references.bib

@book{community2022,
	title = {The Turing Way: A handbook for reproducible, ethical and collaborative research},
	author = {{The Turing Way Community}},
	year = {2022},
	month = {07},
	date = {2022-07-27},
	publisher = {Zenodo},
	doi = {10.5281/zenodo.3233853},
	url = {https://zenodo.org/record/3233853},
	note = {License: \href{https://creativecommons.org/licenses/by/4.0/}{CC BY 4.0}. Source: \url{https://github.com/the-turing-way/the-turing-way}. Website: \url{https://the-turing-way.netlify.app/}}
}

@book{chacon2014,
	title = {Pro Git},
	author = {Chacon, Scott and Straub, Ben},
	year = {2014},
	date = {2014},
	publisher = {Apress},
	doi = {10.1007/978-1-4842-0076-6},
	url = {http://dx.doi.org/10.1007/978-1-4842-0076-6},
	note = {License: \href{https://creativecommons.org/licenses/by-nc/4.0/}{CC BY-NC}. Source: \url{https://github.com/progit/progit2}. Website: \url{https://git-scm.com/book/en/v2}}
}

@software{allaire2022,
	title = {Quarto},
	author = {Allaire, J.J. and Teague, Charles and Xie, Yihui and Dervieux, Christophe},
	year = {2022},
	month = {01},
	date = {2022-01-10},
	doi = {10.5281/zenodo.5960048},
	url = {https://github.com/quarto-dev/quarto-cli},
	version = {1.2},
	note = {License: \href{https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html}{GNU GPL v2}. \url{https://github.com/quarto-dev/quarto-web}. Website: \url{https://quarto.org/}}
}

@article{millman2018,
	title = {Teaching Computational Reproducibility for Neuroimaging},
	author = {Millman, K. Jarrod and Brett, Matthew and Barnowski, Ross and Poline, Jean-Baptiste},
	year = {2018},
	month = {10},
	date = {2018-10-22},
	journal = {Frontiers in Neuroscience},
	volume = {12},
	doi = {10.3389/fnins.2018.00727},
	url = {https://dx.doi.org/10.3389/fnins.2018.00727},
	note = {License: \href{https://creativecommons.org/licenses/by/4.0/}{CC BY 4.0}. Website: \url{http://dx.doi.org/10.3389/fnins.2018.00727}}
}

@article{milligan2014,
	title = {Introduction to the Bash Command Line},
	author = {Milligan, Ian and Baker, James},
	editor = {Crymble, Adam},
	year = {2014},
	month = {09},
	date = {2014-09-20},
	journal = {Programming Historian},
	number = {3},
	doi = {10.46430/phen0037},
	url = {https://dx.doi.org/10.46430/phen0037},
	langid = {en}
}

@misc{mcbain2019,
  author = {McBain, Miles},
  title = {Git for Scientists},
  year = {2019},
  url = {https://milesmcbain.github.io/git_4_sci/},
  note = {License: \href{http://creativecommons.org/licenses/by-sa/4.0/}{CC BY-SA 4.0}. Source: \url{https://github.com/MilesMcBain/git_4_sci/}. Website: \url{https://milesmcbain.github.io/git_4_sci/}}
}


@book{capes2023,
	title = {swcarpentry/shell-novice: Software Carpentry: the UNIX shell},
	author = {Capes, Gerard and {Bkmgit} and Deppen, Jacob and Devenyi, G. A. and Ball, Alexander James and Fowler-Wright, Piper and Visconti, Alessia and Dusenberry, Jeff and Vera, Jessica and Harrison, Randal Sean and Bilke, Andreas and Welch, Jessica Nicole and Thorp, Kelly and Hernandez, Alfredo and {Ashkan Mirzaee} and Winjum, Benjamin and Daley, Chris and Wright, Clay and {Colinmorris} and George, Dave and {Ephantus2017} and Myklebust, Erik and {Löffler}, Frank and {HariEpuri} and Wolff, Holger and {Kairsten Fay} and Reyes, Luna Luisa Sanchez and Politze, Marius and Belkin, Maxim and Porter, Nathaniel and {, Nkicg6} and Ziegner, Norman and Stevens, Sarah LR and McCartney, Sean and Njambi, Serah and {Ramisetti} and Borrego, Stacey and Brown, Andrew Christopher and Cryan, Ashley and {Mehrdadbn9} and {Md Intekhabul Hafiz} and {Niketagrawal} and Benson, Noah and McDivitt, Aaron and Budd, Aidan and Stahlke, Amanda and {Andra{\v{s}} T{\v{s}}it{\v{s}}kan} and Stewart, Andrew and Smith, Becky and Martlin, Catherine and {Knüpfer}, Christian and McKain, David and Wilby, David and Salmanidou, Dimitra and Turner, Dave and Scriven, Edan and Wallace, Edward and McAulay, Elizabeth and Roesch, Etienne and Solinsky, Frank and Lipari, Giordano and Starling, Hamish and Barrass, Iain and {Isil Poyraz Bilgin} and {JSheffield159} and Acris, James and Bradley, Jonathan and Juvonen, Matti and Napier, Kathryn and Ross, Kenton and Ernst, Kevin and Trombach, Lukas and Chorley, Martin and {, Melissa} and Lake, Mike and Renfro, Mike and Renfro, Mike and {NJ} and {, Natali} and McKinlay, Nathan and Soranzo, Nicola and {Rodríguez-Sánchez}, Pablo and Wiringa, Peter and Viktorin, Petr and Rigby, Richard and {, Rkm} and Elliott, Ryan S. and {Lelièvre}, Samuel and Lacalle, Santiago and Kumar, Sujai and Liang, Tong and Gatua, Winfred and Sun, Yi and {Cgmerrick} and {Daking4} and Patel, Deep and {Erich333} and {Karl-Holten} and {Kathymd} and {Laporpe} and {Naveendangeti} and {Nbehrnd} and {, Sophie} and {Tbert} and Couch, Tom and Shrestha, Ram Krishna and {Zzhang60} and {{"}Eli}},
	year = {2023},
	month = {05},
	date = {2023-05-02},
	publisher = {Zenodo},
	doi = {10.5281/ZENODO.595899},
	url = {https://zenodo.org/record/595899},
	note = {License: \href{https://creativecommons.org/licenses/by/4.0/}{CC BY 4.0}. Source: \url{https://github.com/swcarpentry/shell-novice}. Website: \url{https://swcarpentry.github.io/shell-novice/}}
}

