Operating System Basics for Linux

Department of Engineering Science, University of Oxford

Izzi Mear & Eric Peasley, Version 1.0 July 21

An operating system is a large, complex collection of software that manages the

computer. All communication between the central processor and the keyboard,
mouse, screen, computer disk and network is controlled by the operating system. It
is the operating system that detects the click of a button or the movement of the
mouse. Other programs cannot communicate with these peripheral devices directly.
They have to ask the operating system to carry out these tasks.

The Linux operating system is based on the much older Unix operating system, first
developed in 1969 at Bell Labs in New Jersey.

This document introduces you to the basics such as accessing free applications,
managing your files and using the terminal. There are many Linux distributions, and
this guide does not cover all case. The examples will usually be from Ubuntu.

Contents
• Useful Applications (e.g. Free access to Office365) Page 2
• Managing Applications (e.g. Split Screen and Virtual Desktops) Page 5
• Managing your Files (e.g. Organising files/folders and backups) Page 7
• Using a Terminal (e.g. Text-based commands to create folders) Page 13

Comments, corrections and suggestions to [email protected]

Icons throughout sourced from FlatIcon.com, made by Freepik, Eucalyp, smashicons, wanicon, icongeek26 and tHose icons.

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 Useful Applications
Your operating system will come bundled with some applications. Departmental
computers will already have all the software you need, however if you are working on
a personal computer there may be some software you need to install.

Office 365

Students and staff at the University can access Office 365, which contains many
useful applications for University work. The University of Oxford Office 365 system
includes a cloud based working environment (called Nexus365). Follow the
instructions here to get started: https://help.it.ox.ac.uk/nexus365/getting-started

Here you will find :-

Outlook: The Microsoft email client to view your University emails.

One Drive: A cloud based filing system. You can use this to backup
your files and share files with other people.

Word: The Microsoft word processor. You can save files as a Word
document(.docx) to One Drive or your own computer.

Excel: The Microsoft spreadsheet. You can save files as an Excel

spreadsheet(.xlsx) to One Drive or your own computer.

One Note: A digital notebook, you can use this for taking notes.

Powerpoint: Used for creating presentations.

Each of these can be used online, in your browser. This is the most reliable option as
there is no official installation from Microsoft for Linux systems. Some browsers work
better than others, so having multiple installed (e.g. Chrome & Firefox) can be useful.

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You can only get full functionality by installing the software directly onto your
machine. There are options for getting a full installation working on Linux using
Virtual Machines. See for example the instructions on makeuseof.com.

Microsoft Teams App

Another part of Nexus365 is the Application Teams. It is an online chat/conferencing

tool. Teams lets you message, talk to and see other members of the University. It will
be used for the online laboratories. There is a web based version.

Logging into the Teams App

Log in using your SSO and password:

Sign in using [email protected]

Replacing abc123 with your own Single Sign On (SSO) username.

Sometimes it capitalizes the first letter of the SSO, if so change it back to lower case.

PDF Reader

You will need to use PDFs. Whichever PDF Reader you use, make sure you can:
• Make notes and highlight
• Search within PDFs: You will often work with many documents, searching for
key terms using the Search bar is much faster than scrolling.
• Viewing Headings for Navigation: You can save a lot of time by enabling
the navigation pane to click through Headings, shown here circled in yellow:

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 Creating Text Files

You will not always want files where the text is formatted. In some cases
you will want something very simple: just words as a .txt file. This could because of:
• personal preference (some people prefer the minimalist environment)
• the wider range of compatibility (all OS will be able to read a .txt even if Word
is not installed).

Most Linux distributions should have a Text Editor installed. For some distributions,
you can create a New Document by right clicking on the background in the File
Browser. Then double click on the Document and it will open in a Text Editor.

There are two different types of files it can save:

• Plain Text format just contains ASCII character codes.
You can't change the font. These save to .txt files.

• Rich Text format contains extra formatting codes for changing the font and
size of the text and other formatting commands. These save to .rtf files.

