paper.bib

@Manual{allaire_rmarkdown_2018,
  title = {{rmarkdown}: Dynamic Documents for {R}},
  author = {JJ Allaire and Yihui Xie and Jonathan McPherson and Javier Luraschi and Kevin Ushey and Aron Atkins and Hadley Wickham and Joe Cheng and Winston Chang and Richard Iannone},
  year = {2018},
  note = {R package version 1.11},
  url = {https://rmarkdown.rstudio.com}
}

@article{beaulieu-jones_reproducibility_2017,
	title = {Reproducibility of computational workflows is automated using continuous analysis},
	volume = {advance online publication},
	issn = {1087-0156},
	doi = {10.1038/nbt.3780},
	journal = {Nature Biotechnology},
	author = {Beaulieu-Jones, Brett K. and Greene, Casey S.},
	month = mar,
	year = {2017}
}

@article{belmann_bioboxes_2015,
	title = {Bioboxes: standardised containers for interchangeable bioinformatics software},
	volume = {4},
	issn = {2047-217X},
	doi = {10.1186/s13742-015-0087-0},
	number = {1},
	journal = {GigaScience},
	author = {Belmann, Peter and Dröge, Johannes and Bremges, Andreas and McHardy, Alice C. and Sczyrba, Alexander and Barton, Michael D.},
	month = oct,
	year = {2015},
	pmid = {26473029},
	pages = {47}
}

@article{boettiger_introduction_2015,
	title = {An introduction to {Docker} for reproducible research, with examples from the {R} environment},
	volume = {49},
	issn = {01635980},
	doi = {10.1145/2723872.2723882},
	number = {1},
	journal = {ACM SIGOPS Operating Systems Review},
	author = {Boettiger, Carl},
	month = jan,
	year = {2015},
	pages = {71--79}
}

@article{RJ-2017-065,
  author = {Boettiger, Carl and Eddelbuettel, Dirk},
  title = {{An Introduction to Rocker: Docker Containers for R}},
  year = {2017},
  journal = {{The R Journal}},
  doi = {10.32614/RJ-2017-065},
  pages = {527--536},
  volume = {9},
  number = {2}
}

@Manual{brokamp_automagic_2017,
  title = {automagic: Automagically Document and Install Packages Necessary to Run {R} Code},
  author = {Cole Brokamp},
  year = {2017},
  note = {R package version 0.3},
  url = {https://CRAN.R-project.org/package=automagic},
}

@inproceedings{ChirigatiRSF16,
  title = {{ReproZip}: Computational Reproducibility With Ease},
  author = {Chirigati, Fernando and Rampin, R{\'e}mi and Shasha, Dennis and Freire, Juliana},
  year = {2016},
  isbn = {978-1-4503-3531-7},
  location = {San Francisco, California, USA},
  doi = {10.1145/2882903.2899401},
  booktitle = {Proceedings of the 2016 International Conference on Management of Data},
  series = {SIGMOD '16},
  pages = {2085--2088},
  numpages = {4},
  publisher = {ACM},
  keywords = {computational reproducibility, provenance, reprozip},
}

@inproceedings{cito_using_2016,
	series = {{ICSE} '16},
	title = {Using {Docker} {Containers} to {Improve} {Reproducibility} in {Software} {Engineering} {Research}},
	isbn = {978-1-4503-4205-6},
	doi = {10.1145/2889160.2891057},
	booktitle = {Proceedings of the 38th {International} {Conference} on {Software} {Engineering} {Companion}},
	publisher = {ACM},
	author = {Cito, Jürgen and Gall, Harald C.},
	year = {2016},
	pages = {906--907}
}

@Manual{csardi_sysreqs_2019,
  title = {sysreqs: Install SystemRequirements of Packages},
  author = {Csardi, Gabor},
  year = {2019},
  note = {R package version 1.0.0.9000},
  url = {https://github.com/r-hub/sysreqs},
}

@Manual{csardi_callr_2018,
  title = {callr: Call {R} from {R}},
  author = {Gábor Csárdi and Winston Chang},
  year = {2018},
  note = {R package version 3.1.1},
  url = {https://CRAN.R-project.org/package=callr},
}

@article{emsley_framework_2018,
	title = {A {Framework} for the {Preservation} of a {Docker} {Container} {\textbar} {International} {Journal} of {Digital} {Curation}},
	volume = {12},
	doi = {10.2218/ijdc.v12i2.509},
	number = {2},
	journal = {International Journal of Digital Curation},
	author = {Emsley, Iain and De Roure, David},
	month = apr,
	year = {2018}
}

