1 Local computing

1.1 Mac OS

Root = /
Other disks (USB, etc.) mounted under /Volumes
User directories under /Users; your home directory at /Users/yourusername
System wide applications under /Applications; users can also install applications under /Users/username/Applicatons
User specific config files under /Users/username/Library (hidden by default)
Unix related executables under /bin, /sbin, etc.
PATH is an environment variable, settable from command line or ~/.profile

Root = C:\
Other disks mounted as D:\, E:, etc.
User directories under C:\Users; your home directory at C:\Users\yourusername
System wide applications under c:\Program Files (64 bit) and C:\Program Files (x86) (32 bit)
Path variable settable from “System Properties” dialog

Standard shortcuts like “Desktop”, “Documents”, and “Downloads” are usually subdirectories of your home directory
Hidden files and directories can be viewed by setting appropriate options in Finder / Explorer

Avoid spaces (or other non-printing characters) and punctuation other than dashes, underscores, and periods in file names
File names that include dates should preferably follow the ISO-8601 formatting standard, which has the form “YYYY-MM-DD”. For example, an experiment done of Jan 12, 2022 should be named something like “2022-01-12-Expt01.csv”.
- The advantage of this is it makes it easy to sort and search by date
Try and be consistent in your naming schemes. I promise this will make your life (and/or that of your collaborators) easier at some point in your research career!
See further recommendations from Iowa Stat University’s Open Research Data Repository

A “terminal” is a text input/output environment for interacting with your computer. A terminal used to be a physical device attached to a computer. Strictly speaking, these days we run “terminal emulators” – graphical programs that emulate terminals.
A “shell” is a program that runs in a terminal that processes and interprets the command you type. You can run different shells in the same terminal.

Terminal accessed by running “Terminal” program (in the “Applications/Utilities” folder)
Default shell is zsh; but bash also included by default (invoke at command line by typing bash)

Default terminal is “Command Prompt” but new “Windows Terminal” is better choice
Several options for shell but I recommend “PowerShell”

NOTE: The following commands also work in Windows PowerShell

pwd – prints name of your “working” directory (i.e. the directory you’re currently in)
ls – lists the contents of the working directory
cd – change directory
- cd Downloads
- cd ~ (move to your home directory)
mkdir – make a new directory
- mkdir foo_dir
- mkdir bar_dir
rmdir – remove a directory (must be empty)
- rmdir bar_dir
rm – remove a file
- rm bar.txt
cp – copy a file
- cp foo.txt foo_copy.txt
mv – move a file or directory
- mv foo.txt baz.txt
- mv foo_dir foo.dir
cat – write the contents of a file to the terminal:
- cat foo.txt
more – a pager program. View the contents of a file, one page at a time. Type <space> to advance pages, q to quit.

Side note: Why is it common to use names like foo, bar, and baz in examples? See https://en.wikipedia.org/wiki/Foobar

~ – refers to the users home directory.
- cd ~ = change to my home directory
- ls ~/*.txt = list all files ending with the prefix .txt in your home directory
. – the current directory
- cd ./tmp = move to the directory called tmp that is located in the directory the cd command is executed from.
.. – the directory above the current directory (if it exists)
- cd .. = move up one level in the directory hierarchy. For example if pwd is /home/jsmith then cd .. moves you to /home
/ – the root directory of the file system
cd /data = move to the data directory that is the subdirectory of the root
ls / = list all files and directories in the root directory