refs.bib

@article{rob2023,
  title={Defining the roles of research software},
  author={van Nieuwpoort, Rob and Katz, Daniel S},
  journal={Upstream},
  year={2023}
}

@article{Knuth1984,
  title={Literate programming},
  author={Knuth, Donald Ervin},
  journal={The computer journal},
  volume={27},
  number={2},
  pages={97--111},
  year={1984},
  publisher={Oxford University Press}
}

@misc{Gruber2004,
  title={Markdown},
  url={https://daringfireball.net/projects/markdown/},
  journal={Daring Fireball: Markdown},
  author={Gruber, John and Swartz, Aaron},
  year={2004},
  month={Dec}
}

@misc{CommonMark,
  title={CommonMark, A strongly defined, highly compatible specification of Markdown},
  url={https://commonmark.org/},
  journal={CommonMark},
  author={McFarlane, John and Woodward, Martin and Jeff Atwood},
  year={2014},
  month={Oct}
}

@article{Ramsey1994,
  title={Literate programming simplified},
  author={Ramsey, Norman},
  journal={IEEE software},
  volume={11},
  number={5},
  pages={97--105},
  year={1994},
  publisher={IEEE}
}


@book{RMarkdown,
  title={R markdown: The definitive guide},
  author={Xie, Yihui and Allaire, Joseph J and Grolemund, Garrett},
  year={2018},
  publisher={CRC Press}
}

@inproceedings{Wieringa2020,
author = {Wieringa, Maranke},
title = {What to Account for When Accounting for Algorithms: A Systematic Literature Review on Algorithmic Accountability},
year = {2020},
isbn = {9781450369367},
publisher = {Association for Computing Machinery},
address = {New York, NY, USA},
url = {https://doi.org/10.1145/3351095.3372833},
doi = {10.1145/3351095.3372833},
abstract = {As research on algorithms and their impact proliferates, so do calls for scrutiny/accountability of algorithms. A systematic review of the work that has been done in the field of 'algorithmic accountability' has so far been lacking. This contribution puts forth such a systematic review, following the PRISMA statement. 242 English articles from the period 2008 up to and including 2018 were collected and extracted from Web of Science and SCOPUS, using a recursive query design coupled with computational methods. The 242 articles were prioritized and ordered using affinity mapping, resulting in 93 'core articles' which are presented in this contribution. The recursive search strategy made it possible to look beyond the term 'algorithmic accountability'. That is, the query also included terms closely connected to the theme (e.g. ethics and AI, regulation of algorithms). This approach allows for a perspective not just from critical algorithm studies, but an interdisciplinary overview drawing on material from data studies to law, and from computer science to governance studies. To structure the material, Bovens's widely accepted definition of accountability serves as a focal point. The material is analyzed on the five points Bovens identified as integral to accountability: its arguments on (1) the actor, (2) the forum, (3) the relationship between the two, (3) the content and criteria of the account, and finally (5) the consequences which may result from the account. The review makes three contributions. First, an integration of accountability theory in the algorithmic accountability discussion. Second, a cross-sectoral overview of the that same discussion viewed in light of accountability theory which pays extra attention to accountability risks in algorithmic systems. Lastly, it provides a definition of algorithmic accountability based on accountability theory and algorithmic accountability literature.},
booktitle = {Proceedings of the 2020 Conference on Fairness, Accountability, and Transparency},
pages = {1–18},
numpages = {18},
keywords = {data-driven governance, algorithmic accountability, algorithmic systems, accountability theory},
location = {Barcelona, Spain},
series = {FAT* '20}
}

@inproceedings{Rule2018,
  title={Exploration and explanation in computational notebooks},
  author={Rule, Adam and Tabard, Aur{\'e}lien and Hollan, James D},
  booktitle={Proceedings of the 2018 CHI Conference on Human Factors in Computing Systems},
  pages={1--12},
  year={2018}
}