Try the following :-

Select New Document
In the Format menu select Make Plain Text
Enter the following text into the document :-
This is an example text file.
Save as ReadMe.txt. You can move this file later.

Security

Keeping your computer, files and identity safe is hugely important. Sophos Anti-Virus
is available for free from the Central IT pages, using the above link. You should also
consider creating strong passwords and using a password manager. Much can be
found online, for example from Reporters without Borders.

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Managing Applications
Often you will need to work with multiple applications (apps) open. For example, if
you are coding you may need a PDF of instructions open as well as MATLAB. Or if
you are writing a report you may need an internet browser and a Word document.
This section introduces you to different ways to work with multiple apps.

Minimising, Closing and Quitting

To get the best from your computer, it is important to only have the applications open
that you need for your current task. Having too many applications open at once will
cause your machine to be slow. You might think you are quitting applications by
minimising and closing:
• Minimise an app by pressing the - button in the top-right corner of the window
• Close windows of an app by pressing the X button in the top-right corner
However, minimising and even closing windows does not always quit the app.
The app can still be using memory, which will slow down your computer.

Quit rather than close/minimise any applications you are not using.
This will free up RAM (a type of computer memory).

Using Systems Monitor

To check which applications are using memory, use the Systems Monitor.

• Open Applications then scroll to Utilities

• Select Systems Monitor

Under the Processes tab you will see a list of all programs running. To stop an
unresponsive program , simply select it and right-click. You can then select:

• Stop to pause the process

• End which will fully close an application safely.

• Kill which forces the app to quit, only use if End Process does not work.

For more information, see this article on how Linux uses memory.

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 Split Screen View

To work with two applications at once, a simple option is to split the screen between
two applications. To do this:
• Open two applications on a Desktop.
• Move your cursor to the edge of a window, and when an arrow appears resize
the window by holding and dragging.

You can drag the divide between the two applications to the left and right.

Maximising Applications

The approach of splitting the screen is not always the best option – particularly if you
have a small monitor. Sometimes we need to work with an application which has
been maximised to fill the screen. Maximise an application by pressing the square in
the top-right corner of an app window.

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Managing your Files

Files and Folders

A file is just a lot of ones and zeros stored in a permanent location on the
computer. Each file is used to store a particular type of object.

It could contain a picture, a document, a program or many other types of object.

Each file has a name, which may also include a suffix (ending • something) which
helps to show what the file contains. For example:

File name with suffix Type of File

Lecturenotes.pdf A document
ReadMe.txt Plain Text
photo.jpg A Picture
MyScript.m A MATLAB Program

There are thousands of files on a typical computer. A file system is used to keep
track of all the files. The file system is divided into folders.

A folder, also known as a directory, is a location where all the files related to
a particular topic are stored. Folders help keep related files together, so they
do not get mixed up with other files on the system.

Files and folders may seem basic, but keeping them organised can be a difficult
habit to develop. It is always worth taking a few moments to correctly store your files.

When you download a file, it is usually stored automatically in your

Downloads folder. If you want to store it long term, move this file
so it is stored in a sensible folder elsewhere in your file system.

As well as storing files on your computer locally, it is sensible to

store a copy of your files online too. e.g. using OneDrive

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 A File System

The whole file system is organised in a hierarchy of folders within folders. The
diagram on the right represents a very small portion of a Linux file system. Another
name for a folder is a directory.

/ Root Directory
Director
At the top of the file system is the folder known
as the root directory. It is specified with a
etc home usr
forward slash “/”. The root directory contains
many other directories than shown here.
Jack's Home Directory Jack

The diagram looks a bit like a family tree. The Eng

words parent and child are used in computing
to describe the relationship between Year1 Year2

directories.
P5comp P5mech

In the diagram:
MyFrame.mat
• The parent of Sess1 is P5comp. ReadMe.txt Sess1 Sess2

• Sess1 and Sess2 are the children of

prog1.m prog2.m
P5comp.