@book{koziar2023,
	title = {swcarpentry/git-novice: Software Carpentry: Version Control with Git 2023-05},
	author = {Koziar, Katherine E. and {Madicken Munk} and Greene, Andrew and Rasel, Annajiat Alim and Bennett, Ed and Stevens, Sarah LR and Turnator, Ece and {Gorroño}, Jon Haitz Legarreta and Leinweber, Katrin and Nederbragt, Lex and {Lelièvre}, Samuel and {Vyas Ramasubramani} and Gitter, Anthony and Cassol, Daniela and Zhu, Judy and Soranzo, Nicola and Hejazi, Nima S and Deconinck, Wouter and {Laurentheirendt} and Clarke, Alison and Bressan, Camilla and Guan, Charles and Urizar, Cristina and Horsfall, Dave and {, David} and {, Deborah} and Lowther, Ed and {Fwoerister} and Bissey, {François} and {HaoZeke} and Kent, James and Holmes, Jessica and Huddleston, John and Lehtonen, Juho and Word, Karen and Lieret, Kilian and Modenese, Luca and Foscato, Marco and {Bjørnstad}, Marius and Matney, Mark and Juvonen, Matti and Belkin, Maxim and {Mingrui Yang} and Silantyeva, Olga and McCann, Patrick and Lanfear, Riley and Bartholomew, Sadie L. and Cox, Sam and Gruber, Scott and Jamieson, Stewart Christopher and Arabas, Sylwester and Russell, Tom and Koskela, Tuomas and {, Will} and Wolff, Benjamin and {, Catherinef37} and {Huijun ZHU} and {Kerimoff}},
	year = {2023},
	month = {05},
	date = {2023-05-08},
	publisher = {Zenodo},
	doi = {10.5281/ZENODO.7908089},
	url = {https://zenodo.org/record/7908089},
	note = {License: \href{https://creativecommons.org/licenses/by/4.0/}{CC BY 4.0}. Source: \url{https://github.com/swcarpentry/git-novice}. Website: \url{https://swcarpentry.github.io/git-novice/}.}
}

@article{bryan2018,
	title = {Excuse Me, Do You Have a Moment to Talk About Version Control?},
	author = {Bryan, Jennifer},
	year = {2018},
	month = {01},
	date = {2018-01-02},
	journal = {The American Statistician},
	pages = {20--27},
	volume = {72},
	number = {1},
	doi = {10.1080/00031305.2017.1399928},
	url = {http://dx.doi.org/10.1080/00031305.2017.1399928},
	langid = {en},
	note = {Website: \url{https://doi.org/10.1080/00031305.2017.1399928}.}
}

@article{ram2013,
	title = {Git can facilitate greater reproducibility and increased transparency in science},
	author = {Ram, Karthik},
	year = {2013},
	month = {02},
	date = {2013-02-28},
	journal = {Source Code for Biology and Medicine},
	volume = {8},
	number = {1},
	doi = {10.1186/1751-0473-8-7},
	url = {http://dx.doi.org/10.1186/1751-0473-8-7},
	langid = {en},
	note = {License: \href{https://creativecommons.org/licenses/by/2.0/}{CC BY 2.0}. Source: \url{https://github.com/karthik/smb_git}. Website: \url{https://doi.org/10.1186/1751-0473-8-7}}
}

