agencies and journal publishers, as well as changes in the way research institutions receiving public funds manage their intellectual property (IP).},
author = {Morin, A. and Urban, J. and Adams, P. D. and Foster, I. and Sali, A. and Baker, D. and Sliz, P.},
doi = {10.1126/science.1218263},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Morin et al. - 2012 - Shining Light into Black Boxes.pdf:pdf},
isbn = {0036807510959203},
issn = {0036-8075},
journal = {Science},
keywords = {Reproducible Research,public access},
mendeley-tags = {Reproducible Research},
number = {6078},
pages = {159--160},
pmid = {22499926},
title = {{Shining Light into Black Boxes}},
volume = {336},
year = {2012}
}
@misc{Morris2013,
author = {Morris, BD},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Morris - 2013 - Using Make for reproducible scientific analyses.pdf:pdf},
keywords = {R,Reproducible Research,programming},
mendeley-tags = {R,Reproducible Research,programming},
pages = {9--12},
title = {{Using Make for reproducible scientific analyses}},
year = {2013}
}
@article{Nakagawa2015b,
author = {Nakagawa, Shinichi and Parker, Timothy H.},
doi = {10.1186/s12915-015-0196-3},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Nakagawa, Parker - 2015 - Replicating research in ecology and evolution feasibility, incentives, and the cost-benefit conundrum.pdf:pdf},
issn = {1741-7007},
journal = {BMC Biology},
keywords = {Reproducible Research},
mendeley-tags = {Reproducible Research},
number = {1},
pages = {88},
publisher = {BMC Biology},
title = {{Replicating research in ecology and evolution: feasibility, incentives, and the cost-benefit conundrum}},
url = {http://www.biomedcentral.com/1741-7007/13/88},
volume = {13},
year = {2015}
}
@article{Noble2009,
abstract = {Most bioinformatics coursework focuses on algorithms, with perhaps some components devoted to learning programming skills and learning how to use existing bioinformatics software. Unfortunately, for students who are preparing for a research career, this type of curriculum fails to address many of the day-to-day organizational challenges associated with performing computational experiments. In practice, the principles behind organizing and documenting computational experiments are often learned on the fly, and this learning is strongly influenced by personal predilections as well as by chance interactions with collaborators or colleagues. The purpose of this article is to describe one good strategy for carrying out computational experiments. I will not describe profound issues such as how to formulate hypotheses, design experiments, or draw conclusions. Rather, I will focus on relatively mundane issues such as organizing files and directories and documenting progress. These issues are important because poor organizational choices can lead to significantly slower research progress. I do not claim that the strategies I outline here are optimal. These are simply the principles and practices that I have developed over 12 years of bioinformatics research, augmented with various suggestions from other researchers with whom I have discussed these issues.},
author = {Noble, William Stafford},
doi = {10.1371/journal.pcbi.1000424},
file = {:C$\backslash$:/Users/FRS/Documents/Mendeley Desktop/Noble - 2009 - A Quick Guide to Organizing Computational Biology Projects.pdf:pdf},
isbn = {1553-7358},
issn = {1553-7358},
journal = {PLoS Computational Biology},
keywords = {Computational Biology,Computational Biology: methods,Database Management Systems,Information Storage and Retrieval,Information Storage and Retrieval: methods,Reproducible Research,Research Design,VIP},