A folder P5comp A file ReadMe.txt

Home Directory

When using a computer, you don't want to mix up your files with those used by the
operating system and other users. Therefore, each user on a system is allocated a
Home Directory, where they can store their personal files. On most Linux systems,
these are all kept in the home folder. An example of creating folders is given on
the next page. Follow these to create the structure shown in the diagram above.

Make sure that your home is always organised.

This will make it easier to find files, and lead to efficient working.

For a more in-depth guide to the file system on Ubuntu, see this video.

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Example: Creating Folders in your Home Folder
Some Linux systems have a choice of different GUI. There are also many ways of
configuring a GUI. You will need to use a File Browser. The following instructions
show to how build the example file structure on the previous page:

• Open a File Browser, go to your home directory

• Create a New Folder (right-clicking on the background in the File Browser).
• Rename the folder Eng (right-clicking the folder should give you this option).
• Go to the Eng folder (single or double clicking on the folder)
• Inside the new folder, create another new folder called Year1
• Inside Year1, create another folder called P5comp.

The idea is that as you do more work on your computer, you slowly build a hierarchy
structure of folders, so that you can easily find the files that you need. e.g. If you
create files for the mechanics laboratory, put them into a P5mech folder in Year1.

File Paths

The file path is a way to describe the location of a file or folder, based on a fixed
starting point. Every file/folder will have a unique absolute path.

The Absolute Path of a file/folder (e.g. fileA) is the path you would have to
take from the top of the system (root directory) to reach that file/folder.

Example: Absolute Path of ReadMe.txt

Consider the file ReadMe.txt on the previous page. To reach this file starting at the
root directory, you would go into home, then the specific users home directory
(Jack), then Eng, Year1, P5comp until you arrive at ReadMe.txt. The Absolute path
is written /home/Jack/Eng/Year1/P5comp/ReadMe.txt

The absolute path of a file can be very long. A quicker way to specify the path from
the Current Working Directory to the file or folder you are interested in. This is
called the relative path to a file. This describes a files location relative to the
Current Working Directory.

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 The Relative Path of a file/folder is the path you would have to take from
the current Working Directory to the original file/folder.

Example: Relative Path moving Down

Considering our example file structure, if the Current Working Directory is
/home/Jack/Eng/Year1/P5comp
• The Relative Path to ReadMe.txt is just ReadMe.txt
• The Relative Path to Prog1.m is Sess1/prog1.m
A relative path does NOT start with a forward slash.

Example: Relative Path moving Up

You can also have a relative path that goes up the tree as well as down. Two full
stops in a path indicates the parent directory from wherever you are in the path.

If the Current Working Directory is folder / Root Directory

Director

Sess2
• The Relative Path to prog1.m is etc home usr

../Sess1/prog1.m
Jack's Home Directory Jack
• The Relative Path to MyFrame.mat is
../../P5mech/ MyFrame.mat
Eng

Relative paths take some getting used to, but Year1 Year2
can be a powerful tool when managing many
files. P5comp P5mech

MyFrame.mat
ReadMe.txt Sess1 Sess2

prog1.m prog2.m

A folder P5comp A file ReadMe.txt

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Backup using OneDrive

It is always a good idea to take a copy of your files, just in case anything happens to
your computer. As part of your University Single Sign On (SSO) account, you have
access to One Drive. This is a file storage area linked to the Microsoft Office Suite
available online.

• Visit Office.com and click Sign In.

• Use your SSO username with ending

@ox.ac.uk

• At the Shibboleth SSO Sign In page,

use your SSO username and password.

Once you logged in, select OneDrive on your dashboard to open your file storage:

• Use the Upload button to add files or folders to your storage area. You can
also drag and drop. Try uploading a Folder.

• In OneDrive, Right Click any file and select Download to download a file.

If you want to avoid manually uploading a back up to OneDrive,

you can set up a folder on your computer to sync using OneDrive.

