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Bibliography

This file consist of a complete bibliography for this book sorted alphabatically

Bak16

Monya Baker. Reproducibility crisis? Nature, 533(26):353–66, 2016.

Bar18

Lorena A. Barba. Terminologies for Reproducible Research. arXiv, Feb 2018. URL: https://arxiv.org/abs/1802.03311v1, arXiv:1802.03311.

BE15

C. Begley and L. Ellis. Raise standards for preclinical cancer research. Nature, 2015. doi:10.1038/483531a.

BI15

C. Glenn Begley and John P. A. Ioannidis. Reproducibility in Science. Circulation Research, Jan 2015. URL: https://www.ahajournals.org/doi/10.1161/CIRCRESAHA.114.303819, doi:10.1161/CIRCRESAHA.114.303819.

BW18

Karl W Broman and Kara H Woo. Data organization in spreadsheets. The American Statistician, 72(1):2–10, 2018. URL: https://peerj.com/preprints/3183/, doi:10.1080/00031305.2017.1375989.

Bry15

Jenny Bryan. How to name files. May 2015. [Online; accessed 27. May 2020]. URL: https://speakerdeck.com/jennybc/how-to-name-files.

CRKR19

Evan W. Carr, Andrew Reece, Gabriella Rosen Kellerman, and Alexi Robichaux. The value of belonging at work. https://hbr.org/2019/12/the-value-of-belonging-at-work, December 2019. (Accessed on 07/08/2020).

CK92

Jon F. Claerbout and Martin Karrenbach. Electronic documents give reproducible research a new meaning. Jan 1992. [Online; accessed 27. May 2020]. URL: https://library.seg.org/doi/abs/10.1190/1.1822162, doi:https://doi.org/10.1190/1.1822162.

Cow19

Wind Cowles. LibGuides: Research Data Management at Princeton: File naming and structure. Aug 2019. [Online; accessed 27. May 2020]. URL: https://libguides.princeton.edu/c.php?g=102546&p=930626.

Cum20

Tucker Cummings. Does the pomodoro technique work for your productivity? https://www.lifehack.org/articles/productivity/the-pomodoro-technique-is-it-right-for-you.html, April 2020. (Accessed on 07/08/2020).

dVWA+14

Rob B. M. de Vries, Kimberley E. Wever, Marc T. Avey, Martin L. Stephens, Emily S. Sena, and Marlies Leenaars. The Usefulness of Systematic Reviews of Animal Experiments for the Design of Preclinical and Clinical Studies. ILAR J., 55(3):427–437, Dec 2014. doi:10.1093/ilar/ilu043.

DL10

Ulrich Dirnagl and Martin Lauritzen. Fighting publication bias: introducing the negative results section. Journal of Cerebral Blood Flow & Metabolism, 30(7):1263–1264, 2010. PMID: 20596038. URL: https://doi.org/10.1038/jcbfm.2010.51, arXiv:https://doi.org/10.1038/jcbfm.2010.51, doi:10.1038/jcbfm.2010.51.

FK18

Siiri Fuchs and Mari Elisa Kuusniemi. Making a research project understandable - guide for data documentation (version 1.2). Zenodo, 2018. doi:10.5281/zenodo.1914401.

GL07

Robert Gentleman and Duncan Temple Lang. Statistical analyses and reproducible research. Journal of Computational and Graphical Statistics, 16(1):1–23, March 2007. URL: https://doi.org/10.1198/106186007x178663, doi:10.1198/106186007x178663.

HBP+18

Michael A. Heroux, Lorena Barba, Manish Parashar, Victoria Stodden, and Michela Taufer. Toward a Compatible Reproducibility Taxonomy for Computational and Computing Sciences. OSTI.GOV collections, Oct 2018. [Online; accessed 27. May 2020]. URL: https://www.osti.gov/biblio/1481626-toward-compatible-reproducibility-taxonomy-computational-computing-sciences, doi:10.2172/1481626.

Hod15

Amy Hodge. Best practices for file naming. May 2015. [Online; accessed 27. May 2020]. URL: https://library.stanford.edu/research/data-management-services/data-best-practices/best-practices-file-naming.

IGH+14

John P. A. Ioannidis, Sander Greenland, Mark A. Hlatky, Muin J. Khoury, Malcolm R. Macleod, David Moher, Kenneth F. Schulz, and Robert Tibshirani. Increasing value and reducing waste in research design, conduct, and analysis. Lancet, 383(9912):166–175, Jan 2014. URL: https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(13)62227-8/fulltext, doi:10.1016/S0140-6736(13)62227-8.

IT18

Peter Ivie and Douglas Thain. Reproducibility in Scientific Computing. ACM Comput. Surv., 51(3):1–36, Jul 2018. doi:10.1145/3186266.

KPK+09

Carol Kilkenny, Nick Parsons, Ed Kadyszewski, Michael F. W. Festing, Innes C. Cuthill, Derek Fry, Jane Hutton, and Douglas G. Altman. Survey of the quality of experimental design, statistical analysis and reporting of research using animals. PLOS ONE, 4:1–11, 11 2009. URL: https://doi.org/10.1371/journal.pone.0007824, doi:10.1371/journal.pone.0007824.

KGL+20

Kevin Kunzmann, Michael J Grayling, Kim May Lee, David S Robertson, Kaspar Rufibach, and James Wason. A review of Bayesian perspectives on sample size derivation for confirmatory trials. arXiv preprint arXiv:2006.15715, 2020. URL: https://arxiv.org/abs/2006.15715.