@INPROCEEDINGS{Pimentel2019,
  author={Pimentel, João Felipe and Murta, Leonardo and Braganholo, Vanessa and Freire, Juliana},
  booktitle={2019 IEEE/ACM 16th International Conference on Mining Software Repositories (MSR)}, 
  title={A Large-Scale Study About Quality and Reproducibility of Jupyter Notebooks}, 
  year={2019},
  volume={},
  number={},
  pages={507-517},
  doi={10.1109/MSR.2019.00077}}

@software{Pluto,
  author       = {Fons van der Plas and
                  Michiel Dral and
                  Paul Berg and
                  Παναγιώτης Γεωργακόπουλος and
                  Rik Huijzer and
                  Mikołaj Bocheński and
                  Alberto Mengali and
                  Benjamin Lungwitz and
                  Connor Burns and
                  Hirumal Priyashan and
                  Jerry Ling and
                  Eric Zhang and
                  Felipe S. S. Schneider and
                  Ian Weaver and
                  Xiu-zhe (Roger) Luo and
                  Shuhei Kadowaki and
                  Gabriel Wu and
                  Jelmar Gerritsen and
                  Rok Novosel and
                  Supanat and
                  Zachary Moon and
                  Luis Müller and
                  tecosaur and
                  Michael Abbott and
                  Nicholas Bauer and
                  pbouffard and
                  Satoshi Terasaki and
                  Shashank Polasa},
  title        = {fonsp/Pluto.jl},
  month        = may,
  year         = 2023,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.4792401},
  url          = {https://doi.org/10.5281/zenodo.4792401}
}

@book{beck2003test,
  title={Test-driven development: by example},
  author={Beck, Kent},
  year={2003},
  publisher={Addison-Wesley Professional}
}

@article{schulte2011active,
  title={Active documents with org-mode},
  author={Schulte, Eric and Davison, Dan},
  journal={Computing in Science \& Engineering},
  volume={13},
  number={3},
  pages={66--73},
  year={2011},
  publisher={Citeseer}
}

@article{dominik,
  title={Org Mode Manual},
  author={Dominik, Carsten},
  journal={self published},
  year={2004}
}

@inproceedings{nybom2018systematic,
  title={A systematic mapping study on API documentation generation approaches},
  author={Nybom, Kristian and Ashraf, Adnan and Porres, Ivan},
  booktitle={2018 44th Euromicro Conference on Software Engineering and Advanced Applications (SEAA)},
  pages={462--469},
  year={2018},
  organization={IEEE}
}

@software{Pandoc,
author = {MacFarlane, John and Krewinkel, Albert and Rosenthal, Jesse},
title = {Pandoc},
url = {https://github.com/jgm/pandoc},
doi = {10.5281/zenodo.1038654},
year = {2017}
}

@book{Pharr2016,
  title={Physically based rendering: From theory to implementation},
  author={Pharr, Matt and Jakob, Wenzel and Humphreys, Greg},
  year={2016},
  publisher={Morgan Kaufmann}
}

@book{Sussman2015,
  title={Structure and interpretation of classical mechanics},
  author={Sussman, Gerald Jay and Wisdom, Jack},
  year={2015},
  publisher={The MIT Press}
}

@article{crusoe2022methods,
  title={Methods included: Standardizing computational reuse and portability with the common workflow language},
  author={Crusoe, Michael R and Abeln, Sanne and Iosup, Alexandru and Amstutz, Peter and Chilton, John and Tijani{\'c}, Neboj{\v{s}}a and M{\'e}nager, Herv{\'e} and Soiland-Reyes, Stian and Gavrilovi{\'c}, Bogdan and Goble, Carole and others},
  journal={Communications of the ACM},
  volume={65},
  number={6},
  pages={54--63},
  year={2022},
  publisher={ACM New York, NY, USA}
}

