refs.bib

@article{ziemannGeneNameErrors2016,
	title = {Gene name errors are widespread in the scientific literature},
	volume = {17},
	issn = {1474-760X},
	url = {http://dx.doi.org/10.1186/s13059-016-1044-7},
	doi = {10.1186/s13059-016-1044-7},
	abstract = {The spreadsheet software Microsoft Excel, when used with default settings, is known to convert gene names to dates and floating-point numbers. A programmatic scan of leading genomics journals reveals that approximately one-fifth of papers with supplementary Excel gene lists contain erroneous gene name conversions.},
	number = {1},
	urldate = {2016-08-26},
	journal = {Genome Biology},
	author = {Ziemann, Mark and Eren, Yotam and El-Osta, Assam},
	month = aug,
	year = {2016},
	note = {00000},
	keywords = {Microsoft Excel, Gene symbol, Supplementary data, lu},
	pages = {177},
	file = {Full Text PDF:C\:\\Users\\sgranger\\Zotero\\storage\\YKWJ4M7K\\Ziemann et al. - 2016 - Gene name errors are widespread in the scientific .pdf:application/pdf;Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\FA8M3GXG\\s13059-016-1044-7.html:text/html;Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\UXL5FI39\\s13059-016-1044-7.html:text/html}
}

@article{munafoManifestoReproducibleScience2017,
	title = {A manifesto for reproducible science},
	volume = {1},
	copyright = {{\textcopyright} 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.},
	issn = {2397-3374},
	url = {http://www.nature.com/articles/s41562-016-0021},
	doi = {10.1038/s41562-016-0021},
	abstract = {Leading voices in the reproducibility landscape call for the adoption of measures to optimize key elements of the scientific process.},
	language = {en},
	number = {1},
	urldate = {2017-02-03},
	journal = {Nature Human Behaviour},
	author = {Munaf{\`o}, Marcus R. and Nosek, Brian A. and Bishop, Dorothy V. M. and Button, Katherine S. and Chambers, Christopher D. and Sert, Nathalie Percie du and Simonsohn, Uri and Wagenmakers, Eric-Jan and Ware, Jennifer J. and Ioannidis, John P. A.},
	month = jan,
	year = {2017},
	keywords = {lu},
	pages = {0021},
	file = {Full Text PDF:C\:\\Users\\sgranger\\Zotero\\storage\\F585CUQX\\Munaf{\`o} et al. - 2017 - A manifesto for reproducible science.pdf:application/pdf;Full Text PDF:C\:\\Users\\sgranger\\Zotero\\storage\\4IZGS9RH\\Munaf{\`o} et al. - 2017 - A manifesto for reproducible science.pdf:application/pdf;Full Text PDF:C\:\\Users\\sgranger\\Zotero\\storage\\CP7VPM64\\Munaf{\`o} et al. - 2017 - A manifesto for reproducible science.pdf:application/pdf;Full Text PDF:C\:\\Users\\sgranger\\Zotero\\storage\\WG7XA4QD\\R. Munaf{\`o} et al. - 2017 - A manifesto for reproducible science.pdf:application/pdf;Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\T8IE4PXN\\s41562-016-0021.html:text/html;Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\KR5VQZCM\\s41562-016-0021.html:text/html;Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\KTCHABQI\\s41562-016-0021.html:text/html;Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\TKV28KSB\\s41562-016-0021.html:text/html}
}

@misc{inriaGuixLogicielLibre,
	title = {Guix, un logiciel libre pour la reproductibilit{\'e} des sciences en {HPC}},
	url = {https://www.inria.fr/centre/bordeaux/actualites/guix-un-logiciel-libre-pour-la-reproductibilite-des-sciences-en-hpc},
	abstract = {Guix est un logiciel libre, d{\'e}velopp{\'e} sous les auspices du projet GNU*~par une communaut{\'e} enthousiaste d{\textquoteright}organisations grandissantes~:~aujourd{\textquoteright}hui~entre 40 et 50 personnes y contribuent chaque mois. Il permet de reproduire des environnements ...},
	urldate = {2017-09-08},
	journal = {Inria},
	author = {{Inria}},
	keywords = {lu},
	file = {Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\3J8WKXUD\\guix-un-logiciel-libre-pour-la-reproductibilite-des-sciences-en-hpc.html:text/html}
}

@article{benureauRerunRepeatReproduce2017,
	title = {Re-run, {Repeat}, {Reproduce}, {Reuse}, {Replicate}: {Transforming} {Code} into {Scientific} {Contributions}},
	shorttitle = {Re-run, {Repeat}, {Reproduce}, {Reuse}, {Replicate}},
	url = {http://arxiv.org/abs/1708.08205},
	abstract = {Scientific code is not production software. Scientific code participates in the evaluation of a scientific hypothesis. This imposes specific constraints on the code that are often overlooked in practice. We articulate, with a small example, five characteristics that a scientific code in computational science should possess: re-runnable, repeatable, reproducible, reusable and replicable.},
	urldate = {2017-09-25},
	journal = {arXiv:1708.08205 [cs]},
	author = {Benureau, Fabien and Rougier, Nicolas},
	month = aug,
	year = {2017},
	note = {arXiv: 1708.08205},
	keywords = {Computer Science - Computers and Society, Computer Science - General Literature, lu},
	file = {arXiv\:1708.08205 PDF:C\:\\Users\\sgranger\\Zotero\\storage\\E2CXNH7I\\Benureau et Rougier - 2017 - Re-run, Repeat, Reproduce, Reuse, Replicate Trans.pdf:application/pdf;arXiv.org Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\88R4JJ6S\\1708.html:text/html}
}

@article{wilkinsonFAIRGuidingPrinciples2016,
	title = {The {FAIR} {Guiding} {Principles} for scientific data management and stewardship},
	volume = {3},
	copyright = {2016 Nature Publishing Group},
	issn = {2052-4463},
	url = {https://www.nature.com/articles/sdata201618},
	doi = {10.1038/sdata.2016.18},
	abstract = {Comment},
	language = {en},
	urldate = {2017-09-07},
	journal = {Scientific Data},
	author = {Wilkinson, Mark D. and Dumontier, Michel and Aalbersberg, IJsbrand Jan and Appleton, Gabrielle and Axton, Myles and Baak, Arie and Blomberg, Niklas and Boiten, Jan-Willem and Santos, Luiz Bonino da Silva and Bourne, Philip E. and Bouwman, Jildau and Brookes, Anthony J. and Clark, Tim and Crosas, Merc{\`e} and Dillo, Ingrid and Dumon, Olivier and Edmunds, Scott and Evelo, Chris T. and Finkers, Richard and Gonzalez-Beltran, Alejandra and Gray, Alasdair J. G. and Groth, Paul and Goble, Carole and Grethe, Jeffrey S. and Heringa, Jaap and Hoen, Peter A. C. {\textquoteright}t and Hooft, Rob and Kuhn, Tobias and Kok, Ruben and Kok, Joost and Lusher, Scott J. and Martone, Maryann E. and Mons, Albert and Packer, Abel L. and Persson, Bengt and Rocca-Serra, Philippe and Roos, Marco and Schaik, Rene van and Sansone, Susanna-Assunta and Schultes, Erik and Sengstag, Thierry and Slater, Ted and Strawn, George and Swertz, Morris A. and Thompson, Mark and Lei, Johan van der and Mulligen, Erik van and Velterop, Jan and Waagmeester, Andra and Wittenburg, Peter and Wolstencroft, Katherine and Zhao, Jun and Mons, Barend},
	month = mar,
	year = {2016},
	keywords = {FAIR, RDM, repository},
	pages = {sdata201618}
}

@article{markowetzFiveSelfishReasons2015,
	title = {Five selfish reasons to work reproducibly},
	volume = {16},
	issn = {1474-760X},
	url = {https://doi.org/10.1186/s13059-015-0850-7},
	doi = {10.1186/s13059-015-0850-7},
	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.},
	language = {en},
	number = {1},
	urldate = {2017-10-18},
	journal = {Genome Biology},
	author = {Markowetz, Florian},
	month = dec,
	year = {2015},
	keywords = {replicable\_reproductible, traitement\_donnees, lu},
	pages = {274}
}

@article{vandewalleReproducibleResearchSignal2009,
	title = {Reproducible research in signal processing},
	volume = {26},
	issn = {1053-5888},
	url = {http://ieeexplore.ieee.org/document/4815541/},
	doi = {10.1109/MSP.2009.932122},
	abstract = {What should we do to raise the quality of signal processing publications to an even higher level? We believe it to be crucial to maintain the precision in describing our work in publications, ensured through a high-quality reviewing process. We also believe that if the experiments are performed on a large data set, the algorithm is compared to the state-of-the-art methods, the code and/or data are well documented and available online, we will all benefit and make it easier to build upon each other's work. It is a clear win-win situation for our community: we will have access to more and more algorithms and can spend time inventing new things rather than recreating existing ones.},
	number = {3},
	urldate = {2018-01-10},
	journal = {IEEE Signal Processing Magazine},
	author = {Vandewalle, Patrick and Kovacevic, Jelena and Vetterli, Martin},
	month = may,
	year = {2009},
	keywords = {Education, reproducible research, lu, Reproducibility of results, Testing, Advertising, Digital signal processing, high-quality reviewing process, large data set, Programming, research and development, Scholarships, signal processing, Signal processing, Signal processing algorithms, Wikipedia, win-win situation, pas de full text en acc{\`e}s libre},
	pages = {37--47},
	file = {IEEE Xplore Abstract Record:C\:\\Users\\sgranger\\Zotero\\storage\\KRS85FL2\\4815541.html:text/html;Texte int{\'e}gral:C\:\\Users\\sgranger\\Zotero\\storage\\3Z64FT5Z\\Vandewalle et al. - 2009 - Reproducible research in signal processing.pdf:application/pdf;VandewalleKV09.pdf:C\:\\Users\\sgranger\\Zotero\\storage\\E4RPPHHD\\VandewalleKV09.pdf:application/pdf}
}

@article{sandveTenSimpleRules2013,
	title = {Ten {Simple} {Rules} for {Reproducible} {Computational} {Research}},
	volume = {9},
	issn = {1553-7358},
	url = {http://dx.plos.org/10.1371/journal.pcbi.1003285},
	doi = {10.1371/journal.pcbi.1003285},
	language = {en},
	number = {10},
	urldate = {2018-01-10},
	journal = {PLoS Computational Biology},
	author = {Sandve, Geir Kjetil and Nekrutenko, Anton and Taylor, James and Hovig, Eivind},
	editor = {Bourne, Philip E.},
	month = oct,
	year = {2013},
	keywords = {lu},
	pages = {e1003285}
}

@article{nosekPreregistrationRevolution2017,
	title = {The {Preregistration} {Revolution}},
	url = {https://osf.io/2dxu5/},
	doi = {10.17605/OSF.IO/2DXU5},
	abstract = {Progress in science relies on generating hypotheses with existing observations and testing hypotheses with new observations. This distinction between postdiction and prediction is appreciated conceptually, but is not respected in practice. Mistaking generation of postdictions with testing of predictions reduces the credibility of research findings.  However, ordinary biases in human reasoning such as hindsight bias make it hard to avoid this mistake. An effective solution is to define the research questions and analysis plan prior to observing the research outcomes--a process called preregistration. A variety of practical strategies are available to make the best possible use of preregistration in circumstances that fall short of the ideal application, such as when the data are pre-existing.  Services are now available for preregistration across all disciplines facilitating a rapid increase in the practice.  Widespread adoption of preregistration will increase distinctiveness between hypothesis generation and hypothesis testing and will improve the credibility of research findings.},
	urldate = {2018-01-12},
	journal = {Open Science Framework},
	author = {Nosek, Brian A. and Ebersole, Charles R. and DeHaven, Alexander and Mellor, David},
	month = jun,
	year = {2017},
	keywords = {lu},
	file = {Full Text PDF:C\:\\Users\\sgranger\\Zotero\\storage\\D3PGWISG\\Nosek et al. - 2017 - The Preregistration Revolution.pdf:application/pdf;Full Text PDF:C\:\\Users\\sgranger\\Zotero\\storage\\8ULZNETH\\Nosek et al. - 2017 - The Preregistration Revolution.pdf:application/pdf;Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\QUPLXK7D\\2dxu5.html:text/html;Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\HR8XAR95\\2dxu5.html:text/html}
}

@article{lakensJustifyYourAlpha2017,
	title = {Justify {Your} {Alpha}: {A} {Response} to {\textquotedblleft}{Redefine} {Statistical} {Significance}{\textquotedblright}},
	shorttitle = {Justify {Your} {Alpha}},
	url = {https://psyarxiv.com/9s3y6/},
	doi = {10.17605/OSF.IO/9S3Y6},
	abstract = {In response to recommendations to redefine statistical significance to p <= .005, we propose that researchers should transparently report and justify all choices they make when designing a study, including the alpha level.},
	urldate = {2018-01-12},
	journal = {PsyArXiv},
	author = {Lakens, Daniel and Adolfi, Federico G. and Albers, Casper and Anvari, Farid and Apps, Matthew A. J. and Argamon, Shlomo Engelson and Assen, Marcel A. L. M. van and Baguley, Thom and Becker, Raymond and Benning, Stephen D. and Bradford, Daniel E. and Buchanan, Erin Michelle and Caldwell, Aaron and Calster, Ben van and Carlsson, Rickard and Chen, Sau-Chin and Chung, Bryan and Colling, Lincoln and Collins, Gary and Crook, Zander and Cross, Emily S. and Daniels, Sameera and Danielsson, Henrik and DeBruine, Lisa and Dunleavy, Daniel and Earp, Brian D. and Feist, Michele and Ferrell, Jason D. and Field, James G. and Fox, Nick and Friesen, Amanda and Gomes, Caio and Grange, James A. and Grieve, Andrew and Guggenberger, Robert and Harmelen, Anne-Laura Van and Hasselman, Fred and Hochard, Kevin D. and Hoffarth, Mark Romeo and Holmes, Nicholas Paul and Ingre, Michael and Isager, Peder M. and Isotalus, Hanna and Johansson, Christer and Juszczyk, Konrad and Kenny, David and Khalil, Ahmed Abdelrahim and Konat, Barbara and Lao, Junpeng and Larsen, Erik Gahner and Lodder, Gerine M. A. and Lukavsky, Jiri and Madan, Christopher and Manheim, David and Gonzalez-Marquez, Monica and Martin, Stephen R. and Martin, Andrea E. and Mayo, Deborah and McCarthy, Randy J. and McConway, Kevin and McFarland, Colin and Nilsonne, Gustav and Nio, Amanda Q. X. and Oliveira, Cilene Lino de and Parsons, Sam and Pfuhl, Gerit and Quinn, Kimberly and Sakon, John and Saribay, Selahattin Adil and Schneider, Iris and Selvaraju, Manojkumar and Sjoerds, Zsuzsika and Smith, Samuel and Smits, Tim and Spies, Jeffrey R. and Sreekumar, Vishnu and Steltenpohl, Crystal and Stenhouse, Neil and {\'S}wi{\k a}tkowski, Wojciech and Vadillo, Miguel A. and Williams, Matt and Williams, Samantha and Williams, Donald R. and Xivry, Jean-Jacques Orban de and Yarkoni, Tal and Ziano, Ignazio and Zwaan, Rolf},
	month = sep,
	year = {2017},
	keywords = {lu},
	file = {Full Text PDF:C\:\\Users\\sgranger\\Zotero\\storage\\5JSMI2RX\\Lakens et al. - 2017 - Justify Your Alpha A Response to {\textquotedblleft}Redefine Statis.pdf:application/pdf;Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\ZLMVW6PP\\9s3y6.html:text/html}
}

