bibliography.bib

@article{brack_ten_2022,
  title = {Ten Simple Rules for Making a Software Tool Workflow-Ready},
  author = {Brack, Paul and Crowther, Peter and {Soiland-Reyes}, Stian and Owen, Stuart and Lowe, Douglas and Williams, Alan R. and Groom, Quentin and Dillen, Mathias and Coppens, Frederik and Gr{\"u}ning, Bj{\"o}rn and Eguinoa, Ignacio and Ewels, Philip and Goble, Carole},
  year = 2022,
  month = mar,
  journal = {PLOS Computational Biology},
  volume = {18},
  number = {3},
  pages = {e1009823},
  publisher = {Public Library of Science},
  issn = {1553-7358},
  doi = {10.1371/journal.pcbi.1009823},
  urldate = {2026-03-10},
  langid = {english},
  keywords = {Automation,Computer software,Genome analysis,Graphical user interfaces,Language,Open source software,Software development,Software tools}
}

@article{roach_ten_2022,
  title = {Ten Simple Rules and a Template for Creating Workflows-as-Applications},
  author = {Roach, Michael J. and {Pierce-Ward}, N. Tessa and Suchecki, Radoslaw and Mallawaarachchi, Vijini and Papudeshi, Bhavya and Handley, Scott A. and Brown, C. Titus and {Watson-Haigh}, Nathan S. and Edwards, Robert A.},
  year = 2022,
  month = dec,
  journal = {PLOS Computational Biology},
  volume = {18},
  number = {12},
  pages = {e1010705},
  issn = {1553-7358},
  doi = {10.1371/journal.pcbi.1010705},
  urldate = {2023-01-10},
  langid = {english},
  keywords = {Bioinformatics,Computer software,Language,Operating systems,Preprocessing,Pythons,Software tools,User interfaces}
}

@article{seemann_ten_2013,
  title = {Ten Recommendations for Creating Usable Bioinformatics Command Line Software},
  author = {Seemann, Torsten},
  year = 2013,
  month = dec,
  journal = {Gigascience},
  volume = {2},
  number = {1},
  pages = {2047-217X-2-15},
  issn = {2047-217X},
  doi = {10.1186/2047-217X-2-15},
  urldate = {2026-03-10},
  abstract = {Bioinformatics software varies greatly in quality. In terms of usability, the command line interface is the first experience a user will have of a tool. Unfortunately, this is often also the last time a tool will be used. Here I present ten recommendations for command line software author's tools to follow, which I believe would greatly improve the uptake and usability of their products, waste less user's time, and improve the quality of scientific analyses.}
}

@article{taschuk_ten_2017,
  title = {Ten Simple Rules for Making Research Software More Robust},
  author = {Taschuk, Morgan and Wilson, Greg},
  year = 2017,
  month = apr,
  journal = {PLoS Comput Biol},
  volume = {13},
  number = {4},
  pages = {e1005412},
  issn = {1553-7358},
  doi = {10.1371/journal.pcbi.1005412},
  urldate = {2019-05-16},
  abstract = {Software produced for research, published and otherwise, suffers from a number of common problems that make it difficult or impossible to run outside the original institution or even off the primary developer's computer. We present ten simple rules to make such software robust enough to be run by anyone, anywhere, and thereby delight your users and collaborators.},
  langid = {english}
}