@Article{Vivian2017,
author="Vivian, John
and Rao, Arjun Arkal
and Nothaft, Frank Austin
and Ketchum, Christopher
and Armstrong, Joel
and Novak, Adam
and Pfeil, Jacob
and Narkizian, Jake
and Deran, Alden D
and Musselman-Brown, Audrey
and Schmidt, Hannes
and Amstutz, Peter
and Craft, Brian
and Goldman, Mary
and Rosenbloom, Kate
and Cline, Melissa
and O'Connor, Brian
and Hanna, Megan
and Birger, Chet
and Kent, W James
and Patterson, David A
and Joseph, Anthony D
and Zhu, Jingchun
and Zaranek, Sasha
and Getz, Gad
and Haussler, David
and Paten, Benedict",
title="Toil enables reproducible, open source, big biomedical data analyses",
journal="Nature Biotechnology",
year="2017",
month="Apr",
day="01",
volume="35",
number="4",
pages="314--316",
issn="1546-1696",
doi="10.1038/nbt.3772",
url="https://doi.org/10.1038/nbt.3772"
}

@article{baker2016,
  title={Reproducibility crisis},
  author={Baker, Monya},
  journal={Nature},
  volume={533},
  number={26},
  pages={353--66},
  year={2016}
}

@article{lamprecht2020,
  title={Towards FAIR principles for research software},
  author={Lamprecht, Anna-Lena and Garcia, Leyla and Kuzak, Mateusz and Martinez, Carlos and Arcila, Ricardo and Martin Del Pico, Eva and Dominguez Del Angel, Victoria and Van De Sandt, Stephanie and Ison, Jon and Martinez, Paula Andrea and others},
  journal={Data Science},
  volume={3},
  number={1},
  pages={37--59},
  year={2020},
  publisher={IOS Press}
}

@article{peng2011,
author = {Roger D. Peng },
title = {Reproducible Research in Computational Science},
journal = {Science},
volume = {334},
number = {6060},
pages = {1226-1227},
year = {2011},
doi = {10.1126/science.1213847},
URL = {https://www.science.org/doi/abs/10.1126/science.1213847},
eprint = {https://www.science.org/doi/pdf/10.1126/science.1213847},
abstract = {Computational science has led to exciting new developments, but the nature of the work has exposed limitations in our ability to evaluate published findings. Reproducibility has the potential to serve as a minimum standard for judging scientific claims when full independent replication of a study is not possible.}
}

@Article{Clark2014,
author="Clark, Tim
and Ciccarese, Paolo N.
and Goble, Carole A.",
title="Micropublications: a semantic model for claims, evidence, arguments and annotations in biomedical communications",
journal="Journal of Biomedical Semantics",
year="2014",
month="Jul",
day="04",
volume="5",
number="1",
pages="28",
abstract="Scientific publications are documentary representations of defeasible arguments, supported by data and repeatable methods. They are the essential mediating artifacts in the ecosystem of scientific communications. The institutional ``goal'' of science is publishing results. The linear document publication format, dating from 1665, has survived transition to the Web.",
issn="2041-1480",
doi="10.1186/2041-1480-5-28",
url="https://doi.org/10.1186/2041-1480-5-28"
}

@inproceedings{baxter2012,
  title={The research software engineer},
  author={Baxter, Rob and Hong, N Chue and Gorissen, Dirk and Hetherington, James and Todorov, Ilian},
  booktitle={Digital Research Conference, Oxford},
  pages={1--3},
  year={2012}
}

@article{hong2022,
  title={FAIR principles for research software (FAIR4RS principles)},
  author={Hong, Neil P Chue and Katz, Daniel S and Barker, Michelle and Lamprecht, Anna-Lena and Martinez, Carlos and Psomopoulos, Fotis E and Harrow, Jen and Castro, Leyla Jael and Gruenpeter, Morane and Martinez, Paula Andrea and others},
  journal={Zenodo},
  year={2022}
}