Kuu10

Arja Kuula. Methodological and ethical dilemmas of archiving qualitative data. IASSIST Quarterly, 34(3-4):35, 2010. URL: http://www.iassistdata.org/sites/default/files/iqvol34_35_kuula.pdf.

Lab16

Mozilla Science Lab. Mozilla science lab’s study group. GitHub, 2016. doi:.

Mar15

Florian Markowetz. Five selfish reasons to work reproducibly. Genome Biology, 2015. doi:10.1186/s13059-015-0850-7.

MBM18

Ben Marwick, Carl Boettiger, and Lincoln Mullen. Packaging data analytical work reproducibly using R (and friends). PeerJ Preprints, Mar 2018. doi:10.7287/peerj.preprints.3192v2.

Mar18

Loyola University Maryland. Why Ethics are Important in Data Science by Loyola University Maryland. Jun 2018. [Online; accessed 8. Jun. 2020]. URL: https://www.loyola.edu/academics/data-science/blog/2018/why-ethics-are-important-in-data-science.

NustKP+17

Daniel Nüst, Markus Konkol, Edzer Pebesma, Christian Kray, Marc Schutzeichel, Holger Przibytzin, and Jörg Lorenz. Opening the publication process with executable research compendia. D-Lib Magazine, January 2017. URL: https://doi.org/10.1045/january2017-nuest, doi:10.1045/january2017-nuest.

NSM+20

Daniel Nüst, Vanessa Sochat, Ben Marwick, Stephen Eglen, Tim Head, Tony Hirst, and Benjamin Evans. Ten simple rules for writing dockerfiles for reproducible data science. OSF Preprints, apr 2020. URL: osf.io/fsd7t, doi:10.31219/osf.io/fsd7t.

PDF07

Heather A. Piwowar, Roger S. Day, and Douglas B. Fridsma. Sharing detailed research data is associated with increased citation rate. PLOS ONE, 2007. doi:10.1371/journal.pone.0000308.

PV13

Heather A. Piwowar and Todd J. Vision. Data reuse and the open data citation advantage. PeerJ, 2013. doi:10.7717/peerj.175.

Ple18

Hans E. Plesser. Reproducibility vs. Replicability: A Brief History of a Confused Terminology. Front. Neuroinf., Jan 2018. doi:10.3389/fninf.2017.00076.

Reg16

Protection Regulation. Regulation (eu) 2016/679 of the european parliament and of the council of 27 april 2016 on the protection of natural persons with regard to the processing of personal data and on the free movement of such data, and repealing directive 95/46/ec (general data protection regulation). Official Journal of the European Union, 2016. URL: http://data.europa.eu/eli/reg/2016/679/oj.

Sha20

Malvika Sharan. The Turing Way: A community built on a culture of collaboration. Zenodo, Apr 2020. doi:10.5281/zenodo.3745008.

Sto14

Victoria Stodden. Edge.org. May 2014. [Online; accessed 27. May 2020]. URL: https://www.edge.org/response-detail/25340.

SBH+18

D. Stuart, G. Baynes, I. Hrynaszkiewicz, K. Allin, D. Penny, Mithu, L., and M. Astell. Whitepaper: Practical challenges for researchers in data sharing. Figshare, 2018. doi:10.6084/m9.figshare.5975011.v1.

WDA+16

Mark D. Wilkinson, Michel Dumontier, IJsbrand Jan Aalbersberg, Gabrielle Appleton, Myles Axton, Arie Baak, Niklas Blomberg, Jan-Willem Boiten, Luiz Bonino da Silva Santos, Philip E. Bourne, Jildau Bouwman, Anthony J. Brookes, Tim Clark, Mercè Crosas, Ingrid Dillo, Olivier Dumon, Scott Edmunds, Chris T. Evelo, Richard Finkers, Alejandra Gonzalez-Beltran, Alasdair J.G. Gray, Paul Groth, Carole Goble, Jeffrey S. Grethe, Jaap Heringa, Peter A.C ‘t Hoen, Rob Hooft, Tobias Kuhn, Ruben Kok, Joost Kok, Scott J. Lusher, Maryann E. Martone, Albert Mons, Abel L. Packer, Bengt Persson, Philippe Rocca-Serra, Marco Roos, Rene van Schaik, Susanna-Assunta Sansone, Erik Schultes, Thierry Sengstag, Ted Slater, George Strawn, Morris A. Swertz, Mark Thompson, Johan van der Lei, Erik van Mulligen, Jan Velterop, Andra Waagmeester, Peter Wittenburg, Katherine Wolstencroft, Jun Zhao, and Barend Mons. The FAIR Guiding Principles for scientific data management and stewardship. Scientific Data, 3:160018, March 2016. URL: https://doi.org/10.1038/sdata.2016.18.

WPA+20

Louise Woodley, Catherine Pratt, Rachael Ainsworth, Eva Amsen, Arne Bakker, Stefanie Butland, Stephanie O’Donnell, Naomi Penfold, Allen Pope, Tom Quigley, and Emmy Tsang. Using virtual events to facilitate community building: event formats. Zenodo, Jul 2020. doi:10.5281/zenodo.3934385.

OpenSCollaboration15

Open Science Collaboration. Estimating the reproducibility of psychological science. Science, 349(6251):aac4716, Aug 2015. doi:10.1126/science.aac4716.

WorldHOrganisation20

World Health Organisation. Events as they happen. Jul 2020. [Online; accessed 7. Jul. 2020]. URL: https://www.who.int/emergencies/diseases/novel-coronavirus-2019/events-as-they-happen.

Glossary Record of Contributions