@Manual{fay_dockerfiler_2018,
  title = {dockerfiler: Easy {Dockerfile} Creation from {R}},
  author = {Colin Fay},
  year = {2018},
  note = {R package version 0.1.1},
  url = {https://CRAN.R-project.org/package=dockerfiler},
}

@Manual{fitzjohn_stevedore_2019,
  title = {stevedore: {Docker} Client},
  author = {Rich FitzJohn},
  year = {2019},
  note = {R package version 0.9.1},
  url = {https://CRAN.R-project.org/package=stevedore},
}

@article{gentleman_statistical_2007,
	title = {Statistical {Analyses} and {Reproducible} {Research}},
	volume = {16},
	issn = {1061-8600},
	url = {https://doi.org/10.1198/106186007X178663},
	doi = {10.1198/106186007X178663},
	number = {1},
	journal = {Journal of Computational and Graphical Statistics},
	author = {Gentleman, Robert and Lang, Duncan Temple},
	month = mar,
	year = {2007},
	pages = {1--23}
}

@article{hosny_algorun_2016,
	title = {{AlgoRun}: a {Docker}-based packaging system for platform-agnostic implemented algorithms},
	volume = {32},
	issn = {1367-4803},
	shorttitle = {{AlgoRun}},
	doi = {10.1093/bioinformatics/btw120},
	number = {15},
	journal = {Bioinformatics},
	author = {Hosny, Abdelrahman and Vera-Licona, Paola and Laubenbacher, Reinhard and Favre, Thibauld},
	month = aug,
	year = {2016},
	pages = {2396--2398}
}

@misc{codemeta,
  doi = {10.5063/schema/codemeta-2.0},
  url = {https://raw.githubusercontent.com/codemeta/codemeta/2.0/codemeta.jsonld},
  author = {Jones,  Matthew B and Boettiger,  Carl and Mayes,  Abby Cabunoc and {Arfon Smith} and Slaughter,  Peter and Niemeyer,  Kyle and Gil,  Yolanda and Fenner,  Martin and Nowak,  Krzysztof and Hahnel,  Mark and Coy,  Luke and Allen,  Alice and Crosas,  Mercè and Sands,  Ashley and Hong,  Neil Chue and Cruse,  Patricia and Katz,  Dan and Goble,  Carole},
  title = {{CodeMeta}: an exchange schema for software metadata},
  publisher = {KNB Data Repository},
  year = {2017}
}

@inproceedings{katz_software_2018,
	series = {Lecture {Notes} in {Computer} {Science}},
	title = {Software {Citation} in {Theory} and {Practice}},
	isbn = {978-3-319-96418-8},
	doi = {10.1007/978-3-319-96418-8_34},
	booktitle = {Mathematical {Software} – {ICMS} 2018},
	publisher = {Springer International Publishing},
	author = {Katz, Daniel S. and Chue Hong, Neil P.},
	editor = {Davenport, James H. and Kauers, Manuel and Labahn, George and Urban, Josef},
	year = {2018},
	pages = {289--296}
}

@article{kim_bio-docklets_2017,
	title = {Bio-{Docklets}: {Virtualization} {Containers} for {Single}-{Step} {Execution} of {NGS} {Pipelines}.},
	shorttitle = {Bio-{Docklets}},
	doi = {10.1101/116962},
	journal = {bioRxiv},
	author = {Kim, Baekdoo and Ali, Thahmina A. and Lijeron, Carlos and Afgan, Enis and Krampis, Konstantinos},
	month = mar,
	year = {2017},
	pages = {116962}
}

@article{knoth_reproducibility_2017,
	title = {Reproducibility and {Practical} {Adoption} of {GEOBIA} with {Open}-{Source} {Software} in {Docker} {Containers}},
	volume = {9},
	doi = {10.3390/rs9030290},
	number = {3},
	journal = {Remote Sensing},
	author = {Knoth, Christian and Nüst, Daniel},
	month = mar,
	year = {2017},
	pages = {290}
}

