What to Learn Next?#
Baker, M. (2016). 1,500 scientists lift the lid on reproducibility. Nature, 533(7604), 452–454. https://doi.org/10.1038/533452a
Barba, L. (2017): Barba-group Reproducibility Syllabus. figshare. Paper. https://doi.org/10.6084/m9.figshare.4879928.v1
Piwowar, H. A., & Vision, T. J. (2013). Data reuse and the open data citation advantage. PeerJ, 1, e175. https://doi.org/10.7717/peerj.175
Whitaker, Kirstie (2018): Barriers to reproducible research (and how to overcome them). figshare. Paper. https://doi.org/10.6084/m9.figshare.7140050.v2
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:
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
cd ..to go in the parent folder (
cdis to move into folders,
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.