@misc{mcnamaraScientistsProgramming2018,
	title = {Scientists {Programming}},
	url = {http://www.science.smith.edu/~amcnamara/blog/conferences/2018/02/11/Scientists-Programming.html},
	urldate = {2018-02-12},
	author = {McNamara, Amelia},
	year = {2018},
	keywords = {lu},
	file = {Amelia McNamara | Blog | Scientists Programming:C\:\\Users\\sgranger\\Zotero\\storage\\ALVR4ULS\\Scientists-Programming.html:text/html}
}

@article{lowndesOurPathBetter2017,
	title = {Our path to better science in less time using open data science tools},
	volume = {1},
	copyright = {2017 Nature Publishing Group},
	issn = {2397-334X},
	url = {https://www.nature.com/articles/s41559-017-0160},
	doi = {10.1038/s41559-017-0160},
	abstract = {Reproducibility has long been a tenet of science but has been challenging to achieve{\textemdash}we learned this the hard way when our old approaches proved inadequate to efficiently reproduce our own work. Here we describe how several free software tools have fundamentally upgraded our approach to collaborative research, making our entire workflow more transparent and streamlined. By describing specific tools and how we incrementally began using them for the Ocean Health Index project, we hope to encourage others in the scientific community to do the same{\textemdash}so we can all produce better science in less time.},
	language = {en},
	number = {6},
	urldate = {2018-02-12},
	journal = {Nature Ecology \& Evolution},
	author = {Lowndes, Julia S. Stewart and Best, Benjamin D. and Scarborough, Courtney and Afflerbach, Jamie C. and Frazier, Melanie R. and O{\textquoteright}Hara, Casey C. and Jiang, Ning and Halpern, Benjamin S.},
	month = jun,
	year = {2017},
	keywords = {lu},
	pages = {0160},
	file = {Full Text PDF:C\:\\Users\\sgranger\\Zotero\\storage\\X68HFLD2\\Lowndes et al. - 2017 - Our path to better science in less time using open.pdf:application/pdf;Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\5KM7H7LE\\s41559-017-0160.html:text/html}
}

@article{mcnamaraKeyAttributesModern2016,
	title = {Key attributes of a modern statistical computing tool},
	url = {http://arxiv.org/abs/1610.00985},
	abstract = {In the 1990s, statisticians began thinking in a principled way about how computation could support statistics and statistics education. Since then, the pace of software development has accelerated, advancements in computing and data science have moved the goalposts, and it is time to reassess. Software continues to be developed to help do and learn statistics, but there is little critical evaluation of the resulting tools, and no accepted framework with which to critique them. In this paper, we present a set of attributes necessary for a modern statistical computing tool. This framework is designed to be broadly applicable to both novice and expert users, but the particular focus is on making a more supportive statistical computing environment. A modern statistical computing tool should be accessible, provide easy entry, privilege data as a first-order object, support exploratory and confirmatory analysis, allow for flexible plot creation, support randomization, be interactive, include inherent documentation, support narrative, publishing, and reproducibility, and be flexible to extensions. Ideally, all these attributes could be incorporated into one tool, supporting users at all levels, but a more reasonable goal is for tools designed for novices and professionals to `reach across the gap,' taking inspiration from each others' strengths.},
	urldate = {2018-02-12},
	journal = {arXiv:1610.00985 [cs, stat]},
	author = {McNamara, Amelia},
	month = sep,
	year = {2016},
	note = {arXiv: 1610.00985},
	keywords = {Computer Science - Computers and Society, Statistics - Computation, lu},
	file = {arXiv\:1610.00985 PDF:C\:\\Users\\sgranger\\Zotero\\storage\\RMANEWZS\\McNamara - 2016 - Key attributes of a modern statistical computing t.pdf:application/pdf;arXiv.org Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\N5CH8EGW\\1610.html:text/html}
}

@misc{britishecologicalsocietyGuidesBetterScience2017,
	title = {Guides to {Better} {Science}},
	url = {https://www.britishecologicalsociety.org/publications/guides-to/},
	abstract = {Free guides to promote research excellence covering: peer review, data management, getting published, and reproducible code.},
	language = {en-GB},
	urldate = {2018-02-15},
	journal = {British Ecological Society},
	author = {{British Ecological Society}},
	year = {2017},
	keywords = {lu},
	file = {Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\667XTT8X\\guides-to.html:text/html}
}

@article{barbaTerminologiesReproducibleResearch2018,
	title = {Terminologies for {Reproducible} {Research}},
	url = {http://arxiv.org/abs/1802.03311},
	abstract = {Reproducible research---by its many names---has come to be regarded as a key concern across disciplines and stakeholder groups. Funding agencies and journals, professional societies and even mass media are paying attention, often focusing on the so-called "crisis" of reproducibility. One big problem keeps coming up among those seeking to tackle the issue: different groups are using terminologies in utter contradiction with each other. Looking at a broad sample of publications in different fields, we can classify their terminology via decision tree: they either, A---make no distinction between the words reproduce and replicate, or B---use them distinctly. If B, then they are commonly divided in two camps. In a spectrum of concerns that starts at a minimum standard of "same data+same methods=same results," to "new data and/or new methods in an independent study=same findings," group 1 calls the minimum standard reproduce, while group 2 calls it replicate. This direct swap of the two terms aggravates an already weighty issue. By attempting to inventory the terminologies across disciplines, I hope that some patterns will emerge to help us resolve the contradictions.},
	urldate = {2018-02-16},
	journal = {arXiv:1802.03311 [cs]},
	author = {Barba, Lorena A.},
	month = feb,
	year = {2018},
	note = {arXiv: 1802.03311},
	keywords = {Computer Science - Digital Libraries, lu},
	file = {arXiv\:1802.03311 PDF:C\:\\Users\\sgranger\\Zotero\\storage\\5MXY8XZ7\\Barba - 2018 - Terminologies for Reproducible Research.pdf:application/pdf;arXiv.org Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\7G2L8963\\1802.html:text/html}
}

@article{brownTenQuickTips2018,
	title = {Ten quick tips for teaching programming},
	volume = {14},
	issn = {1553-7358},
	url = {http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006023},
	doi = {10.1371/journal.pcbi.1006023},
	language = {en},
	number = {4},
	urldate = {2018-04-06},
	journal = {PLOS Computational Biology},
	author = {Brown, Neil C. C. and Wilson, Greg},
	month = apr,
	year = {2018},
	keywords = {Language, Computer software, Computer and information sciences, Drag, Human learning, Instructors, Language acquisition, Learning},
	pages = {e1006023},
	file = {Full Text PDF:C\:\\Users\\sgranger\\Zotero\\storage\\8DNKTG44\\Brown et Wilson - 2018 - Ten quick tips for teaching programming.pdf:application/pdf;Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\HZL6M7YA\\article.html:text/html}
}

@misc{bastianTipsUnderstandingData2017,
	title = {5 {Tips} for {Understanding} {Data} in {Meta}-{Analyses}},
	url = {http://blogs.plos.org/absolutely-maybe/2017/07/03/5-tips-for-understanding-data-in-meta-analyses/},
	abstract = {There's a deluge of scientific studies of all sorts - thousands every day. There's often a few studies looking for answers on the same topic, but there can be dozens or even hundreds of them. Meta-analysis is a group of statistical techniques that enable data from more than one study~to be combined~and analyzed as a new dataset. Meta-analysis didn't start to spread~until the 1970s.~Now there are dozens of publications with meta-analyses~every day and it takes less than 5 years for the number published in a year~to double.* Meta-analytic methods are still a bit of a mystery to many people, though. I've written a couple of "5 things"~posts about meta-analysis, but not enough explaining data basics. So here's the~prequel! This cartoon is a forest plot, a style of data visualization for meta-analysis results. Some people call them "blobbograms". Each of these horizontal lines with a square in the middle represents the results of a different study. The length of that},
	language = {en-US},
	urldate = {2018-04-06},
	author = {Bastian, Hilda},
	month = jul,
	year = {2017},
	keywords = {lu}
}

@article{wurmusReproducibleGenomicsAnalysis2018,
	title = {Reproducible genomics analysis pipelines with {GNU} {Guix}},
	copyright = {{\textcopyright} 2018, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NoDerivs 4.0 International), CC BY-ND 4.0, as described at http://creativecommons.org/licenses/by-nd/4.0/},
	url = {https://www.biorxiv.org/content/biorxiv/early/2018/04/21/298653.full.pdf},
	doi = {10.1101/298653},
	abstract = {In bioinformatics as well as other compute heavy research fields, there is a need for workflows that can be relied upon to produce consistent output, independent of the software environment or configuration settings of the machine on which they are executed. Indeed, this is essential for making controlled comparisons between different observations or distributing software to be used by others. Providing this type of reproducibility, however, is often complicated by the need to accommodate the myriad dependencies included in a larger body of software, each of which often contain multiple versions. In many fields as wells as bioinformatics, these versions are subject to continual change due to rapidly evolving technologies, further complicating problems related to reproducibility. We are proposing a principled approach for building analysis pipelines and taking care of their dependencies. As a case study to demonstrate the utility of our approach, we present a set of highly reproducible pipelines for the analysis of RNA-seq, ChIP-seq, Bisulfite-seq, and single-cell RNA-seq. All pipelines process raw experimental data generating reports containing publication-ready plots and figures, with interactive report elements and standard observables. Users may install these highly reproducible packages and apply them to their own datasets without any special computational expertise apart from using the command line. We hope such a toolkit will provide immediate benefit to laboratory workers wishing to process their own data sets or bioinformaticians who would want to automate parts or all of their analysis. Our approach to reproducibility may also serve as a blueprint for reproducible workflows in other areas. Our pipelines, their documentation and sample reports from the pipelines are available at http://bioinformatics.mdc-berlin.de/pigx},
	language = {en},
	urldate = {2018-04-23},
	journal = {bioRxiv},
	author = {Wurmus, Ricardo and Uyar, Bora and Osberg, Brendan and Franke, Vedran and Gosdschan, Alexander and Wreczycka, Katarzyna and Ronen, Jonathan and Akalin, Altuna},
	month = apr,
	year = {2018},
	pages = {298653},
	file = {Full Text PDF:C\:\\Users\\sgranger\\Zotero\\storage\\QNP5HDU7\\Wurmus et al. - 2018 - Reproducible genomics analysis pipelines with GNU .pdf:application/pdf;Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\TGAWARC5\\298653.html:text/html}
}

@misc{poldrackHowCanOne2018,
	title = {How can one do reproducible science with limited resources?},
	url = {http://www.russpoldrack.org/2018/04/how-can-one-do-reproducible-science.html},
	abstract = {When I visit other universities to talk, we often end up having free-form discussions about reproducibility at some point during the visit...},
	language = {en},
	urldate = {2018-04-24},
	journal = {russpoldrack.org},
	author = {Poldrack, Russ},
	year = {2018},
	keywords = {lu},
	file = {Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\E5YL3U3B\\how-can-one-do-reproducible-science.html:text/html}
}

@article{editorialChecklistsWorkImprove2018,
	title = {Checklists work to improve science},
	volume = {556},
	copyright = {2018 Nature},
	url = {http://www.nature.com/articles/d41586-018-04590-7},
	doi = {10.1038/d41586-018-04590-7},
	abstract = {Nature authors say a reproducibility checklist is a step in the right direction, but more needs to be done.},
	language = {EN},
	number = {7701},
	urldate = {2018-04-27},
	journal = {Nature},
	author = {Editorial, Nature},
	month = apr,
	year = {2018},
	keywords = {lu},
	pages = {273},
	file = {Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\Q24RTIAI\\d41586-018-04590-7.html:text/html}
}

@article{stoddenEmpiricalAnalysisJournal2018,
	title = {An empirical analysis of journal policy effectiveness for computational reproducibility},
	volume = {115},
	copyright = {{\textcopyright} 2018 . Published under the PNAS license.},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/content/115/11/2584},
	doi = {10.1073/pnas.1708290115},
	abstract = {A key component of scientific communication is sufficient information for other researchers in the field to reproduce published findings. For computational and data-enabled research, this has often been interpreted to mean making available the raw data from which results were generated, the computer code that generated the findings, and any additional information needed such as workflows and input parameters. Many journals are revising author guidelines to include data and code availability. This work evaluates the effectiveness of journal policy that requires the data and code necessary for reproducibility be made available postpublication by the authors upon request. We assess the effectiveness of such a policy by (i) requesting data and code from authors and (ii) attempting replication of the published findings. We chose a random sample of 204 scientific papers published in the journal Science after the implementation of their policy in February 2011. We found that we were able to obtain artifacts from 44\% of our sample and were able to reproduce the findings for 26\%. We find this policy{\textemdash}author remission of data and code postpublication upon request{\textemdash}an improvement over no policy, but currently insufficient for reproducibility.},
	language = {en},
	number = {11},
	urldate = {2018-04-30},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Stodden, Victoria and Seiler, Jennifer and Ma, Zhaokun},
	month = mar,
	year = {2018},
	pmid = {29531050},
	keywords = {open science, reproducible research, code access, data access, reproducibility policy, lu},
	pages = {2584--2589},
	file = {Full Text PDF:C\:\\Users\\sgranger\\Zotero\\storage\\UUIV9MT3\\Stodden et al. - 2018 - An empirical analysis of journal policy effectiven.pdf:application/pdf;Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\EP7KW53C\\2584.html:text/html}
}

@article{forstmeierDetectingAvoidingLikely2017,
	title = {Detecting and avoiding likely false-positive findings {\textendash} a practical guide},
	volume = {92},
	copyright = {{\textcopyright} 2016 The Authors. Biological Reviews published by John Wiley \& Sons Ltd on behalf          of Cambridge Philosophical Society.},
	issn = {1469-185X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/brv.12315},
	doi = {10.1111/brv.12315},
	abstract = {Recently there has been a growing concern that many published research findings do not hold up in attempts to replicate them. We argue that this problem may originate from a culture of {\textquoteleft}you can publish if you found a significant effect{\textquoteright}. This culture creates a systematic bias against the null hypothesis which renders meta-analyses questionable and may even lead to a situation where hypotheses become difficult to falsify. In order to pinpoint the sources of error and possible solutions, we review current scientific practices with regard to their effect on the probability of drawing a false-positive conclusion. We explain why the proportion of published false-positive findings is expected to increase with (i) decreasing sample size, (ii) increasing pursuit of novelty, (iii) various forms of multiple testing and researcher flexibility, and (iv) incorrect P-values, especially due to unaccounted pseudoreplication, i.e. the non-independence of data points (clustered data). We provide examples showing how statistical pitfalls and psychological traps lead to conclusions that are biased and unreliable, and we show how these mistakes can be avoided. Ultimately, we hope to contribute to a culture of {\textquoteleft}you can publish if your study is rigorous{\textquoteright}. To this end, we highlight promising strategies towards making science more objective. Specifically, we enthusiastically encourage scientists to preregister their studies (including a priori hypotheses and complete analysis plans), to blind observers to treatment groups during data collection and analysis, and unconditionally to report all results. Also, we advocate reallocating some efforts away from seeking novelty and discovery and towards replicating important research findings of one's own and of others for the benefit of the scientific community as a whole. We believe these efforts will be aided by a shift in evaluation criteria away from the current system which values metrics of {\textquoteleft}impact{\textquoteright} almost exclusively and towards a system which explicitly values indices of scientific rigour.},
	language = {en},
	number = {4},
	urldate = {2018-05-03},
	journal = {Biological Reviews},
	author = {Forstmeier, Wolfgang and Wagenmakers, Eric-Jan and Parker Timothy, H},
	month = nov,
	year = {2017},
	keywords = {replication, confirmation bias, HARKing, hindsight bias, overfitting, P-hacking, power, preregistration, researcher degrees of freedom, Type I error, lu},
	pages = {1941--1968},
	file = {Full Text PDF:C\:\\Users\\sgranger\\Zotero\\storage\\4TV9GILR\\Wolfgang et al. - 2017 - Detecting and avoiding likely false-positive findi.pdf:application/pdf;Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\U2N3FNIB\\brv.html:text/html}
}

