paper.bib

@inproceedings{warren_repeatability_2015,
	title = {Repeatability and {Benefaction} in {Computer} {Systems} {Research} — {A} {Study} and a {Modest} {Proposal}},
	abstract = {We describe a study into the extent to which Computer Systems researchers share their code and data and the extent to which such code builds. Starting with 601 papers from ACM conferences and journals, we examine 402 papers whose results were backed by code. For 32.3\% of these papers we were able to obtain the code and build it within 30 minutes; for 48.3\% of the papers we managed to build the code, but it may have required extra effort; for 54.0\% of the papers either we managed to build the code or the authors stated the code would build with reasonable effort. We also propose a novel sharing specification scheme that requires researchers to specify the level of sharing that reviewers and readers can assume from a paper.},
	author = {Warren, Alex},
	year = {2015},
	keywords = {Aclarubicin, Hardware description language, Paper, Repeatability, Specification}
}

@misc{baker_monya_1500_2016,
	title = {1,500 scientists lift the lid on reproducibility : {Nature} {News} \& {Comment}},
	url = {https://www.nature.com/news/1-500-scientists-lift-the-lid-on-reproducibility-1.19970},
	urldate = {2019-06-12},
	author = {Baker, Monya},
	month = may,
	year = {2016}
}

@article{gruning_practical_2018,
	title = {Practical {Computational} {Reproducibility} in the {Life} {Sciences}},
	volume = {6},
	issn = {2405-4712},
	url = {http://www.sciencedirect.com/science/article/pii/S2405471218301406},
	doi = {10.1016/j.cels.2018.03.014},
	abstract = {Many areas of research suffer from poor reproducibility, particularly in computationally intensive domains where results rely on a series of complex methodological decisions that are not well captured by traditional publication approaches. Various guidelines have emerged for achieving reproducibility, but implementation of these practices remains difficult due to the challenge of assembling software tools plus associated libraries, connecting tools together into pipelines, and specifying parameters. Here, we discuss a suite of cutting-edge technologies that make computational reproducibility not just possible, but practical in both time and effort. This suite combines three well-tested components—a system for building highly portable packages of bioinformatics software, containerization and virtualization technologies for isolating reusable execution environments for these packages, and workflow systems that automatically orchestrate the composition of these packages for entire pipelines—to achieve an unprecedented level of computational reproducibility. We also provide a practical implementation and five recommendations to help set a typical researcher on the path to performing data analyses reproducibly.},
	number = {6},
	urldate = {2019-06-12},
	journal = {Cell Systems},
	author = {Grüning, Björn and Chilton, John and Köster, Johannes and Dale, Ryan and Soranzo, Nicola and van den Beek, Marius and Goecks, Jeremy and Backofen, Rolf and Nekrutenko, Anton and Taylor, James},
	month = jun,
	year = {2018},
	pages = {631--635}
}

@article{wilkinson_fair_2016,
	title = {The {FAIR} {Guiding} {Principles} for scientific data management and stewardship},
	volume = {3},
	url = {https://doi.org/10.1038/sdata.2016.18},
	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 da Silva Santos, Luiz Bonino and Bourne, Philip E. and Bouwman, Jildau and Brookes, Anthony J. and Clark, Tim and Crosas, Mercè 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 ’t Hoen, Peter A.C 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 van Schaik, Rene and Sansone, Susanna-Assunta and Schultes, Erik and Sengstag, Thierry and Slater, Ted and Strawn, George and Swertz, Morris A. and Thompson, Mark and van der Lei, Johan and van Mulligen, Erik and Velterop, Jan and Waagmeester, Andra and Wittenburg, Peter and Wolstencroft, Katherine and Zhao, Jun and Mons, Barend},
	month = mar,
	year = {2016},
	pages = {160018}
}

@misc{FAIR_Bioinfo_Figure1,
author = "Thomas Denecker and Claire Toffano-Nioche",
title = "{7-steps.png}",
year = "2019",
month = "7",
url = "https://figshare.com/articles/7-steps_png/8950505",
doi = "10.6084/m9.figshare.8950505.v1"
}

@misc{FAIR_Bioinfo_github,
author = {{Denecker, Thomas and Toffano-Nioche, Claire}},
title = {FAIR_Bioinfo},
doi = {10.5281/zenodo.3238205},
howpublished = {\url{https://github.com/thomasdenecker/FAIR_Bioinfo}}
}
@misc{fair_bioinfo_docker,
author = {{Denecker, Thomas}},
title = {fair_bioinfo},
howpublished = {\url{https://hub.docker.com/r/tdenecker/fair_bioinfo}}
}
@misc{FAIR_Bioinfo_gitbook,
author = {{Denecker, Thomas and Toffano-Nioche, Claire}},
title = {FAIR_Bioinfo},
doi = {10.5281/zenodo.3341392},
howpublished = {\url{https://fair-bioinfo.gitbook.io/fair-bioinfo/}}
}