@article{perez-riverol2016,
	title = {Ten Simple Rules for Taking Advantage of Git and GitHub},
	author = {Perez-Riverol, Yasset and Gatto, Laurent and Wang, Rui and Sachsenberg, Timo and Uszkoreit, Julian and Leprevost, Felipe da Veiga and Fufezan, Christian and Ternent, Tobias and Eglen, Stephen J. and Katz, Daniel S. and Pollard, Tom J. and Konovalov, Alexander and Flight, Robert M. and Blin, Kai and {Vizcaíno}, Juan Antonio},
	editor = {Markel, Scott},
	year = {2016},
	month = {07},
	date = {2016-07-14},
	journal = {PLOS Computational Biology},
	pages = {e1004947},
	volume = {12},
	number = {7},
	doi = {10.1371/journal.pcbi.1004947},
	url = {http://dx.doi.org/10.1371/journal.pcbi.1004947},
	langid = {en},
	note = {License: \href{https://creativecommons.org/licenses/by/4.0/}{CC BY 4.0}. Source: \url{https://github.com/ypriverol/github-paper}. Website: \url{https://doi.org/10.1371/journal.pcbi.1004947}}
}

@book{bryan2023,
  author = {Bryan, Jenny},
  title = {Happy Git and GitHub for the useR},
  year = {2023},
  publisher = {Jenny Bryan},
  url = {https://happygitwithr.com},
  note = {License: \href{https://creativecommons.org/licenses/by-nc/4.0/}{CC BY-NC 4.0}. Source: \url{https://github.com/jennybc/happy-git-with-r}. Website: \url{https://happygitwithr.com/}}
}

@article{lowndes2022,
	title = {Openscapes Champions Lesson Series},
	author = {Lowndes, Julia Stewart and Robinson, Erin},
	year = {2022},
	month = {12},
	date = {2022-12-06},
	doi = {10.5281/ZENODO.7407247},
	url = {https://zenodo.org/record/7407247},
	langid = {en},
	note = {License: \href{https://creativecommons.org/licenses/by/4.0/}{CC BY 4.0}. Source: \url{https://github.com/Openscapes/series}. Website: \url{https://openscapes.github.io/series/}}
}

@book{GitHub2023,
  author = {GitHub},
  title = {GitHub Docs},
  year = {2023},
  publisher = {GitHub},
  url = {https://docs.github.com/en},
  note = {License: \href{https://creativecommons.org/licenses/by-nc/4.0/}{CC BY-NC 4.0}. Source: \href{https://docs.github.com/en}{https://docs.github.com/en}}
}

@article{blischak2016,
	title = {A Quick Introduction to Version Control with Git and GitHub},
	author = {Blischak, John D. and Davenport, Emily R. and Wilson, Greg},
	editor = {Ouellette, Francis},
	year = {2016},
	month = {01},
	date = {2016-01-19},
	journal = {PLOS Computational Biology},
	pages = {e1004668},
	volume = {12},
	number = {1},
	doi = {10.1371/journal.pcbi.1004668},
	url = {http://dx.doi.org/10.1371/journal.pcbi.1004668},
	langid = {en},
	note = {License: \href{https://creativecommons.org/licenses/by/4.0/}{CC BY 4.0}. Source: \href{https://doi.org/10.1371/journal.pcbi.1004668}{https://doi.org/10.1371/journal.pcbi.1004668}}
}

@online{aimrsf2023,
  author = {{AI for Multiple Long-term Conditions Research Support Facility}},
  title = {Introduction to version control with git},
  year = {2023},
  month = {06},
  url = {https://www.youtube.com/watch?v=z9-qAGq78qE},
  note = {License: \href{https://creativecommons.org/licenses/by/4.0/}{CC BY 4.0}. Source: \url{https://github.com/aim-rsf/training/tree/main/version-control}}
}

@book{coderefinery2023,
  author = {coderefinery},
  title = {GitHub without the command line},
  year = {2023},
  publisher = {coderefinery},
  url = {https://coderefinery.github.io/github-without-command-line/},
  note = {License: \href{https://creativecommons.org/licenses/by-nc/4.0/}{CC BY-NC 4.0}. Source: \url{https://github.com/coderefinery/github-without-command-line/tree/master}. Website: \url{https://coderefinery.github.io/github-without-command-line/}}
}

@online{amin2023,
  author = {Amin, Abhay},
  title = {Naming conventions for Git Branches — a Cheatsheet},
  year = {2023},
  url = {https://medium.com/@abhay.pixolo/naming-conventions-for-git-branches-a-cheatsheet-8549feca2534},
  note = {License: \href{NA}{NA}. Source: \url{NA}. Website: \url{https://medium.com/@abhay.pixolo/naming-conventions-for-git-branches-a-cheatsheet-8549feca2534}}
}