Basic Unix

Biochemistry laboratories - 201

Jean-Yves Sgro

Find this document here (short URL) today:

*Note*: To see as slides click on **"Gift icon"** at the top right. To revert back to page view click on **"book icon"** when on the first slide.


  • check your name on the attendees list
  • choose an iMac
  • login with your NetID ( is not necessary)
  • If this is the first time this Mac "sees" you it will go through a quick set-up: simply skip using "Apple ID"

Finding Terminal on the iMac

Method 1

  • Click on the "Finder" at the bottom left of the "Dock" on the bottom of the screen. This will open a new window.
  • On the left click on "Applications"
  • In the alphabetical list open folder Utilities
  • double click to open Terminal

Method 2

  • Spotlight Search: Click the magnifying glass at the top right corner of your screen
  • type Terminal
  • press the return key

Web Linux Terminal

Today we'll work in Mac OS Terminal.

You can try the Linux option later within a web-based terminal

Choice URL


Unix Exercise Files

Hand-outs are in HTML format:

Note: other formats and other tutorials are at

Class evaluation

After class:

  • fill-in the one page "evaluation" form for this class

The evaluation is anonymous. Evaluation link on Qualtrics or type:

Note: Survey will be unlocked when workshops are held.

Hard drive file system



Command-line operation: The Shell

The prompt


Your hard drive area

Your user space


Home directory


Print working directory (current directory)


Current and Parent directories

Diagram Naming convention


*dot dot*

Parent directory:
directory “above” containing the “current” directory.



Current directory

Absolute and Relative path

Absolute: starts with / root level

Relative: relative to another directory

For example using





List files


Long list of home directory

ls ~

total 0 drwx------+ 5 YOU AD\Domain Users 170 Mar 15 18:36 Desktop
drwx------+ 3 YOU AD\Domain Users 102 Jun 19 2014 Documents
drwx------+ 5 YOU AD\Domain Users 170 Mar 15 18:36 Downloads
drwx------@ 43 YOU AD\Domain Users 1462 Mar 15 18:36 Library
drwx------+ 3 YOU AD\Domain Users 102 Jun 19 2014 Movies
drwx------+ 3 YOU AD\Domain Users 102 Jun 19 2014 Music
drwx------+ 3 YOU AD\Domain Users 102 Jun 19 2014 Pictures
drwxr-xr-x+ 5 YOU AD\Domain Users 170 Jun 19 2014 Public

Groups and Privileges

In order to organize privileges and permissions the Unix system is designed around the following definitions:

User group Definition
user A user of the computer. Your specific user name is shown with whoami.
group Multiple users can be assembled into a group e.g. from the same lab. The system administrator of the computer will create the group.
others This is "anyone" else; on older system this was called "the world".
all Contains everyone including user, group and anyone but not present in this listing.

Table: Definitions of user groups. In the listing above they belong to user YOU and group AD\Domain Users.


Privilege Definition
d This is a directory
r The file can be read.
w The file can be writen or even overwriten.
x The execute privilege. For a directory it means its content can be listed.
- The privilege within that column is not granted.

Table: Privilege tags

Standard Input/Output streams

Handle Name Description
0 stdin Standard input
1 stdout Standard output
2 stderr Standard error

Table: Understanding I/O streams numbers


The glass content can vary. The glass is the variable, the content is the variable value.

Separating the container and the content:
‘glass’ is the container ‘$glass’ is the content and can vary.

This website does not host notebooks, it only renders notebooks available on other websites.

Delivered by Fastly, Rendered by OVHcloud

nbviewer GitHub repository.

nbviewer version: d25d3c3

nbconvert version: 5.6.1

Rendered (Sat, 26 Nov 2022 11:43:39 UTC)