@article{gelmanFailureNullHypothesis2018,
	title = {The {Failure} of {Null} {Hypothesis} {Significance} {Testing} {When} {Studying} {Incremental} {Changes}, and {What} to {Do} {About} {It}},
	volume = {44},
	issn = {0146-1672},
	url = {https://doi.org/10.1177/0146167217729162},
	doi = {10.1177/0146167217729162},
	abstract = {A standard mode of inference in social and behavioral science is to establish stylized facts using statistical significance in quantitative studies. However, in a world in which measurements are noisy and effects are small, this will not work: selection on statistical significance leads to effect sizes which are overestimated and often in the wrong direction. After a brief discussion of two examples, one in economics and one in social psychology, we consider the procedural solution of open postpublication review, the design solution of devoting more effort to accurate measurements and within-person comparisons, and the statistical analysis solution of multilevel modeling and reporting all results rather than selection on significance. We argue that the current replication crisis in science arises in part from the ill effects of null hypothesis significance testing being used to study small effects with noisy data. In such settings, apparent success comes easy but truly replicable results require a more serious connection between theory, measurement, and data.},
	language = {en},
	number = {1},
	urldate = {2018-05-09},
	journal = {Personality and Social Psychology Bulletin},
	author = {Gelman, Andrew},
	month = jan,
	year = {2018},
	keywords = {lu},
	pages = {16--23},
	file = {SAGE PDF Full Text:C\:\\Users\\sgranger\\Zotero\\storage\\9NBKLC6A\\Gelman - 2018 - The Failure of Null Hypothesis Significance Testin.pdf:application/pdf}
}

@article{leonelliReThinkingReproducibilityCriterion2018,
	title = {Re-{Thinking} {Reproducibility} as a {Criterion} for {Research} {Quality}},
	url = {http://philsci-archive.pitt.edu/14352/},
	abstract = {A heated debate surrounds the significance of reproducibility as an indicator for research quality and reliability, with many commentators linking a {\textquotedblleft}crisis of reproducibility{\textquotedblright} to the rise of fraudulent, careless and unreliable practices of knowledge production. Through the analysis of discourse and practices across research fields, I point out that reproducibility is not only interpreted in different ways, but also serves a variety of epistemic functions depending on the research at hand. Given such variation, I argue that the uncritical pursuit of reproducibility as an overarching epistemic value is misleading and potentially damaging to scientific advancement. Requirements for reproducibility, however they are interpreted, are one of many available means to secure reliable research outcomes. Furthermore, there are cases where the focus on enhancing reproducibility turns out not to foster high-quality research. Scientific communities and Open Science advocates should learn from inferential reasoning from irreproducible data, and promote incentives for all researchers to explicitly and publicly discuss (1) their methodological commitments, (2) the ways in which they learn from mistakes and problems in everyday practice, and (3) the strategies they use to choose which research component of any project needs to be preserved in the long term, and how.},
	language = {en},
	journal = {History of Economic thought and Methodology},
	author = {Leonelli, Sabina},
	month = jan,
	year = {2018},
	keywords = {lu},
	pages = {19}
}

@techreport{desquilbetGuidePratiqueValidation2019,
	address = {Maison Alfort},
	title = {Guide pratique de validation statistique de m{\'e}thodes de mesure : r{\'e}p{\'e}tabilit{\'e}, reproductibilit{\'e}, et concordance},
	url = {https://bit.ly/2ZKcQGL},
	urldate = {2018-05-15},
	institution = {Ecole Nationale V{\'e}t{\'e}rinaire Maison Alfort},
	author = {Desquilbet, Lo{\"i}c},
	year = {2019},
	keywords = {lu}
}

@article{ioannidisWhyMostPublished2005,
	title = {Why {Most} {Published} {Research} {Findings} {Are} {False}},
	volume = {2},
	issn = {1549-1676},
	url = {http://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.0020124},
	doi = {10.1371/journal.pmed.0020124},
	abstract = {Summary There is increasing concern that most current published research findings are false. The probability that a research claim is true may depend on study power and bias, the number of other studies on the same question, and, importantly, the ratio of true to no relationships among the relationships probed in each scientific field. In this framework, a research finding is less likely to be true when the studies conducted in a field are smaller; when effect sizes are smaller; when there is a greater number and lesser preselection of tested relationships; where there is greater flexibility in designs, definitions, outcomes, and analytical modes; when there is greater financial and other interest and prejudice; and when more teams are involved in a scientific field in chase of statistical significance. Simulations show that for most study designs and settings, it is more likely for a research claim to be false than true. Moreover, for many current scientific fields, claimed research findings may often be simply accurate measures of the prevailing bias. In this essay, I discuss the implications of these problems for the conduct and interpretation of research.},
	language = {en},
	number = {8},
	urldate = {2018-05-24},
	journal = {PLOS Medicine},
	author = {Ioannidis, John P. A.},
	month = aug,
	year = {2005},
	keywords = {Meta-analysis, Research design, lu, Clinical research design, Finance, Genetic epidemiology, Genetics of disease, Randomized controlled trials, Schizophrenia},
	pages = {e124},
	file = {Full Text PDF:C\:\\Users\\sgranger\\Zotero\\storage\\N473CLLN\\Ioannidis - 2005 - Why Most Published Research Findings Are False.pdf:application/pdf;Full Text PDF:C\:\\Users\\sgranger\\Zotero\\storage\\3WTJNLBD\\Ioannidis - 2005 - Why Most Published Research Findings Are False.pdf:application/pdf;Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\J65K3WRR\\article.html:text/html;Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\23ZTNQ9R\\article.html:text/html}
}

@article{gelmanDifferenceSignificantNot2006,
	title = {The {Difference} {Between} {\textquotedblleft}{Significant}{\textquotedblright} and {\textquotedblleft}{Not} {Significant}{\textquotedblright} is not {Itself} {Statistically} {Significant}},
	volume = {60},
	issn = {0003-1305},
	url = {https://doi.org/10.1198/000313006X152649},
	doi = {10.1198/000313006X152649},
	abstract = {It is common to summarize statistical comparisons by declarations of statistical significance or nonsignificance. Here we discuss one problem with such declarations, namely that changes in statistical significance are often not themselves statistically significant. By this, we are not merely making the commonplace observation that any particular threshold is arbitrary{\textemdash}for example, only a small change is required to move an estimate from a 5.1\% significance level to 4.9\%, thus moving it into statistical significance. Rather, we are pointing out that even large changes in significance levels can correspond to small, nonsignificant changes in the underlying quantities.The error we describe is conceptually different from other oft-cited problems{\textemdash}that statistical significance is not the same as practical importance, that dichotomization into significant and nonsignificant results encourages the dismissal of observed differences in favor of the usually less interesting null hypothesis of no difference, and that any particular threshold for declaring significance is arbitrary. We are troubled by all of these concerns and do not intend to minimize their importance. Rather, our goal is to bring attention to this additional error of interpretation. We illustrate with a theoretical example and two applied examples. The ubiquity of this statistical error leads us to suggest that students and practitioners be made more aware that the difference between {\textquotedblleft}significant{\textquotedblright} and {\textquotedblleft}not significant{\textquotedblright} is not itself statistically significant.},
	number = {4},
	urldate = {2018-05-25},
	journal = {The American Statistician},
	author = {Gelman, Andrew and Stern, Hal},
	month = nov,
	year = {2006},
	keywords = {Meta-analysis, lu, Hypothesis testing, Pairwise comparison, Replication},
	pages = {328--331},
	file = {Full Text PDF:C\:\\Users\\sgranger\\Zotero\\storage\\IW7KJA6E\\Gelman et Stern - 2006 - The Difference Between {\textquotedblleft}Significant{\textquotedblright} and {\textquotedblleft}Not Sign.pdf:application/pdf;Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\4NKK78V6\\000313006X152649.html:text/html}
}

@article{fanelliScienceReallyFacing2018,
	title = {Is science really facing a reproducibility crisis, and do we need it to?},
	volume = {115},
	copyright = {{\textcopyright} 2018 . Published under the PNAS license.},
	issn = {0027-8424, 1091-6490},
	shorttitle = {Opinion},
	url = {http://www.pnas.org/content/115/11/2628},
	doi = {10.1073/pnas.1708272114},
	abstract = {Efforts to improve the reproducibility and integrity of science are typically justified by a narrative of crisis, according to which most published results are unreliable due to growing problems with research and publication practices. This article provides an overview of recent evidence suggesting that this narrative is mistaken, and argues that a narrative of epochal changes and empowerment of scientists would be more accurate, inspiring, and compelling.},
	language = {en},
	number = {11},
	urldate = {2018-05-25},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Fanelli, Daniele},
	month = mar,
	year = {2018},
	pmid = {29531051},
	keywords = {reproducible research, lu, bias, crisis, integrity, misconduct},
	pages = {2628--2631},
	file = {Full Text PDF:C\:\\Users\\sgranger\\Zotero\\storage\\SU7P2L89\\Fanelli - 2018 - Opinion Is science really facing a reproducibilit.pdf:application/pdf;Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\LP4LANNV\\2628.html:text/html}
}

@book{randallIrreproducibilityCrisisModern2018,
	address = {New York},
	title = {The {Irreproducibility} {Crisis} of {Modern} {Science}. {Causes}, {Consequences}, and the {Road} to {Reform}},
	url = {https://www.nas.org/images/documents/NAS_irreproducibilityReport.pdf},
	language = {en},
	publisher = {National Association of Scholars},
	author = {Randall, David and Welser, Christopher},
	year = {2018},
	keywords = {lu},
	file = {NAS_irreproducibilityReport.pdf:C\:\\Users\\sgranger\\Zotero\\storage\\BX5BVUIS\\NAS_irreproducibilityReport.pdf:application/pdf}
}

@article{barbaHardRoadReproducibility2016,
	title = {The hard road to reproducibility},
	volume = {354},
	copyright = {Copyright {\textcopyright} 2016, American Association for the Advancement of Science},
	issn = {0036-8075, 1095-9203},
	url = {http://science.sciencemag.org/content/354/6308/142},
	doi = {10.1126/science.354.6308.142},
	abstract = {Early in my Ph.D. studies, my supervisor assigned me the task of running computer code written by a previous student who was graduated and gone. It was hell. I had to sort through many different versions of the code, saved in folders with a mysterious numbering scheme. There was no documentation and},
	language = {en},
	number = {6308},
	urldate = {2018-06-07},
	journal = {Science},
	author = {Barba, Lorena A.},
	month = oct,
	year = {2016},
	pmid = {27846503},
	keywords = {lu},
	pages = {142--142},
	file = {Full Text PDF:C\:\\Users\\sgranger\\Zotero\\storage\\AZAESZW4\\Barba - 2016 - The hard road to reproducibility.pdf:application/pdf;Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\5QJRA9HS\\142.html:text/html}
}

@article{pernetRobustCorrelationAnalyses2013,
	title = {Robust {Correlation} {Analyses}: {False} {Positive} and {Power} {Validation} {Using} a {New} {Open} {Source} {Matlab} {Toolbox}},
	volume = {3},
	issn = {1664-1078},
	shorttitle = {Robust {Correlation} {Analyses}},
	url = {https://www.frontiersin.org/articles/10.3389/fpsyg.2012.00606/full},
	doi = {10.3389/fpsyg.2012.00606},
	abstract = {Pearson{\textquoteright}s correlation measures the strength of the association between two variables. The technique is, however, restricted to linear associations and is overly sensitive to outliers. Indeed, a single outlier can result in a highly inaccurate summary of the data. Yet, it remains the most commonly used measure of association in psychology research. Here we describe a free Matlab(R) based toolbox (http://sourceforge.net/projects/robustcorrtool/) that computes robust measures of association between two or more random variables: the percentage-bend correlation and skipped-correlations. After illustrating how to use the toolbox, we show that robust methods, where outliers are down weighted or removed and accounted for in significance testing, provide better estimates of the true association with accurate false positive control and without loss of power. The different correlation methods were tested with normal data and normal data contaminated with marginal or bivariate outliers. We report estimates of effect size, false positive rate and power, and advise on which technique to use depending on the data at hand.},
	language = {English},
	urldate = {2018-06-11},
	journal = {Frontiers in Psychology},
	author = {Pernet, Cyril R. and Wilcox, Rand R. and Rousselet, Guillaume A.},
	year = {2013},
	keywords = {MATLAB, power, lu, Correlation, outliers, robust statistics},
	file = {Full Text PDF:C\:\\Users\\sgranger\\Zotero\\storage\\WL2PLRLW\\Pernet et al. - 2013 - Robust Correlation Analyses False Positive and Po.pdf:application/pdf}
}

@article{wilcoxGuideRobustStatistical2018,
	title = {A {Guide} to {Robust} {Statistical} {Methods} in {Neuroscience}},
	volume = {82},
	issn = {1934-8576},
	doi = {10.1002/cpns.41},
	abstract = {There is a vast array of new and improved methods for comparing groups and studying associations that offer the potential for substantially increasing power, providing improved control over the probability of a Type I error, and yielding a deeper and more nuanced understanding of data. These new techniques effectively deal with four insights into when and why conventional methods can be unsatisfactory. But for the non-statistician, the vast array of new and improved techniques for comparing groups and studying associations can seem daunting, simply because there are so many new methods that are now available. This unit briefly reviews when and why conventional methods can have relatively low power and yield misleading results. The main goal is to suggest some general guidelines regarding when, how, and why certain modern techniques might be used. {\textcopyright} 2018 by John Wiley \& Sons, Inc.},
	language = {eng},
	journal = {Current Protocols in Neuroscience},
	author = {Wilcox, Rand R. and Rousselet, Guillaume A.},
	month = jan,
	year = {2018},
	pmid = {29357109},
	keywords = {curvature, heteroscedasticity, lu, non-normality, outliers, skewed distributions},
	pages = {8.42.1--8.42.30}
}

@book{knuthLiterateProgramming1992,
	address = {[Stanford, Calif.]},
	series = {{CSLI} lecture notes no. 27},
	title = {Literate programming},
	isbn = {0-937073-81-4},
	publisher = {Center for the Study of Language and Information},
	author = {Knuth, Donald Ervin},
	year = {1992}
}