@article{kurtzer_singularity_2017,
	title = {Singularity: {Scientific} containers for mobility of compute},
	volume = {12},
	issn = {1932-6203},
	shorttitle = {Singularity},
	doi = {10.1371/journal.pone.0177459},
	number = {5},
	journal = {PLOS ONE},
	author = {Kurtzer, Gregory M. and Sochat, Vanessa and Bauer, Michael W.},
	month = may,
	year = {2017},
	pages = {e0177459}
}

@article{marwick_computational_2017,
	title = {Computational {Reproducibility} in {Archaeological} {Research}: {Basic} {Principles} and a {Case} {Study} of {Their} {Implementation}},
	volume = {24},
	issn = {1573-7764},
	doi = {10.1007/s10816-015-9272-9},
	number = {2},
	journal = {Journal of Archaeological Method and Theory},
	author = {Marwick, Ben},
	month = jun,
	year = {2017},
	pages = {424--450}
}

@article{molenaar_klikoscientific_2018,
	title = {Kliko—{The} scientific compute container format},
	volume = {25},
	issn = {2213-1337},
	doi = {10.1016/j.ascom.2018.08.003},
	journal = {Astronomy and Computing},
	author = {Molenaar, G. and Makhathini, S. and Girard, J. N. and Smirnov, O.},
	month = oct,
	year = {2018},
	keywords = {Astronomy, Containerization, Data reduction, Docker, Pipelines, Scientific computing},
	pages = {1--9},
}

@misc{nust_reproducibility_2018,
	title = {Reproducibility {Service} for {Executable} {Research} {Compendia}: {Technical} {Specifications} and {Reference} {Implementation}},
	publisher = {Zenodo},
	author = {Nüst, Daniel},
	month = dec,
	year = {2018},
	doi = {10.5281/zenodo.2203844}
}

@article{nust_opening_2017,
	title = {Opening the {Publication} {Process} with {Executable} {Research} {Compendia}},
	volume = {23},
	issn = {1082-9873},
	doi = {10.1045/january2017-nuest},
	number = {1/2},
	journal = {D-Lib Magazine},
	author = {Nüst, Daniel and Konkol, Markus and Pebesma, Edzer and Kray, Christian and Schutzeichel, Marc and Przibytzin, Holger and Lorenz, Jörg},
	month = jan,
	year = {2017}
}

@misc{osnat_brief_2018,
	title = {A {Brief} {History} of {Containers}: {From} the 1970s to 2017},
	shorttitle = {A {Brief} {History} of {Containers}},
	url = {https://blog.aquasec.com/a-brief-history-of-containers-from-1970s-chroot-to-docker-2016},
	urldate = {2019-02-05},
	author = {Osnat, Rani},
	month = mar,
	year = {2018}
}

@inproceedings{jupyter_binder_2018,
  title = {Binder 2.0 - Reproducible, interactive, sharable environments for science at scale},
  author = {{Project Jupyter et al.}},
  year = {2018},
  booktitle = {Proceedings of the 17th Python in Science Conference},
  url = {https://conference.scipy.org/proceedings/scipy2018/pdfs/project_jupyter.pdf},
  doi = {10.25080/Majora-4af1f417-011}
}

@Manual{r_2018,
  title = {R: A Language and Environment for Statistical Computing},
  author = {{R Core Team}},
  organization = {R Foundation for Statistical Computing},
  address = {Vienna, Austria},
  year = {2018},
  url = {https://www.R-project.org/},
}

@inproceedings{rechert_preserving_2017,
	title = {Preserving {Containers}},
	isbn = {978-3-946531-75-3},
	doi = {10.11588/heibooks.285.377},
	booktitle = {Forschungsdaten managen},
	author = {Rechert, Klaus and Liebetraut, Thomas and Kombrink, Stefan and Wehrle, Dennis and Mocken, Susanne and Rohland, Maximilian},
	editor = {Kratzke, Jonas and Heuveline, Vincent},
	year = {2017},
	pages = {143--151}
}

@Manual{xiao_liftr_2018,
  title = {liftr: Containerize {R} {Markdown} Documents for Continuous Reproducibility},
  author = {Nan Xiao},
  year = {2018},
  note = {R package version 0.9},
  url = {https://CRAN.R-project.org/package=liftr},
}

@Manual{xie_xfun_2018,
  title = {xfun: Miscellaneous Functions by '{Yihui} {Xie}'},
  author = {Yihui Xie},
  year = {2018},
  note = {R package version 0.4},
  url = {https://CRAN.R-project.org/package=xfun}
}