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The discipline of open science

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This page lists selected literature and online resources. Some are related to existing tutorial pages, while others are not. They are supposed to be of high interest to this site’s users.

Several of the resources were added based on an inspiring talk by Julia Lowndes at the SAFRED conference, Brussels, 27 Feb 2018.

These resources focus on the discipline as a whole, its perception, principles, etc., while they often also give an overview of scientific computing workflows.

  • Ibanez et al. (2014): open and reproducible science: vision, routine practices, collaboration, literate computing
  • Hampton et al. (2015): workflows, tools, obstacles and needed mindshifts for open science
  • Donati & Woolston (2017): how data science is becoming a large discipline

Focus on reproducible research

  • Stodden et al. (2014): book on computational reproducibility and (experiment) replicability; the three parts are Tools, Practices and Guidelines, Platforms
  • Stodden & Miguez (2014): a formalized set of best practice recommendations for reproducible research
  • Begley et al. (2015): current irreproducibility and good institutional practice
  • ROpenSci Contributors (2018): a comprehensive overview of aspects and R-oriented tools in reproducible research

Bibliography

Begley C.G., Buchan A.M. & Dirnagl U. (2015). Institutions must do their part for reproducibility. Nature 525 (7567): 25–27. https://doi.org/10.1038/525025a.

Donati G. & Woolston C. (2017). Information management: Data domination. Nature 548 (7669): 613–614. https://doi.org/10.1038/nj7669-613a.

Hampton S.E., Anderson S.S., Bagby S.C., Gries C., Han X., Hart E.M., Jones M.B., Lenhardt W.C., MacDonald A., Michener W.K., Mudge J., Pourmokhtarian A., Schildhauer M.P., Woo K.H. & Zimmerman N. (2015). The Tao of open science for ecology. Ecosphere 6 (7): 1–13. https://doi.org/10.1890/ES14-00402.1.

Ibanez L., Schroeder W.J. & Hanwell M.D. (2014). Practicing open science. In: Stodden V., Leisch F. & Peng R.D. (eds.). Implementing reproducible research. CRC Press, Boca Raton, FL.

ROpenSci Contributors (2018). Reproducibility Guide [WWW document]. https://ropensci.github.io/reproducibility-guide/ (accessed September 22, 2020).

Stodden V., Leisch F. & Peng R.D. (2014). Implementing reproducible research. CRC Press, Boca Raton, FL.

Stodden V. & Miguez S. (2014). Best Practices for Computational Science: Software Infrastructure and Environments for Reproducible and Extensible Research. Journal of Open Research Software 2 (1). https://doi.org/10.5334/jors.ay.