@article{gigerenzerStatisticalRitualsReplication2018,
	title = {Statistical {Rituals}: {The} {Replication} {Delusion} and {How} {We} {Got} {There}                                                    ,                                                             {Statistical} {Rituals}: {The} {Replication} {Delusion} and {How} {We} {Got} {There}},
	volume = {1},
	issn = {2515-2459},
	shorttitle = {Statistical {Rituals}},
	url = {https://doi.org/10.1177/2515245918771329},
	doi = {10.1177/2515245918771329},
	abstract = {The {\textquotedblleft}replication crisis{\textquotedblright} has been attributed to misguided external incentives gamed by researchers (the strategic-game hypothesis). Here, I want to draw attention to a complementary internal factor, namely, researchers{\textquoteright} widespread faith in a statistical ritual and associated delusions (the statistical-ritual hypothesis). The {\textquotedblleft}null ritual,{\textquotedblright} unknown in statistics proper, eliminates judgment precisely at points where statistical theories demand it. The crucial delusion is that the p value specifies the probability of a successful replication (i.e., 1 {\textendash} p), which makes replication studies appear to be superfluous. A review of studies with 839 academic psychologists and 991 students shows that the replication delusion existed among 20\% of the faculty teaching statistics in psychology, 39\% of the professors and lecturers, and 66\% of the students. Two further beliefs, the illusion of certainty (e.g., that statistical significance proves that an effect exists) and Bayesian wishful thinking (e.g., that the probability of the alternative hypothesis being true is 1 {\textendash} p), also make successful replication appear to be certain or almost certain, respectively. In every study reviewed, the majority of researchers (56\%{\textendash}97\%) exhibited one or more of these delusions. Psychology departments need to begin teaching statistical thinking, not rituals, and journal editors should no longer accept manuscripts that report results as {\textquotedblleft}significant{\textquotedblright} or {\textquotedblleft}not significant.{\textquotedblright}, The {\textquotedblleft}replication crisis{\textquotedblright} has been attributed to misguided external incentives gamed by researchers (the strategic-game hypothesis). Here, I want to draw attention to a complementary internal factor, namely, researchers{\textquoteright} widespread faith in a statistical ritual and associated delusions (the statistical-ritual hypothesis). The {\textquotedblleft}null ritual,{\textquotedblright} unknown in statistics proper, eliminates judgment precisely at points where statistical theories demand it. The crucial delusion is that the p value specifies the probability of a successful replication (i.e., 1 {\textendash} p), which makes replication studies appear to be superfluous. A review of studies with 839 academic psychologists and 991 students shows that the replication delusion existed among 20\% of the faculty teaching statistics in psychology, 39\% of the professors and lecturers, and 66\% of the students. Two further beliefs, the illusion of certainty (e.g., that statistical significance proves that an effect exists) and Bayesian wishful thinking (e.g., that the probability of the alternative hypothesis being true is 1 {\textendash} p), also make successful replication appear to be certain or almost certain, respectively. In every study reviewed, the majority of researchers (56\%{\textendash}97\%) exhibited one or more of these delusions. Psychology departments need to begin teaching statistical thinking, not rituals, and journal editors should no longer accept manuscripts that report results as {\textquotedblleft}significant{\textquotedblright} or {\textquotedblleft}not significant.{\textquotedblright}},
	language = {en},
	number = {2},
	urldate = {2018-06-22},
	journal = {Advances in Methods and Practices in Psychological Science},
	author = {Gigerenzer, Gerd},
	month = jun,
	year = {2018},
	keywords = {lu},
	pages = {198--218}
}

@article{bishopFallibilityScienceResponding2018,
	title = {Fallibility in {Science}: {Responding} to {Errors} in the {Work} of {Oneself} and {Others}:},
	shorttitle = {Fallibility in {Science}},
	url = {http://journals.sagepub.com/doi/abs/10.1177/2515245918776632?journalCode=ampa#articleShareContainer},
	doi = {10.1177/2515245918776632},
	language = {en},
	urldate = {2018-07-04},
	journal = {Advances in Methods and Practices in Psychological Science},
	author = {Bishop, D. V. M.},
	month = jul,
	year = {2018},
	keywords = {lu},
	file = {Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\Q35RQ7ZH\\2515245918776632.html:text/html}
}

@book{bakerBookSprints2014,
	address = {Berlin},
	title = {On {Book} {Sprints}},
	url = {https://www.booksprints.net/en/blog/book-sprint-on-book-sprints/},
	publisher = {Booksprints.net},
	author = {Baker, Rachel and Berry, David and Brokering, Mark and Dieter, Michael and French, Amanda and R{\"u}hling, Barbara},
	collaborator = {Hyde, Adam},
	year = {2014},
	keywords = {lu}
}

@misc{grusDonNotebooks2018,
	title = {I {Don}'t {Like} {Notebooks}},
	url = {https://docs.google.com/presentation/d/1n2RlMdmv1p25Xy5thJUhkKGvjtV-dkAIsUXP-AL4ffI},
	urldate = {2018-08-27},
	author = {Grus, Joel},
	month = aug,
	year = {2018},
	keywords = {lu, important},
	file = {Full Text PDF:C\:\\Users\\sgranger\\Zotero\\storage\\IR4IRRZT\\Grus - 2018 - I Donx27t Like Notebooks - Joel Grus - #JupyterCo.pdf:application/pdf}
}

@book{adlinEssentialPersonaLifecycle2010,
	title = {The {Essential} {Persona} {Lifecycle}: {Your} {Guide} to {Building} and {Using} {Personas}},
	isbn = {978-0-12-381418-0},
	shorttitle = {The {Essential} {Persona} {Lifecycle}},
	url = {https://linkinghub.elsevier.com/retrieve/pii/C20090624752},
	language = {en},
	urldate = {2018-10-08},
	publisher = {Elsevier},
	author = {Adlin, Tamara and Pruitt, John},
	year = {2010},
	doi = {10.1016/C2009-0-62475-2}
}

@book{chambersSevenDeadlySins2017,
	address = {Princeton},
	title = {The {Seven} {Deadly} {Sins} of {Psychology}: {A} {Manifesto} for {Reforming} the {Culture} of {Scientific} {Practice}},
	isbn = {978-0-691-15890-7},
	shorttitle = {The {Seven} {Deadly} {Sins} of {Psychology}},
	abstract = {Why psychology is in peril as a scientific discipline{\textemdash}and how to save itPsychological science has made extraordinary discoveries about the human mind, but can we trust everything its practitioners are telling us? In recent years, it has become increasingly apparent that a lot of research in psychology is based on weak evidence, questionable practices, and sometimes even fraud. The Seven Deadly Sins of Psychology diagnoses the ills besetting the discipline today and proposes sensible, practical solutions to ensure that it remains a legitimate and reliable science in the years ahead.In this unflinchingly candid manifesto, Chris Chambers draws on his own experiences as a working scientist to reveal a dark side to psychology that few of us ever see. Using the seven deadly sins as a metaphor, he shows how practitioners are vulnerable to powerful biases that undercut the scientific method, how they routinely torture data until it produces outcomes that can be published in prestigious journals, and how studies are much less reliable than advertised. He reveals how a culture of secrecy denies the public and other researchers access to the results of psychology experiments, how fraudulent academics can operate with impunity, and how an obsession with bean counting creates perverse incentives for academics. Left unchecked, these problems threaten the very future of psychology as a science{\textemdash}but help is here.Outlining a core set of best practices that can be applied across the sciences, Chambers demonstrates how all these sins can be corrected by embracing open science, an emerging philosophy that seeks to make research and its outcomes as transparent as possible.},
	language = {English},
	publisher = {Princeton University Press},
	author = {Chambers, Chris},
	year = {2017}
}

@techreport{reseauqualiteenrechercheTracabiliteActivitesRecherche2018,
	title = {Tra{\c c}abilit{\'e} des activit{\'e}s de recherche et gestion des connaissances - {Guide} pratique de mise en place},
	url = {http://qualite-en-recherche.cnrs.fr/spip.php?article315},
	urldate = {2019-03-28},
	institution = {Mission pour les Initiatives Transverses et Interdisciplinaire},
	author = {{R{\'e}seau Qualit{\'e} en Recherche} and Rivet, Alain and Bach{\`e}lerie, Marie-Laure and Denis-Meyere, Auriane and Tisserand, Delphine},
	year = {2018},
	file = {R{\'e}seau Qualit{\'e} en Recherche - Tra{\c c}abilit{\'e} des activit{\'e}s de recherche et gestion des connaissances - Guide pratique de mise en place:C\:\\Users\\sgranger\\Zotero\\storage\\BTH58K7C\\spip.html:text/html}
}

@article{gronenschildEffectsFreeSurferVersion2012,
	title = {The {Effects} of {FreeSurfer} {Version}, {Workstation} {Type}, and {Macintosh} {Operating} {System} {Version} on {Anatomical} {Volume} and {Cortical} {Thickness} {Measurements}},
	volume = {7},
	issn = {1932-6203},
	url = {http://dx.plos.org/10.1371/journal.pone.0038234},
	doi = {10.1371/journal.pone.0038234},
	language = {en},
	number = {6},
	urldate = {2019-04-17},
	journal = {PLoS ONE},
	author = {Gronenschild, Ed H. B. M. and Habets, Petra and Jacobs, Heidi I. L. and Mengelers, Ron and Rozendaal, Nico and van Os, Jim and Marcelis, Machteld},
	editor = {Hayasaka, Satoru},
	month = jun,
	year = {2012},
	pages = {e38234},
	file = {Texte int{\'e}gral:C\:\\Users\\sgranger\\Zotero\\storage\\VJUAM5AM\\Gronenschild et al. - 2012 - The Effects of FreeSurfer Version, Workstation Typ.pdf:application/pdf}
}

@misc{maurelDonneesPersonnellesVie2018,
	title = {Donn{\'e}es personnelles et vie priv{\'e}e : ce qui va changer avec le {RGPD}},
	shorttitle = {Donn{\'e}es personnelles et vie priv{\'e}e},
	url = {https://scinfolex.com/2018/05/29/donnees-personnelles-et-vie-privee-ce-qui-va-changer-avec-le-rgpd-support-dintervention-et-video/},
	abstract = {Il y a quinze jours, j{\textquoteright}{\'e}tais {\`a} l{\textquoteright}Universit{\'e} de Technologie de Compi{\`e}gne pour donner une conf{\'e}rence intitul{\'e}e {\guillemotleft}~Donn{\'e}es personnelles et vie priv{\'e}e : ce qui va changer avec le {\textellipsis}},
	language = {fr-FR},
	urldate = {2019-04-18},
	journal = {S.I.Lex},
	author = {Maurel, Lionel},
	month = may,
	year = {2018},
	file = {Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\YM6PHA7C\\donnees-personnelles-et-vie-privee-ce-qui-va-changer-avec-le-rgpd-support-dintervention-et-vide.html:text/html}
}

@misc{comitepourlascienceouverteRessourcesGuidesJuridiques,
	title = {Ressources : guides juridiques},
	url = {https://www.ouvrirlascience.fr/category/ressources/?type=guides_juridiques},
	urldate = {2019-04-18},
	journal = {Ouvrir la science},
	author = {{Comit{\'e} pour la science ouverte}},
	file = {Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\G3FZ2VWW\\ressources.html:text/html}
}

@article{begleyDrugDevelopmentRaise2012,
	title = {Drug development : {Raise} standards for preclinical cancer research},
	volume = {483},
	copyright = {2012 Nature Publishing Group},
	issn = {1476-4687},
	shorttitle = {Drug development},
	url = {https://www.nature.com/articles/483531a},
	doi = {10.1038/483531a},
	abstract = {C. Glenn Begley and Lee M. Ellis propose how methods, publications and incentives must change if patients are to benefit.},
	language = {en},
	urldate = {2019-04-30},
	journal = {Nature},
	author = {Begley, C. Glenn and Ellis, Lee M.},
	month = mar,
	year = {2012},
	pages = {531--533},
	file = {Full Text PDF:C\:\\Users\\sgranger\\Zotero\\storage\\9B76C4NF\\Begley et Ellis - 2012 - Drug development Raise standards for preclinical .pdf:application/pdf;Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\PE6NWGJM\\483531a.html:text/html}
}

@article{perrinPreclinicalResearchMake2014,
	title = {Preclinical research : {Make} mouse studies work},
	volume = {507},
	shorttitle = {Preclinical research},
	url = {http://www.nature.com/news/preclinical-research-make-mouse-studies-work-1.14913},
	doi = {10.1038/507423a},
	abstract = {More investment to characterize animal models can boost the ability of preclinical work to predict drug effects in humans, says Steve Perrin.},
	language = {en},
	number = {7493},
	urldate = {2019-04-30},
	journal = {Nature News},
	author = {Perrin, Steve},
	month = mar,
	year = {2014},
	pages = {423},
	file = {Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\6VJ74KRL\\preclinical-research-make-mouse-studies-work-1.html:text/html}
}

@article{nuzzoScientificMethodStatistical2014,
	title = {Scientific method: {Statistical} errors},
	volume = {506},
	shorttitle = {Scientific method},
	url = {http://www.nature.com/news/scientific-method-statistical-errors-1.14700},
	doi = {10.1038/506150a},
	abstract = {P values, the 'gold standard' of statistical validity, are not as reliable as many scientists assume.},
	language = {en},
	number = {7487},
	urldate = {2019-04-30},
	journal = {Nature News},
	author = {Nuzzo, Regina},
	month = feb,
	year = {2014},
	pages = {150},
	file = {Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\ZYEGX9H5\\scientific-method-statistical-errors-1.html:text/html}
}

@article{kerrHARKingHypothesizingResults1998,
	title = {{HARKing} : hypothesizing after the results are known},
	volume = {2},
	issn = {1088-8683},
	shorttitle = {{HARKing}},
	doi = {10.1207/s15327957pspr0203_4},
	abstract = {This article considers a practice in scientific communication termed HARKing (Hypothesizing After the Results are Known). HARKing is defined as presenting a post hoc hypothesis (i.e., one based on or informed by one's results) in one's research report as i f it were, in fact, an a priori hypotheses. Several forms of HARKing are identified and survey data are presented that suggests that at least some forms of HARKing are widely practiced and widely seen as inappropriate. I identify several reasons why scientists might HARK. Then I discuss several reasons why scientists ought not to HARK. It is conceded that the question of whether HARKing ' s costs exceed its benefits is a complex one that ought to be addressed through research, open discussion, and debate. To help stimulate such discussion (and for those such as myself who suspect that HARKing's costs do exceed its benefits), I conclude the article with some suggestions for deterring HARKing.},
	language = {eng},
	number = {3},
	journal = {Personality and Social Psychology Review: An Official Journal of the Society for Personality and Social Psychology, Inc},
	author = {Kerr, N. L.},
	year = {1998},
	pmid = {15647155},
	keywords = {pas de full text en acc{\`e}s libre},
	pages = {196--217},
	file = {Version soumise:C\:\\Users\\sgranger\\Zotero\\storage\\GKAIAUDF\\Kerr - 1998 - HARKing hypothesizing after the results are known.pdf:application/pdf}
}

@article{wacholderAssessingProbabilityThat2004,
	title = {Assessing the {Probability} {That} a {Positive} {Report} is {False}: {An} {Approach} for {Molecular} {Epidemiology} {Studies}},
	volume = {96},
	issn = {0027-8874},
	shorttitle = {Assessing the {Probability} {That} a {Positive} {Report} is {False}},
	url = {https://academic.oup.com/jnci/article/96/6/434/2606750},
	doi = {10.1093/jnci/djh075},
	abstract = {Abstract.  Too many reports of associations between genetic variants and common cancer sites and other complex diseases are false positives. A major reason for},
	language = {en},
	number = {6},
	urldate = {2019-04-30},
	journal = {JNCI: Journal of the National Cancer Institute},
	author = {Wacholder, Sholom and Chanock, Stephen and Garcia-Closas, Montserrat and El ghormli, Laure and Rothman, Nathaniel},
	month = mar,
	year = {2004},
	pages = {434--442},
	file = {Full Text PDF:C\:\\Users\\sgranger\\Zotero\\storage\\ZS6YHBBA\\Wacholder et al. - 2004 - Assessing the Probability That a Positive Report i.pdf:application/pdf;Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\YHDAHY7S\\2606750.html:text/html}
}

