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Resources¶

For additional resources like videos and reference papers on reproducibility, see the Further Reading and Additional Material sections.

What to Learn Next?¶

Open Research would be a good chapter to read next. If you want to start learning hands-on practices, we recommend reading the Version Control chapter next.

Further Reading¶

• Baker, M. (2016). 1,500 scientists lift the lid on reproducibility. Nature, 533(7604), 452–454. Baker (2016)

• Barba, L. (2017): Barba-group Reproducibility Syllabus. figshare. Paper. Barba (2017)

• Piwowar, H. A., & Vision, T. J. (2013). Data reuse and the open data citation advantage. PeerJ, 1, e175. Piwowar & Vision (2013)

• Whitaker, Kirstie (2018): Barriers to reproducible research (and how to overcome them). figshare. Paper. Whitaker (2018)

Additional Material¶

Using the command line¶

While most of what this book is about does not require the use of the command line, it often actually makes things easier. Writing commands in the terminal, PowerShell, command-line, or command prompt provides an alternative means of interacting with the computer. It offers several advantages and can be considered a beneficial approach for various reasons, including efficiency, independence on graphical user interfaces, flexibility, automation of tasks. Often, advanced tasks or options are only available as command line tools (for example advanced git, datalad. You first need to know that linux and OSX use bash code natively, while the command line in windows uses batch script, which is a different language.

List of some tools and training materials for using the command-line:

• A game to teach one the basics of using a POSIX (Linux, BSD, UNIX) terminal
• Carpentries lesson on The Unix Shell
• An article on Command Line Tutorial: Usage in Linux and macOS
• A lesson on Introduction to the Bash Command Line

Some nice-to-know tips:

• When working on the terminal please make sure that you are in the correct folder (also called as directory):

  • If you right click folders, you may have a function to open a terminal there
  • use cd .. to go in the parent folder (cd is to move into folders, .. means up)
  • you can also type cd (note the space) and then drag and drop a folder. This action would autocomplete the folder’s path into the terminal.

• The superpower developers use all the time and will never think you do not know about it: use the tab on your keyboard to get automatic text completion.

Useful Links¶

Reproducibility¶

• Markowetz, F. (2018). 5 selfish reasons to work reproducibly. Slides available at https://osf.io/a8wq4/. Recording from a talk at Data Stewardship TU Delft in 2019. https://youtu.be/yVT07Sukv9Q.

• Leipzig, J (2020). Awesome Reproducible Research: A curated list of reproducible research case studies, projects, tutorials, and media. Github repo. https://github.com/leipzig/awesome-reproducible-research

Data Science¶

• Data science: A guide for society. Ask for Evidence. (2019). Retrieved October 26, 2021, from https://askforevidence.org/articles/data-science-a-guide-for-society.

• Riley, E. (2019). Data Science Guide for Society. London; senseaboutscience.org.

• The Open Data Institute. (2019). Knowledge & opinion. The ODI. Retrieved October 26, 2021, from https://theodi.org/article/data-ethics-canvas.