@techreport{bureauinternationaldespoidsetdesmesuresVocabulaireInternationalMetrologie2012,
	address = {S{\`e}vres},
	title = {Vocabulaire international de m{\'e}trologie {\textendash} {Concepts} fondamentaux et g{\'e}n{\'e}raux et termes associ{\'e}s},
	url = {https://www.bipm.org/utils/common/documents/jcgm/JCGM_200_2012.pdf},
	number = {JCGM 200:2012},
	urldate = {2019-04-30},
	institution = {Bureau International des Poids et des Mesures},
	author = {{Bureau International des Poids et des Mesures}},
	year = {2012},
	file = {JCGM_200_2012.pdf:C\:\\Users\\sgranger\\Zotero\\storage\\BXGMYK3B\\JCGM_200_2012.pdf:application/pdf}
}

@misc{jetpropulsionlaboratory-californiainstituteoftechnologyMarsClimateOrbiter,
	title = {Mars {Climate} {Orbiter}},
	url = {https://www.jpl.nasa.gov/missions/mars-climate-orbiter/},
	abstract = {Designed to study Mars from orbit and serve as a communications relay for the Mars Polar Lander and Deep Space probes, the Mars Climate Orbiter was unsuccessful due to a navigation error caused by a failure to translate English units to metric.},
	urldate = {2019-04-30},
	journal = {Jet Propulsion Laboratory - California Institute of Technology - NASA},
	author = {{Jet Propulsion Laboratory - California Institute of Technology}},
	file = {Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\N6V2I8U4\\mars-climate-orbiter.html:text/html}
}

@article{spinellisDecayFailuresWeb2003,
	title = {The decay and failures of web references},
	volume = {46},
	issn = {00010782},
	url = {http://portal.acm.org/citation.cfm?doid=602421.602422},
	doi = {10.1145/602421.602422},
	number = {1},
	urldate = {2019-04-30},
	journal = {Communications of the ACM},
	author = {Spinellis, Diomidis},
	month = jan,
	year = {2003},
	keywords = {pas de full text en acc{\`e}s libre},
	pages = {71--77}
}

@misc{wikipediaLinkRot2019,
	title = {Link rot},
	copyright = {Creative Commons Attribution-ShareAlike License},
	url = {https://en.wikipedia.org/w/index.php?title=Link_rot&oldid=893134620},
	abstract = {Link rot (or linkrot) is the process by which hyperlinks on individual websites or the Internet in general tend to point to web pages, servers or other resources that have become permanently unavailable. There is no reliable data on how long web pages and other resources survive: the estimates vary dramatically between different studies, as well as between different sets of links on which these studies are based (see the \#Prevalence section).},
	language = {en},
	urldate = {2019-04-30},
	journal = {Wikipedia},
	author = {{Wikipedia}},
	month = apr,
	year = {2019},
	note = {Page Version ID: 893134620},
	file = {Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\QTEPWKEI\\index.html:text/html}
}

@article{collbergRepeatabilityComputerSystems2016,
	title = {Repeatability in computer systems research},
	volume = {59},
	issn = {0001-0782},
	url = {https://arizona.pure.elsevier.com/en/publications/repeatability-in-computer-systems-research},
	doi = {10.1145/2812803},
	language = {English (US)},
	number = {3},
	urldate = {2019-04-30},
	journal = {Communications of the ACM},
	author = {Collberg, Christian S. and Proebsting, Todd A.},
	month = feb,
	year = {2016},
	pages = {62--69},
	file = {Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\BU8RPWUT\\repeatability-in-computer-systems-research.html:text/html}
}

@book{abelsonStructureInterpretationComputer1996,
	address = {Cambridge, Etats-Unis d'Am{\'e}rique},
	title = {Structure and {Interpretation} of {Computer} {Programs}},
	isbn = {978-0-262-01153-2 978-0-262-51087-5},
	language = {anglais},
	publisher = {MIT Press},
	author = {Abelson, Harold and Sussman, Gerald Jay and Sussman, Julie and Perlis, Alan J.},
	year = {1996},
	keywords = {Electronic digital computers -- Programming, LISP (Computer program language), LISP (langage de programmation), Ordinateurs -- Programmation -- Manuels d'enseignement sup{\'e}rieur, Programmation structur{\'e}e, Structured programming},
	file = {Library Catalog Entry Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\V6NPUPMX\\SRCH.html:text/html}
}

@misc{broukhisInternationalObfuscatedCode,
	title = {The {International} {Obfuscated} {C} {Code} {Contest}},
	url = {http://ioccc.org/},
	urldate = {2019-04-30},
	journal = {The International Obfuscated C Code Contest},
	author = {Broukhis, Leo and Cooper, Simon and Curt Noll, Landon},
	file = {The International Obfuscated C Code Contest:C\:\\Users\\sgranger\\Zotero\\storage\\T2UPVQTD\\ioccc.org.html:text/html}
}

@misc{arnoldPatriotMissileFailure2000,
	title = {The {Patriot} {Missile} {Failure}},
	url = {http://www-users.math.umn.edu/~arnold/disasters/patriot.html},
	urldate = {2019-04-30},
	journal = {Douglas N. Arnold  McKnight, Presidential Professor of Mathematics},
	author = {Arnold, Douglas N.},
	month = aug,
	year = {2000},
	file = {The Patriot Missile Failure:C\:\\Users\\sgranger\\Zotero\\storage\\4H4BXCPA\\patriot.html:text/html}
}

@article{feherNumericalErrorsMinimization2012,
	title = {Numerical {Errors} in {Minimization} {Based} {Binding} {Energy} {Calculations}},
	volume = {52},
	issn = {1549-9596},
	url = {https://doi.org/10.1021/ci300298d},
	doi = {10.1021/ci300298d},
	abstract = {This work examines the effect of small input perturbations on binding energies computed from differences between energy minimized structures, such as the Prime MM-GBSA and MOE MM-GB/VI methods. The applied perturbations include translations of the cognate ligand in the binding site by a maximum of 0.1 {\r A} along each coordinate or the permutation of the order of atoms of the cognate ligand without any changes to the atom coordinates. These seemingly inconsequential input changes can lead to as much as 17 kcal/mol differences in the computed binding energy. The calculated binding energies cluster around discrete values, which correspond to specific ligand poses. It appears that the largest variations are observed for target-ligand systems in which there is a possibility for multiple poses with strong hydrogen bonds. The barriers between different poses can appear fractal-like, making it difficult to predict which solution will be produced from a given input. Including protein flexibility in MM-GBSA calculations further increases numerical instability, and the protein strain terms seem to be the major factor contributing to this sensitivity. In such calculations it appears unwise to extend the flexible region beyond 6 {\r A}.},
	number = {12},
	urldate = {2019-04-30},
	journal = {Journal of Chemical Information and Modeling},
	author = {Feher, Miklos and Williams, Christopher I.},
	month = dec,
	year = {2012},
	pages = {3200--3212},
	file = {ACS Full Text PDF w/ Links:C\:\\Users\\sgranger\\Zotero\\storage\\4P8ZWA3C\\Feher et Williams - 2012 - Numerical Errors in Minimization Based Binding Ene.pdf:application/pdf;ACS Full Text Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\2HXMB9BT\\ci300298d.html:text/html}
}

@article{feherNumericalErrorsChaotic2012,
	title = {Numerical {Errors} and {Chaotic} {Behavior} in {Docking} {Simulations}},
	volume = {52},
	issn = {1549-9596},
	url = {https://doi.org/10.1021/ci200598m},
	doi = {10.1021/ci200598m},
	abstract = {This work examines the sensitivity of docking programs to tiny changes in ligand input files. The results show that nearly identical ligand input structures can produce dramatically different top-scoring docked poses. Even changing the atom order in a ligand input file can produce significantly different poses and scores. In well-behaved cases the docking variations are small and follow a normal distribution around a central pose and score, but in many cases the variations are large and reflect wildly different top scores and binding modes. The docking variations are characterized by statistical methods, and the sensitivity of high-throughput and more precise docking methods are compared. The results demonstrate that part of docking variation is due to numerical sensitivity and potentially chaotic effects in current docking algorithms and not solely due to incomplete ligand conformation and pose searching. These results have major implications for the way docking is currently used for pose prediction, ranking, and virtual screening.},
	number = {3},
	urldate = {2019-04-30},
	journal = {Journal of Chemical Information and Modeling},
	author = {Feher, Miklos and Williams, Christopher I.},
	month = mar,
	year = {2012},
	pages = {724--738},
	file = {ACS Full Text PDF w/ Links:C\:\\Users\\sgranger\\Zotero\\storage\\DT54ZEQ6\\Feher et Williams - 2012 - Numerical Errors and Chaotic Behavior in Docking S.pdf:application/pdf;ACS Full Text Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\WHZS5BHQ\\ci200598m.html:text/html}
}

@article{goldbergWhatEveryComputer1991,
	title = {What {Every} {Computer} {Scientist} {Should} {Know} {About} {Floating}-point {Arithmetic}},
	volume = {23},
	issn = {0360-0300},
	url = {https://www.itu.dk/~sestoft/bachelor/IEEE754_article.pdf},
	doi = {10.1145/103162.103163},
	abstract = {Floating-point arithmetic is considered as esoteric subject by many people. This is rather surprising, because floating-point is ubiquitous in computer systems: Almost every language has a floating-point datatype; computers from PCs to supercomputers have floating-point accelerators; most compilers will be called upon to compile floating-point algorithms from time to time; and virtually every operating system must respond to floating-point exceptions such as overflow. This paper presents a tutorial on the aspects of floating-point that have a direct impact on designers of computer systems. It begins with background on floating-point representation and rounding error, continues with a discussion of the IEEE floating point standard, and concludes with examples of how computer system builders can better support floating point.},
	number = {1},
	urldate = {2019-04-30},
	journal = {ACM Comput. Surv.},
	author = {Goldberg, David},
	month = mar,
	year = {1991},
	keywords = {denormalized number, exception, floating-point, floating-point standard, gradual underflow, guard digit, NaN, overflow, relative error, rounding error, rounding mode, ulp, underflow},
	pages = {5--48}
}

@article{stoddenAssessingReproducibilityAstrophysical2018,
	title = {Assessing {Reproducibility} : {An} {Astrophysical} {Example} of {Computational} {Uncertainty} in the {HPC} {Context}},
	url = {https://web.stanford.edu/~vcs/papers/ResCuE2018-VSMK.pdf},
	abstract = {We present an experiment using the Enzo simulation code on NCSA{\textquoteright}s Blue Waters system to highlight the importance of computational and numerical uncertainty in scientific computing on HPC systems. We quantify the (surprising) variability of outputs from 200 identical simulation runs. We make two recommendations to improve the assessment of reproducibility of computational results: the inclusion of computational variability measures in standard reporting practices; and modular software designs that permit localized assessments of the source of computational uncertainty.},
	language = {en},
	urldate = {2019-04-30},
	author = {Stodden, Victoria and Krafczyk, Matthew S},
	month = aug,
	year = {2018},
	pages = {5},
	file = {Stodden et Krafczyk - Assessing Reproducibility An Astrophysical Exampl.pdf:C\:\\Users\\sgranger\\Zotero\\storage\\WR6Q6LJ2\\Stodden et Krafczyk - Assessing Reproducibility An Astrophysical Exampl.pdf:application/pdf}
}

@misc{legrandSeriesWebinarsDocuments2016,
	title = {Series of webinars and documents on {Reproducible} {Research} - {Controling} your environment},
	shorttitle = {Series of webinars and documents on {Reproducible} {Research}},
	url = {https://github.com/alegrand/RR_webinars/blob/master/2_controling_your_environment/index.org},
	urldate = {2019-04-30},
	journal = {Reproducible Research Webinars},
	author = {Legrand, Arnaud},
	month = feb,
	year = {2016},
	note = {original-date: 2016-02-08T08:41:51Z}
}

@article{hebrardHowMeasurementsRate2009,
	title = {How {Measurements} of {Rate} {Coefficients} at {Low} {Temperature} {Increase} the {Predictivity} of {Photochemical} {Models} of {Titan}{\textquoteright}s {Atmosphere}},
	volume = {113},
	issn = {1089-5639},
	url = {https://doi.org/10.1021/jp905524e},
	doi = {10.1021/jp905524e},
	abstract = {The predictivity of photochemical models of Titan{\textquoteright}s atmosphere depends strongly on the precision and accuracy of reaction rates. For many reactions, large uncertainty results from the extrapolation of rate laws to low temperatures. A few reactions have been measured directly at temperatures relevant to Titan{\textquoteright}s atmosphere. In the present study, we observed the consequences of the reduced uncertainty attributed to these reactions. The global predictivity of the model was improved, i.e., most species are predicted with lower uncertainty factors. Nevertheless, high uncertainty factors are still observed, and a new list of key reactions has been established.},
	number = {42},
	urldate = {2019-04-30},
	journal = {The Journal of Physical Chemistry A},
	author = {H{\'e}brard, E. and Dobrijevic, M. and Pernot, P. and Carrasco, N. and Bergeat, A. and Hickson, K. M. and Canosa, A. and Le Picard, S. D. and Sims, I. R.},
	month = oct,
	year = {2009},
	pages = {11227--11237},
	file = {ACS Full Text PDF w/ Links:C\:\\Users\\sgranger\\Zotero\\storage\\ENYQ4HM9\\H{\'e}brard et al. - 2009 - How Measurements of Rate Coefficients at Low Tempe.pdf:application/pdf;ACS Full Text Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\QVFIVE5J\\jp905524e.html:text/html}
}

@article{ezhelaInconstancyFundamentalPhysical2004,
	title = {The {Inconstancy} of the {Fundamental} {Physical} {Constants}: {Computational} {Status}},
	shorttitle = {The {Inconstancy} of the {Fundamental} {Physical} {Constants}},
	url = {http://arxiv.org/abs/physics/0409117},
	abstract = {It is argued that the CODATA recommended values of the fundamental physical constants could not be used as the reference data in searching the hypothetical space-time variations of the fundamental physical constants. It is shown that the CODATA data permanently suffers a loss of self-consistency of the released data due to unjustified over-rounding of their estimates. The simple estimates of the critical numbers of decimal digits that should be saved in the independently rounded correlation coefficients, the average values and uncertainties to save the self-consistency is obtained. The set of high level quality requirements to the computerized presentation of the numerical data on the jointly measured or estimated physical values are formulated. It is argued (once again) that the common standard for presentation of the numerical values of correlated quantities in publications and sites is urgently needed.},
	urldate = {2019-04-30},
	journal = {arXiv:physics/0409117},
	author = {Ezhela, V. V. and Kuyanov, Yu V. and Larin, V. N. and Siver, A. S.},
	month = sep,
	year = {2004},
	note = {arXiv: physics/0409117},
	keywords = {Physics - Data Analysis, Statistics and Probability},
	file = {arXiv\:physics/0409117 PDF:C\:\\Users\\sgranger\\Zotero\\storage\\6M2V6G9Z\\Ezhela et al. - 2004 - The Inconstancy of the Fundamental Physical Consta.pdf:application/pdf;arXiv.org Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\48XVFVGM\\0409117.html:text/html}
}

@misc{cnrsCahierLaboratoire,
	title = {Le cahier de laboratoire},
	url = {http://www.cnrs.fr/infoslabos/cahier-laboratoire/},
	urldate = {2019-04-30},
	journal = {Informations aux laboratoires CNRS},
	author = {{CNRS}},
	file = {CNRS - Informations aux laboratoires:C\:\\Users\\sgranger\\Zotero\\storage\\CJQVUVBN\\cahier-laboratoire.html:text/html}
}

@techreport{bureauinternationaldespoidsetdesmesuresEvaluationDonneesMesure,
	address = {S{\`e}vres},
	title = {{\'E}valuation des donn{\'e}es de mesure - {Guide} pour l{\textquoteright}expression de l{\textquoteright}incertitude de mesure},
	url = {https://www.bipm.org/utils/common/documents/jcgm/JCGM_100_2008_F.pdf},
	language = {FR},
	number = {JCGM 100:2008(F)},
	urldate = {2019-04-30},
	institution = {Bureau International des Poids et des Mesures},
	author = {{Bureau International des Poids et des Mesures}}
}

@techreport{bureauinternationaldespoidsetdesmesuresEvaluationMeasurementData,
	address = {S{\`e}vres},
	title = {Evaluation of measurement data - {Supplement} 2 to the {\textquotedblleft}{Guide} to the expression of uncertainty in measurement{\textquotedblright} - {Extension} to any number of  output quantities},
	url = {https://www.bipm.org/utils/common/documents/jcgm/JCGM_102_2011_E.pdf},
	number = {JCGM 102 : 2011},
	urldate = {2019-04-30},
	institution = {Bureau International des Poids et des Mesures},
	author = {{Bureau International des Poids et des Mesures}}
}

@article{wickhamTidyData2014,
	title = {Tidy {Data}},
	volume = {59},
	copyright = {Copyright (c) 2013 Hadley  Wickham},
	issn = {1548-7660},
	url = {https://www.jstatsoft.org/index.php/jss/article/view/v059i10},
	doi = {10.18637/jss.v059.i10},
	language = {en},
	number = {1},
	urldate = {2019-04-30},
	journal = {Journal of Statistical Software},
	author = {Wickham, Hadley},
	month = sep,
	year = {2014},
	pages = {1--23},
	file = {Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\YEFH4V88\\v059i10.html:text/html;Texte int{\'e}gral:C\:\\Users\\sgranger\\Zotero\\storage\\SKDBL5BS\\Wickham - 2014 - Tidy Data.pdf:application/pdf}
}

@article{marwickPackagingDataAnalytical2018,
	title = {Packaging {Data} {Analytical} {Work} {Reproducibly} {Using} {R} (and {Friends})},
	volume = {72},
	issn = {0003-1305},
	url = {https://amstat.tandfonline.com/doi/full/10.1080/00031305.2017.1375986},
	doi = {10.1080/00031305.2017.1375986},
	abstract = {Computers are a central tool in the research process, enabling complex and large-scale data analysis. As computer-based research has increased in complexity, so have the challenges of ensuring that this research is reproducible. To address this challenge, we review the concept of the research compendium as a solution for providing a standard and easily recognizable way for organizing the digital materials of a research project to enable other researchers to inspect, reproduce, and extend the research. We investigate how the structure and tooling of software packages of the R programming language are being used to produce research compendia in a variety of disciplines. We also describe how software engineering tools and services are being used by researchers to streamline working with research compendia. Using real-world examples, we show how researchers can improve the reproducibility of their work using research compendia based on R packages and related tools.},
	number = {1},
	urldate = {2019-04-30},
	journal = {The American Statistician},
	author = {Marwick, Ben and Boettiger, Carl and Mullen, Lincoln},
	month = jan,
	year = {2018},
	pages = {80--88},
	file = {Full Text PDF:C\:\\Users\\sgranger\\Zotero\\storage\\TEDRQHJR\\Marwick et al. - 2017 - Packaging data analytical work reproducibly using .pdf:application/pdf;Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\5W3KXWZH\\00031305.2017.html:text/html;Version soumise:C\:\\Users\\sgranger\\Zotero\\storage\\JDLBUGIC\\Marwick et al. - 2018 - Packaging Data Analytical Work Reproducibly Using .pdf:application/pdf}
}

@misc{wikipediaFigshare2019,
	title = {Figshare},
	copyright = {Creative Commons Attribution-ShareAlike License},
	url = {https://en.wikipedia.org/w/index.php?title=Figshare&oldid=879496564},
	abstract = {Figshare is an online open access repository where researchers can preserve and share their research outputs, including figures, datasets, images, and videos.  It is free to upload content and free to access, in adherence to the principle of open data. Figshare is one of a number of portfolio businesses supported by Digital Science.},
	language = {en},
	urldate = {2019-04-30},
	journal = {Wikipedia},
	author = {{Wikipedia}},
	month = jan,
	year = {2019},
	note = {Page Version ID: 879496564},
	file = {Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\IA9YB3YJ\\index.html:text/html}
}

@misc{wikipediaZenodo2019,
	title = {Zenodo},
	copyright = {Creative Commons Attribution-ShareAlike License},
	url = {https://fr.wikipedia.org/w/index.php?title=Zenodo&oldid=157645684},
	abstract = {Zenodo est un r{\'e}pertoire de travaux de recherche et de donn{\'e}es.},
	language = {fr},
	urldate = {2019-04-30},
	journal = {Wikip{\'e}dia},
	author = {{Wikipedia}},
	month = mar,
	year = {2019},
	note = {Page Version ID: 157645684},
	file = {Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\8V7I9WN6\\index.html:text/html}
}

@misc{softwareheritageSoftwareHeritage,
	title = {Software {Heritage}},
	url = {https://www.softwareheritage.org/?lang=fr},
	abstract = {Les logiciels sontnotre patrimoine Les logiciels sont fragiles contrairement aux mots grav{\'e}s dans la pierre, ils peuvent {\^e}tre d{\'e}truits ou alt{\'e}r{\'e}s Les logiciels sont la cl{\'e} pour acc{\'e}der {\`a} l{\textquoteright}information et {\`a} une part essentielle du patrimoine de l{\textquoteright}humanit{\'e} Software Heritage pr{\'e}serve le code source des logiciels, pour les g{\'e}n{\'e}rations actuelles et futures Nous construisons [{\textellipsis}]},
	language = {fr-FR},
	urldate = {2019-04-30},
	journal = {Software Heritage},
	author = {{Software Heritage}},
	file = {Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\SW26WDL5\\www.softwareheritage.org.html:text/html}
}

@misc{gofairFAIRPrinciples,
	title = {{FAIR} {Principles}},
	url = {https://www.go-fair.org/fair-principles/},
	abstract = {In 2016, the {\textquoteleft}FAIR Guiding Principles for scientific data management and stewardship{\textquoteright}~were published in~Scientific Data. The authors intended to provide guidelines to improve the findability, accessibility, interoperability, and reuse of digital assets. The principles emphasise machine-actionability (i.e., the capacity of{\textellipsis} Continue reading {\textrightarrow}},
	language = {en-US},
	urldate = {2019-04-30},
	journal = {GO FAIR Initiative},
	author = {{GO FAIR}},
	file = {Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\HBAGGZ6D\\fair-principles.html:text/html}
}

@misc{legrandSeriesWebinarsDocuments2016a,
	title = {Series of webinars and documents on {Reproducible} {Research} - {Preserving} software: ensuring availability and traceability},
	shorttitle = {Series of webinars and documents on {Reproducible} {Research}},
	url = {https://github.com/alegrand/RR_webinars/blob/master/5_archiving_software_and_data/index.org},
	urldate = {2019-04-30},
	journal = {Reproducible Research Webinars},
	author = {Legrand, Arnaud},
	month = feb,
	year = {2016},
	note = {original-date: 2016-02-08T08:41:51Z}
}

@misc{bryanHowNameFiles2015,
	address = {Duke},
	title = {How to name files},
	url = {https://speakerdeck.com/jennybc/how-to-name-files},
	abstract = {Low-tech common sense about filenames. Prepared under the auspices of the Reproducible Science Curriculum (https://github.com/Reproducible-Science-Curriculum). Slides made for a workshop at Duke in May 2015.},
	urldate = {2019-04-30},
	author = {Bryan, Jenny},
	month = may,
	year = {2015},
	file = {How to name files - Speaker Deck:C\:\\Users\\sgranger\\Zotero\\storage\\U6SFR7JQ\\how-to-name-files.html:text/html}
}

@misc{gitlabGitlabINRIA,
	title = {Gitlab at {INRIA}},
	url = {https://gitlab.inria.fr/users/sign_in},
	abstract = {Gitlab at INRIA},
	urldate = {2019-04-30},
	journal = {GitLab},
	author = {{Gitlab}},
	file = {Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\MBYBMP4I\\sign_in.html:text/html}
}

@misc{gitlabGitlabIN2P3,
	title = {Gitlab {IN}2P3},
	url = {https://gitlab.in2p3.fr/users/sign_in},
	abstract = {Gitlab IN2P3},
	urldate = {2019-04-30},
	journal = {GitLab},
	author = {{Gitlab}},
	file = {Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\XT4VH4FM\\sign_in.html:text/html}
}

@misc{wikipediaGitHub2019,
	title = {{GitHub}},
	copyright = {Creative Commons Attribution-ShareAlike License},
	url = {https://fr.wikipedia.org/w/index.php?title=GitHub_(entreprise)&oldid=156072313},
	abstract = {Github est une entreprise de d{\'e}veloppement logiciel et de service dont le si{\`e}ge est situ{\'e} aux {\'E}tats-Unis. Github d{\'e}veloppe notamment la plateforme Github, l'{\'e}diteur de texte Atom ou encore le framework Electron.
Le 4 juin 2018, Microsoft annonce l{\textquoteright}acquisition de l{\textquoteright}entreprise pour la somme de 7,5 milliards de dollars am{\'e}ricains,.},
	language = {fr},
	urldate = {2019-04-30},
	journal = {Wikip{\'e}dia},
	author = {{Wikipedia}},
	month = jan,
	year = {2019},
	note = {Page Version ID: 156072313},
	file = {Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\L735DFQR\\index.html:text/html}
}

@misc{inrialearninglabMOOCRechercheReproductible2018,
	title = {{MOOC} {\guillemotleft} {Recherche} reproductible : principes m{\'e}thodologiques pour une science transparente {\guillemotright} {\textendash} {Session} 2},
	shorttitle = {{MOOC} {\guillemotleft} {Recherche} reproductible},
	url = {https://learninglab.inria.fr/mooc-recherche-reproductible-principes-methodologiques-pour-une-science-transparente/},
	language = {fr-FR},
	urldate = {2019-04-30},
	journal = {Inria Learning Lab},
	author = {{Inria Learning Lab}},
	month = sep,
	year = {2018},
	file = {Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\67W2DFQ9\\mooc-recherche-reproductible-principes-methodologiques-pour-une-science-transparente.html:text/html}
}

@misc{hesterHappyGitGitHub,
	title = {Happy {Git} and {GitHub} for the {useR}},
	url = {https://happygitwithr.com/},
	abstract = {Using Git and GitHub with R, Rstudio, and R Markdown},
	urldate = {2019-04-30},
	author = {Hester, Jim and Bryan, Jenny},
	file = {Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\N3GKFBJ2\\happygitwithr.com.html:text/html}
}

@misc{softwarecarpentryVersionControlGit,
	title = {Version {Control} with {Git}},
	url = {http://swcarpentry.github.io/git-novice/},
	urldate = {2019-04-30},
	journal = {Software Carpentry},
	author = {{Software Carpentry}},
	file = {Version Control with Git:C\:\\Users\\sgranger\\Zotero\\storage\\55GWEPZK\\git-novice.html:text/html}
}

@book{chaconProGitBook2014,
	address = {New York},
	edition = {2nd},
	title = {Pro {Git} book. {Everything} {You} {Need} to {Know} {About} {Git}},
	url = {https://git-scm.com/book/en/v2},
	urldate = {2019-04-30},
	publisher = {Apress},
	author = {Chacon, Scott and Straub, Ben},
	year = {2014},
	file = {Git - Book:C\:\\Users\\sgranger\\Zotero\\storage\\8BMLUYJ9\\v2.html:text/html}
}

@book{chaconProGitTout2019,
	address = {New York},
	edition = {2nd},
	title = {Pro {Git}. {Tout} ce que vous devez savoir sur {Git}},
	url = {https://git-scm.com/book/fr/v2},
	urldate = {2019-04-30},
	publisher = {APress},
	author = {Chacon, Scott and Straub, Ben},
	year = {2019},
	file = {Git - Book:C\:\\Users\\sgranger\\Zotero\\storage\\CIKJ9PSF\\v2.html:text/html}
}

@misc{cottleLearnGitBranching,
	title = {Learn {Git} {Branching}},
	url = {https://pcottle.github.io/learnGitBranching/index.html?demo},
	abstract = {An interactive Git visualization tool to educate and challenge!},
	language = {fr},
	urldate = {2019-04-30},
	author = {Cottle, Peter},
	file = {Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\9R826JUR\\learngitbranching.js.org.html:text/html}
}

@misc{scipySciPyConferences,
	title = {{SciPy} {Conferences}},
	url = {http://conference.scipy.org/},
	urldate = {2019-04-30},
	author = {{SciPy}},
	file = {SciPy Conferences:C\:\\Users\\sgranger\\Zotero\\storage\\L26KBVES\\conference.scipy.org.html:text/html}
}

@misc{euroscipyEuroSciPyHome,
	title = {{EuroSciPy} home},
	url = {https://www.euroscipy.org/},
	urldate = {2019-04-30},
	author = {{EuroSciPy}},
	file = {EuroSciPy home:C\:\\Users\\sgranger\\Zotero\\storage\\2V28759E\\www.euroscipy.org.html:text/html}
}

@misc{user!UseR2019,
	title = {{useR}! 2019},
	url = {http://www.user2019.fr/},
	urldate = {2019-04-30},
	author = {{useR!}},
	file = {useR! 2019 - Toulouse:C\:\\Users\\sgranger\\Zotero\\storage\\MS2WK45I\\www.user2019.fr.html:text/html}
}

@misc{rencontresr7eRencontres2018,
	title = {7e {Rencontres} {R}},
	url = {https://r2018-rennes.sciencesconf.org/},
	urldate = {2019-04-30},
	author = {{Rencontres R}},
	year = {2018},
	file = {7e Rencontres R - Rennes 2018 - Sciencesconf.org:C\:\\Users\\sgranger\\Zotero\\storage\\V6V7DS9R\\r2018-rennes.sciencesconf.org.html:text/html}
}

@misc{universiteparissudIntroductionStatistiqueAvec,
	title = {Introduction {\`a} la statistique avec {R} - session 6},
	url = {//www.fun-mooc.fr/courses/UPSUD/42001S06/session06/about},
	abstract = {Ce cours permet d{\textquoteright}apprendre la statistique {\`a} l{\textquoteright}aide du logiciel libre R. Le recours aux math{\'e}matiques est minimal. L{\textquoteright}objectif est de savoir analyser des donn{\'e}es en comprenant ce que l{\textquoteright}on fait.},
	language = {fr},
	urldate = {2019-04-30},
	journal = {FUN-MOOC},
	author = {{Universit{\'e} Paris Sud}},
	file = {Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\TNTGYSVD\\about.html:text/html}
}

@misc{inriaPythonFondamentauxUtilisation,
	title = {Python : des fondamentaux {\`a} l'utilisation du langage},
	shorttitle = {Python},
	url = {//www.fun-mooc.fr/courses/inria/41001S03/session03/about},
	abstract = {Dans ce cours, vous apprendrez {\`a} bien programmer en Python. On vous m{\`e}nera des premiers pas dans le langage {\`a} l'{\'e}tude des concepts les plus {\'e}volu{\'e}s au travers de nombreuses vid{\'e}os courtes, d'exercices et de mini-projets.},
	language = {fr},
	urldate = {2019-04-30},
	journal = {FUN-MOOC},
	author = {{Inria}},
	file = {Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\IHESWTGV\\about.html:text/html}
}

@misc{arnalBegin,
	title = {Begin{\textquoteright}{R}},
	url = {http://beginr.u-bordeaux.fr/},
	urldate = {2019-04-30},
	journal = {Begin'R},
	author = {Arnal, Florent and Bombrun, Lionel and Da Costa, Jean-Pierre and Dantzer, C{\'e}cile and Genuer, Robin and Jutand, Marthe-Aline and Lebreton, Marie and Moutault, S{\'e}bastien and Saracco, J{\'e}r{\^o}me and Savoire, Rapha{\"e}lle},
	file = {Begin{\textquoteright}R:C\:\\Users\\sgranger\\Zotero\\storage\\HKL4E9DC\\beginr.u-bordeaux.fr.html:text/html}
}

@misc{pythonsoftwarefoundationTutorielPythonDocumentation,
	title = {Le tutoriel {Python} - {Documentation} {Python} 3.7.3},
	url = {https://docs.python.org/fr/3/tutorial/},
	urldate = {2019-04-30},
	journal = {Documentation Python},
	author = {{Python Software Foundation}},
	file = {Le tutoriel Python {\textemdash} Documentation Python 3.7.3:C\:\\Users\\sgranger\\Zotero\\storage\\3RT6IP9B\\tutorial.html:text/html}
}

@book{wickhamPourDataSciences2018,
	address = {Paris, France},
	title = {R pour les data sciences: importer, classer, transformer, visualiser et mod{\'e}liser les donn{\'e}es},
	isbn = {978-2-212-67571-9},
	shorttitle = {R pour les data sciences},
	abstract = {La 4e de couv. indique : "R : le langage de r{\'e}f{\'e}rence pour le big data. Les data sciences constituent une discipline fascinante, qui vous servira {\`a} transformer des donn{\'e}es brutes en id{\'e}es et connaissances ais{\'e}ment compr{\'e}hensibles. L'objectif de ce livre est de vous aider {\`a} ma{\^i}triser les outils essentiels qui vous permettront d'utiliser R dans la pratique des data sciences. Apr{\`e}s l'avoir lu, vous pourrez faire face {\`a} la plupart des situations que vous rencontrerez dans vos projets, en exploitant au mieux les fonctionnalit{\'e}s de R. Mais avant de devenir un expert en R, vous devrez tout d'abord importer vos donn{\'e}es, c'est-{\`a}-dire les lire, en g{\'e}n{\'e}ral depuis un fichier, une base de donn{\'e}es ou une API web. et les charger dans un cadre de donn{\'e}es dans R. Si vous ne pouvez pas transf{\'e}rer vos donn{\'e}es dans R, vous ne pourrez pas les analyser ! Une fois vos donn{\'e}es import{\'e}es, vous gagnerez beaucoup {\`a} les ranger. Une fois vos donn{\'e}es rang{\'e}es, vous passerez bien souvent par une {\'e}tape de transformation. Une fois vos donn{\'e}es rang{\'e}es avec les variables dont vous avez besoin, la g{\'e}n{\'e}ration de connaissances reposera principalement sur deux moteurs : la visualisation et la mod{\'e}lisation. Leurs forces et faiblesses sont compl{\'e}mentaires, et toute bonne analyse doit tenir compte des deux. Inutile d'{\^e}tre un programmeur expert pour {\^e}tre un bon analyste de donn{\'e}es, mais apprendre {\`a} programmer plus efficacement vous permettra d'automatiser des t{\^a}ches courantes et de r{\'e}soudre plus facilement de nouveaux probl{\`e}mes."},
	language = {fran{\c c}ais},
	publisher = {Eyrolles},
	author = {Wickham, Hadley and Grolemund, Garrett},
	translator = {Payen, Rapha{\"e}l},
	year = {2018},
	keywords = {R (logiciel), Data visualisation, Donn{\'e}es massives, Exploration de donn{\'e}es},
	file = {Library Catalog Entry Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\JADE5B78\\SRCH.html:text/html}
}

@book{pilgrimDivePython2009,
	address = {New York},
	title = {Dive into {Python} 3},
	isbn = {978-1-4302-2415-0},
	url = {https://www.diveinto.org/python3/},
	language = {anglais},
	publisher = {Apress},
	author = {Pilgrim, Mark},
	year = {2009},
	keywords = {Object-oriented programming (Computer science), Python (Computer program language), Python (langage de programmation) -- Guides pratiques, Python (langage de programmation) -- Probl{\`e}mes et exercices, QA76.73.P98},
	file = {Library Catalog Entry Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\UNDFIGTE\\SRCH.html:text/html}
}

@misc{softwarecarpentryProgramming,
	title = {Programming with {R}},
	url = {http://swcarpentry.github.io/r-novice-inflammation/},
	urldate = {2019-04-30},
	journal = {Software Carpentry},
	author = {{Software Carpentry}},
	file = {Programming with R:C\:\\Users\\sgranger\\Zotero\\storage\\XIXM664T\\r-novice-inflammation.html:text/html}
}

@misc{softwarecarpentryReproducibleScientificAnalysisa,
	title = {R for {Reproducible} {Scientific} {Analysis}},
	url = {http://swcarpentry.github.io/r-novice-gapminder/},
	urldate = {2019-04-30},
	journal = {Software Carpentry},
	author = {{Software Carpentry}},
	file = {R for Reproducible Scientific Analysis:C\:\\Users\\sgranger\\Zotero\\storage\\E7YD9DZS\\r-novice-gapminder.html:text/html}
}

@misc{softwarecarpentryProgrammingPython,
	title = {Programming with {Python}},
	url = {http://swcarpentry.github.io/python-novice-inflammation/},
	urldate = {2019-04-30},
	journal = {Software Carpentry},
	author = {{Software Carpentry}},
	file = {Programming with Python:C\:\\Users\\sgranger\\Zotero\\storage\\SCDRXTJV\\python-novice-inflammation.html:text/html}
}

@misc{softwarecarpentryPlottingProgrammingPython,
	title = {Plotting and {Programming} in {Python}},
	url = {http://swcarpentry.github.io/python-novice-gapminder/},
	urldate = {2019-04-30},
	journal = {Software Carpentry},
	author = {{Software Carpentry}},
	file = {Plotting and Programming in Python:C\:\\Users\\sgranger\\Zotero\\storage\\XHADHFM5\\python-novice-gapminder.html:text/html}
}

@misc{gruberMarkdown2004,
	title = {Markdown},
	url = {https://daringfireball.net/projects/markdown/},
	urldate = {2019-04-30},
	journal = {Daring Fireball},
	author = {Gruber, John},
	month = dec,
	year = {2004},
	file = {Daring Fireball\: Markdown:C\:\\Users\\sgranger\\Zotero\\storage\\WAHZ67DN\\markdown.html:text/html}
}

@misc{legrandVitrineEnversDecor2018,
	type = {Mooc {Recherche} {Reproductible} : ressources publiques},
	title = {La vitrine et l'envers du d{\'e}cor : {Le} document computationnel},
	url = {https://gitlab.inria.fr/learninglab/mooc-rr/mooc-rr-ressources/blob/master/module2/slides/C028AL_slides_module2-fr-gz.pdf},
	language = {en},
	urldate = {2019-04-30},
	journal = {GitLab},
	author = {Legrand, Arnaud},
	month = sep,
	year = {2018},
	file = {Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\L23ESRIX\\C028AL_slides_module2-fr-gz.html:text/html}
}

@misc{projectjupyterProjectJupyter,
	title = {Project {Jupyter}},
	url = {https://www.jupyter.org},
	abstract = {The Jupyter Notebook is a web-based interactive computing platform. The notebook combines live code, equations, narrative text, visualizations, interactive dashboards and other media.},
	urldate = {2019-04-30},
	journal = {Project Jupyter},
	author = {{Project Jupyter}},
	file = {Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\EM5IHIHI\\jupyter.org.html:text/html}
}

@misc{lalanneLangageMarkdown,
	title = {Le langage {R} {Markdown}},
	url = {https://www.fun-mooc.fr/c4x/UPSUD/42001S02/asset/RMarkdown.html},
	urldate = {2019-04-30},
	author = {Lalanne, Christophe and Falissard, Bruno},
	file = {Le langage R Markdown:C\:\\Users\\sgranger\\Zotero\\storage\\E2EALYRK\\RMarkdown.html:text/html}
}

@misc{carstenOrgModeEmacs,
	title = {Org mode for {Emacs} - {Votre} vie en texte brut},
	url = {https://www.orgmode.org/fr/index.html},
	urldate = {2019-04-30},
	journal = {Org mode for Emacs},
	author = {Carsten, Dominik and Guerry, Bastien},
	file = {Org mode for Emacs {\textendash} Votre vie en texte brut:C\:\\Users\\sgranger\\Zotero\\storage\\RTEFYXUZ\\index.html:text/html}
}

@misc{wikipediaScientificWorkflowSystem2019,
	title = {Scientific workflow system},
	copyright = {Creative Commons Attribution-ShareAlike License},
	url = {https://en.wikipedia.org/w/index.php?title=Scientific_workflow_system&oldid=889416610},
	abstract = {A scientific workflow system is a specialized form of a workflow management system designed specifically to compose and execute a series of computational or data manipulation steps, or workflow, in a scientific application.},
	language = {en},
	urldate = {2019-04-30},
	journal = {Wikipedia},
	author = {{Wikipedia}},
	month = mar,
	year = {2019},
	note = {Page Version ID: 889416610},
	file = {Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\E8QF9HCB\\index.html:text/html}
}

@misc{legrandSeriesWebinarsDocuments2016b,
	title = {Series of webinars and documents on {Reproducible} {Research}. {Reproducible} {Science} in {Bioinformatics} : {Current} {Status}, {Solutions} and {Research} {Opportunities}},
	shorttitle = {Series of webinars and documents on {Reproducible} {Research}},
	url = {https://github.com/alegrand/RR_webinars},
	urldate = {2019-04-30},
	journal = {Reproducible Research Webinars},
	author = {Legrand, Arnaud},
	month = feb,
	year = {2016},
	note = {original-date: 2016-02-08T08:41:51Z}
}

@misc{travisciTestDeployYour,
	title = {Test and {Deploy} {Your} {Code} with {Confidence}},
	url = {https://travis-ci.org/},
	urldate = {2019-04-30},
	journal = {Travis CI},
	author = {{Travis CI}},
	file = {Travis CI - Test and Deploy Your Code with Confidence:C\:\\Users\\sgranger\\Zotero\\storage\\XRM4M5GV\\travis-ci.org.html:text/html}
}

@misc{appveyorContinuousIntegrationDeployment,
	title = {Continuous {Integration} and {Deployment} service for {Windows} and {Linux}},
	url = {https://www.appveyor.com/},
	abstract = {\#1 Continuous Delivery service for Windows},
	language = {en},
	urldate = {2019-04-30},
	journal = {AppVeyor},
	author = {{AppVeyor}},
	file = {Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\UA3ICDKB\\www.appveyor.com.html:text/html}
}

@article{wickhamTestthatGetStarted2011,
	title = {testthat: {Get} {Started} with {Testing}},
	volume = {3},
	issn = {2073-4859},
	shorttitle = {testthat},
	url = {https://journal.r-project.org/archive/2011/RJ-2011-002/RJ-2011-002.pdf},
	doi = {10.32614/RJ-2011-002},
	abstract = {Software testing is important, but many of us don{\textquoteright}t do it because it is frustrating and boring. testthat is a new testing framework for R that is easy learn and use, and integrates with your existing workflow. This paper shows how, with illustrations from existing packages.},
	language = {en},
	number = {1},
	urldate = {2019-04-30},
	journal = {The R Journal},
	author = {Wickham, Hadley},
	year = {2011},
	pages = {5},
	file = {Wickham - 2011 - testthat Get Started with Testing.pdf:C\:\\Users\\sgranger\\Zotero\\storage\\GWTBR3GM\\Wickham - 2011 - testthat Get Started with Testing.pdf:application/pdf}
}

@misc{silgeBeginnerGuideTravisCI2016,
	title = {A {Beginner}'s {Guide} to {Travis}-{CI} for {R}},
	url = {https://juliasilge.com/blog/beginners-guide-to-travis/},
	urldate = {2019-04-30},
	journal = {Julia Silge},
	author = {Silge, Julia},
	month = may,
	year = {2016},
	file = {Julia Silge - A Beginner's Guide to Travis-CI for R:C\:\\Users\\sgranger\\Zotero\\storage\\YKFI48QQ\\beginners-guide-to-travis.html:text/html}
}

@misc{wikipediaDocker2019,
	title = {Docker},
	copyright = {Creative Commons Attribution-ShareAlike License},
	url = {https://fr.wikipedia.org/w/index.php?title=Docker_(logiciel)&oldid=158485394},
	abstract = {Docker  est un logiciel libre permettant  facilement de lancer des applications dans des conteneurs logiciels.
Selon la firme de recherche sur l'industrie 451 Research, {\guillemotleft} Docker est un outil qui peut empaqueter une application et ses d{\'e}pendances dans un conteneur isol{\'e}, qui pourra {\^e}tre ex{\'e}cut{\'e} sur n'importe quel serveur {\guillemotright}. Il ne s'agit pas de virtualisation, mais de conteneurisation, une forme plus l{\'e}g{\`e}re qui s'appuie sur certaines parties de la machine h{\^o}te pour son fonctionnement. Cette approche permet d'accro{\^i}tre la flexibilit{\'e} et la portabilit{\'e} d{\textquoteright}ex{\'e}cution d'une application, laquelle va pouvoir tourner de fa{\c c}on fiable et pr{\'e}dictible sur une grande vari{\'e}t{\'e} de machines h{\^o}tes, que ce soit sur la machine locale, un cloud priv{\'e} ou public, une machine nue, etc..
Techniquement, Docker {\'e}tend le format de conteneur Linux standard, LXC, avec une API de haut niveau fournissant une solution pratique de virtualisation qui ex{\'e}cute les processus de fa{\c c}on isol{\'e}e. Pour arriver {\`a} ses fins, Docker utilise entre autre LXC, cgroups et le noyau Linux lui-m{\^e}me. Contrairement aux machines virtuelles traditionnelles, un conteneur Docker n'inclut pas de syst{\`e}me d'exploitation, mais s'appuie au contraire sur les fonctionnalit{\'e}s du syst{\`e}me d{\textquoteright}exploitation fournies par la machine h{\^o}te.
La technologie de conteneur de Docker peut {\^e}tre utilis{\'e}e pour {\'e}tendre des syst{\`e}mes distribu{\'e}s de fa{\c c}on qu'ils s'ex{\'e}cutent de mani{\`e}re autonome depuis une seule machine physique ou une seule instance par n{\oe}ud. Cela permet aux n{\oe}uds d'{\^e}tre d{\'e}ploy{\'e}s au fur et {\`a} mesure que les ressources sont disponibles, offrant un d{\'e}ploiement transparent et similaire aux PaaS pour des syst{\`e}mes comme Apache Cassandra, Riak ou d'autres syst{\`e}mes distribu{\'e}s.},
	language = {fr},
	urldate = {2019-04-30},
	journal = {Wikip{\'e}dia},
	author = {{Wikipedia}},
	month = apr,
	year = {2019},
	note = {Page Version ID: 158485394},
	file = {Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\MJL9CN7Q\\index.html:text/html}
}

@misc{tandonschoolofengineering.polytechnicinstituteReproZipReproducibilityPacker,
	title = {{ReproZip}! {The} {Reproducibility} {Packer}},
	url = {https://www.reprozip.org/},
	urldate = {2019-04-30},
	journal = {Reprozip},
	author = {{Tandon School of Engineering. Polytechnic Institute}},
	file = {ReproZip! The Reproducibility Packer:C\:\\Users\\sgranger\\Zotero\\storage\\JLABMZKR\\www.reprozip.org.html:text/html}
}

@inproceedings{chirigatiReproZipComputationalReproducibility2016,
	title = {{ReproZip}: {Computational} reproducibility with ease},
	shorttitle = {{ReproZip}},
	url = {https://nyuscholars.nyu.edu/en/publications/reprozip-computational-reproducibility-with-ease},
	doi = {10.1145/2882903.2899401},
	language = {English (US)},
	urldate = {2019-04-30},
	booktitle = {{SIGMOD} 2016 - {Proceedings} of the 2016 {International} {Conference} on {Management} of {Data}},
	publisher = {Association for Computing Machinery},
	author = {Chirigati, Fernando and Rampin, R{\'e}mi and Shasha, Dennis and Freire, Juliana},
	month = jun,
	year = {2016},
	pages = {2085--2088},
	file = {Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\NDJURTSV\\reprozip-computational-reproducibility-with-ease.html:text/html;Texte int{\'e}gral:C\:\\Users\\sgranger\\Zotero\\storage\\A5C2U6NU\\Chirigati et al. - 2016 - ReproZip Computational reproducibility with ease.pdf:application/pdf}
}

@misc{gnuguixGNUAdvancedDistro,
	title = {{GNU}'s advanced distro and transactional package manager},
	url = {https://www.gnu.org/software/guix/},
	urldate = {2019-04-30},
	journal = {GNU Guix},
	author = {{GNU Guix}},
	file = {GNU's advanced distro and transactional package manager {\textemdash} GNU~Guix:C\:\\Users\\sgranger\\Zotero\\storage\\KREHM8WQ\\guix.html:text/html}
}

@misc{nixosNixOSLinux,
	title = {{NixOS} {Linux}},
	url = {https://nixos.org/},
	urldate = {2019-04-30},
	journal = {NixOS},
	author = {{NixOS}},
	file = {NixOS Linux:C\:\\Users\\sgranger\\Zotero\\storage\\Z5XRKIN9\\nixos.org.html:text/html}
}

@misc{pouzatVersEtudeReproductible,
	title = {Vers une {\'e}tude reproductible : {La} r{\'e}alit{\'e} du terrain},
	url = {https://gitlab.inria.fr/learninglab/mooc-rr/mooc-rr-ressources/blob/master/module4/slides/C028AL_slides_module4-fr-gz.pdf},
	language = {en},
	urldate = {2019-04-30},
	journal = {Mooc Recherche Reproductible : ressources publiques},
	author = {Pouzat, Christophe and Legrand, Arnaud and Hinsen, Konrad},
	file = {Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\MMCCQ4ER\\C028AL_slides_module4-fr-gz.html:text/html}
}

@misc{legrandBienControlerSon,
	title = {Bien contr{\^o}ler son environnement logiciel},
	url = {https://gitlab.inria.fr/learninglab/mooc-rr/mooc-rr-ressources/blob/master/module4/ressources/resources_environment_fr.org},
	abstract = {Mooc Recherche Reproductible ressources publiques (https://learninglab.gitlabpages.inria.fr/mooc-rr/mooc-rr-ressources)},
	language = {en},
	urldate = {2019-04-30},
	journal = {Mooc Recherche Reproductible : ressources publiques},
	author = {Legrand, Arnaud},
	file = {Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\N6XAG437\\resources_environment_fr.html:text/html}
}

@misc{legrandControlingYourEnvironment2016,
	title = {Controling your environment},
	shorttitle = {Series of webinars and documents on {Reproducible} {Research}},
	url = {https://github.com/alegrand/RR_webinars/blob/master/2_controling_your_environment/index.org},
	urldate = {2019-04-30},
	journal = {Series of webinars and documents on Reproducible Research},
	author = {Legrand, Arnaud},
	month = feb,
	year = {2016},
	note = {original-date: 2016-02-08T08:41:51Z}
}

@misc{githubChooseOpenSource,
	title = {Choose an open source license},
	url = {https://choosealicense.com/},
	abstract = {Non-judgmental guidance on choosing a license for your open source project},
	language = {en},
	urldate = {2019-04-30},
	journal = {Choose a License},
	author = {{GitHub}},
	file = {Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\CTM9UZFQ\\choosealicense.com.html:text/html}
}

@misc{creativecommonsChooseLicense,
	title = {Choose a {License}},
	url = {https://creativecommons.org/choose/},
	urldate = {2019-04-30},
	journal = {Creative Commons},
	author = {{Creative Commons}},
	file = {Choose a License:C\:\\Users\\sgranger\\Zotero\\storage\\RQ3W6CMZ\\choose.html:text/html}
}

@misc{universitedelilleWillODroitsObligations,
	title = {{WillO}. {Droits} et obligations des chercheurs de diffuser leurs publications en libre acc{\`e}s},
	url = {https://decadoc.typeform.com/to/W2ZZMV},
	abstract = {Faites de votre collecte de donn{\'e}es une formidable exp{\'e}rience avec Typeform. Cr{\'e}ez de superbes formulaires en ligne, des sondages, des quiz, et bien plus encore. Testez-le GRATUITEMENT.},
	language = {fr},
	urldate = {2019-04-30},
	journal = {Willo},
	author = {{Universit{\'e} de Lille}},
	file = {Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\SDKNINQF\\W2ZZMV.html:text/html}
}

@misc{cnilTextesOfficiels,
	title = {Textes officiels},
	url = {https://www.cnil.fr/fr/textes-officiels-europeens-protection-donnees},
	urldate = {2019-04-30},
	journal = {CNIL},
	author = {{CNIL}},
	file = {Textes officiels | CNIL:C\:\\Users\\sgranger\\Zotero\\storage\\JMB744UJ\\textes-officiels-europeens-protection-donnees.html:text/html}
}

@misc{inraDatapartageGestionPartage,
	title = {Datapartage - {Gestion} et partage des donn{\'e}es scientifiques. {Services}, outils et bonnes pratiques recommand{\'e}s par l{\textquoteright}{Inra}},
	url = {https://www6.inra.fr/datapartage},
	urldate = {2019-04-30},
	author = {{Inra}},
	file = {Datapartage - Accueil:C\:\\Users\\sgranger\\Zotero\\storage\\ZCFGE5XD\\datapartage.html:text/html}
}

@misc{ciradGererDonneesRecherche,
	title = {G{\'e}rer les donn{\'e}es de la recherche  - {Gestion} de l'information},
	url = {https://coop-ist.cirad.fr/gestion-de-l-information/gerer-les-donnees-de-la-recherche},
	urldate = {2019-04-30},
	journal = {Coop{\'e}rer en information scientifique et technique},
	author = {{Cirad}},
	file = {G{\'e}rer les donn{\'e}es de la recherche / Gestion de l'information - Coop{\'e}rer en information scientifique et technique - Cirad:C\:\\Users\\sgranger\\Zotero\\storage\\AUNB42N3\\gerer-les-donnees-de-la-recherche.html:text/html}
}

@misc{fosteropenscienceResourcesLegalIssues,
	title = {Resources : {Legal} {Issues}},
	url = {https://www.fosteropenscience.eu/resources},
	urldate = {2019-04-30},
	journal = {Foster Open Science},
	author = {{Foster Open Science}},
	file = {Resources | FOSTER:C\:\\Users\\sgranger\\Zotero\\storage\\XR6ZKF3M\\resources.html:text/html}
}

@misc{wikipediaFLOSSManualsFoundation2018,
	title = {{FLOSS} {Manuals} {Foundation}},
	copyright = {Creative Commons Attribution-ShareAlike License},
	url = {https://fr.wikipedia.org/w/index.php?title=FLOSS_Manuals&oldid=153970983},
	abstract = {FLOSS Manuals, ou FM, est une fondation sans but lucratif cr{\'e}{\'e}e en 2006 et bas{\'e}e aux Pays-Bas. Son objectif est de rem{\'e}dier au d{\'e}faut de documentation de qualit{\'e} sur les logiciels libres. La m{\'e}thode utilis{\'e}e repose notamment sur l'usage d'un wiki (TWiki puis Booki et {\`a} pr{\'e}sent Booktype) supportant le d{\'e}veloppement collaboratif de manuels sur les logiciels libres  et sur la mise en place de booksprints qui rassemblent les collaborateurs au manuel dans un espace donn{\'e}.},
	language = {fr},
	urldate = {2019-04-30},
	journal = {Wikip{\'e}dia},
	author = {{Wikipedia}},
	month = nov,
	year = {2018},
	note = {Page Version ID: 153970983},
	file = {Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\4KK8ZF82\\index.html:text/html}
}

@book{wickhamDataScienceImport2016,
	address = {Etats-Unis},
	title = {R for {Data} {Science} : {Import}, {Tidy}, {Transform}, {Visualize} and {Model} {Data}},
	isbn = {978-1-4919-1036-8},
	shorttitle = {R for data science},
	url = {https://r4ds.had.co.nz/},
	language = {anglais},
	publisher = {O'Reilly},
	author = {Wickham, Hadley and Grolemund, Garrett},
	year = {2016},
	keywords = {R (logiciel), Data visualisation, Exploration de donn{\'e}es, Statistique -- Informatique},
	file = {Library Catalog Entry Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\GGGZLMNX\\SRCH.html:text/html}
}

@misc{collbergRepeatabilityComputerScience,
	title = {Repeatability in {Computer} {Science}},
	url = {http://reproducibility.cs.arizona.edu/},
	abstract = {Research is repeatable if we can re-run the researchers' experiment using the same method in the same environment and obtain the same results. A prerequisite for repeatability is for the research artifacts that back up the published results to be shared. Sharing for repeatability is essential to ensure that colleagues and reviewers can evaluate our results based on accurate and complete evidence.

In this study, we examine the extent to which Computer Systems researchers share their research artifacts (source code), and the extent to which shared code builds. We refer to this as weak repeatability. In our study we examined 601 papers from ACM conferences and journals, attempted to locate any source code that backed up the published results, and, if found, tried to build the code.},
	urldate = {2019-05-02},
	journal = {Repeatability in Computer Science},
	author = {Collberg, Christian S. and Proebsting, Todd A. and Warren, Alex M.},
	file = {Repeatability in Computer Science:C\:\\Users\\sgranger\\Zotero\\storage\\PUTGYVVT\\reproducibility.cs.arizona.edu.html:text/html}
}

@techreport{collbergRepeatabilityBenefactionComputer2015,
	address = {University of Arizona},
	title = {Repeatability and {Benefaction} in {Computer} {Systems} {Research}. {A} {Study} and a {Modest} {Proposal}},
	url = {http://reproducibility.cs.arizona.edu/v2/RepeatabilityTR.pdf},
	institution = {University of Arizona},
	author = {Collberg, Christian S. and Proebsting, Todd A. and Warren, Alex M.},
	month = feb,
	year = {2015}
}

@book{reinhartStatisticsDoneWrong2015,
	address = {San Francisco},
	title = {Statistics {Done} {Wrong}},
	isbn = {978-1-59327-620-1},
	url = {https://www.statisticsdonewrong.com/index.html},
	urldate = {2019-05-02},
	publisher = {No Starch Press},
	author = {Reinhart, Alex},
	year = {2015},
	file = {Welcome {\textemdash} Statistics Done Wrong:C\:\\Users\\sgranger\\Zotero\\storage\\WS8RHXHD\\index.html:text/html}
}

@misc{centerforopenscienceOpenScienceFramework,
	title = {Open {Science} {Framework}. {A} scholarly commons to connect the entire research cycle},
	url = {https://osf.io/},
	urldate = {2019-05-02},
	author = {{Center for Open Science}},
	file = {OSF | Home:C\:\\Users\\sgranger\\Zotero\\storage\\KPFQ9VW7\\osf.io.html:text/html}
}

@misc{rougier3615EULA2015,
	title = {3615 {EULA}},
	url = {http://binaire.blog.lemonde.fr/2015/11/24/3615-eula/},
	abstract = {Vous avez peut-{\^e}tre d{\'e}j{\`a} bloqu{\'e} devant des parfois {\guillemotleft} inf{\^a}mes {\guillemotright} EULA, en anglais pour {\guillemotleft} End User License Agreement {\guillemotright}, ou CGU en fran{\c c}ais pour Conditions g{\'e}n{\'e}rale d{\textquoteright}utilisation (voir Dangerous Terms: A User{\textquoteright}s Guide to EULAs). Ces conditions sous lesquelles vous avez acc{\`e}s {\`a} un produit ou {\`a} un service sur le Web sont souvent  longues, r{\'e}barbatives, incompr{\'e}hensives pour un profane. D{\textquoteright}ailleurs, on ne les lit pas, on clique, et on se livre {\`a} la merci de leur contenu. C{\textquoteright}est le syndrome du {\guillemotleft} TL;DR {\guillemotright}, pour {\guillemotleft} Too long; didn{\textquoteright}t read {\guillemotright} : trop long, pas lu. Binaire a demand{\'e} {\`a} Nicolas Rougier de nous parler du sujet. Serge Abiteboul.},
	language = {fr-FR},
	urldate = {2019-05-03},
	journal = {binaire. L'informatique : science et technique au c{\oe}ur du num{\'e}rique},
	author = {Rougier, Nicolas},
	month = nov,
	year = {2015},
	file = {Snapshot:C\:\\Users\\sgranger\\Zotero\\storage\\V759DD2J\\3615-eula.html:text/html}
}

@article{baker500ScientistsLift2016a,
	title = {1,500 scientists lift the lid on reproducibility},
	volume = {533},
	issn = {0028-0836, 1476-4687},
	url = {http://www.nature.com/doifinder/10.1038/533452a},
	doi = {10.1038/533452a},
	number = {7604},
	urldate = {2019-05-03},
	journal = {Nature},
	author = {Baker, Monya},
	month = may,
	year = {2016},
	pages = {452--454}
}


@article{opensciencecollaboration2015Estimating,
  title = {Estimating the Reproducibility of Psychological Science},
  volume = {349},
  number = {6251},
  journal = {Science},
  doi = {10.1126/science.aac4716},
  author = {{Open Science Collaboration}},
  year = {2015},
  pages = {aac4716}
}