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 Using Zip Folders

An easy way to transfer multiple files or folders between computers is to

use a zip file. This stores all the data into a single file. It also uses compression
software to reduce the size of the data.

Zipping Items into a File

• Open the file or folder in File Browser

• Control-click it or tap it using two fingers

• Select Compress from the menu.

You will now see a .zip file is created.

Extracting a Zip File

Double clicking on a zip file will extract the contents.

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Using a Terminal
So far we have shown the the easiest way of interacting with the operating system:
using a Graphical User Interface or GUI. This is where you interact with the
computer using a mouse pointer and click to interact with applications.

Operating systems (OS) are designed like a nut:

• The main part of the OS is called the Kernel. This contains Shell
all the programs to manage the computer and hardware.
Kernel
• Surrounding the kernel is the Shell. The shell contains the
software that allows you to interact with the kernel.

The GUI that you use to interact with your computer is a part of the Shell. However,
this is not the only way of interacting with the Kernel. There are also text based
commands that allow you to control the OS without a mouse. This is known as using
the Command Line.
To use the command line, we use a Terminal environment.
It is a simple window where we can type text.

Why use the Terminal?

Imagine Errol the Engineer has just returned from a six-month survey of materials in
different off-shore structures. The 1430 samples have been run through a testing
machine, resulting in 1430 data files. The research group has worked with files from
this machine before, and know before they can graph the results the files need to be
put through a program called reformatData.sh. In the past, they only had 20 files, so
this script was run 20 times by hand. If Errol has to run reformatData.sh by hand
using a GUI, they will have to select and open a file 1430 times! If it takes even 30
seconds to run each file, the whole process will take more than 12 hours. With the
shell, Errol can instead assign the computer this mundane task!

It is important to know the shell exists and what it can do. The next few pages
give a brief introduction. For a full introduction to shell, see this online course.

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Navigating Files using the Terminal

You cannot do anything in a terminal without knowing some commands. Different

terminals will expect different commands. Most Linux system, when you open the
Terminal it expects bash (for Bourne Again Shell) commands. This section will
introduce some key commands for looking at your files in the Terminal, like you
would using File Browser. The basic tasks covered will be: Launching the Terminal,
Checking the starting location, moving to a subfolder, listing the folders contents and
then creating a folder.

1. Launch Terminal
This can be found in Applications.

2. Check Starting Location

When using the terminal, you have a Current Working Directory. That is your
current location within the file system. This is like when you open a File Browser and
have a particular Folder open. You can also think of it as looking at one folder.

/ Root Directory
Director
In the terminal, enter the command :

etc home usr

pwd

Jack's Home Directory Jack

This Prints your Current Working Directory,

your current location in the file system. To start Eng

with, the Current Working Directory is usually

Year1 Year2
set to your Home directory.

P5comp P5mech
Notice that when you press Enter,
you will see a path returned. MyFrame.mat
ReadMe.txt Sess1 Sess2
In our example it would be:
/home/Jack
prog1.m prog2.m

A folder P5comp A file ReadMe.txt

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 3. List items in Current Folder
To list the content of the Current Working Directory enter

ls This is a lower case L followed by a lower case s

You should see a list of all the files and folders in your Home directory.
In our example, it would simply list one folder Eng.

4. Move into a Subfolder

To move around to look at other files/folders, use the command cd. It changes the
current working directory. Here we move to subfolder called Eng then list contents.

cd Eng
pwd
ls

In our example, we would see the current path printed (due to the pwd command):
/home/Jack/Eng
Then a list of folders Year1 and Year2.

5. Create a new folder

To create a new folder, use the command mkdir. This stands for make directory.

mkdir Year3
ls

You should then see the new folder listed after the list command.

Further Examples using List

We can use the ls command to list the contents of any folder on the file system. We
can specify the folder we want by using the folder's absolute path :

ls /
ls /usr
ls /home

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or the relative path of the folder:

ls Year1
ls Year1/P5computing

You can use the tilde ~ to indicate your Home directory:

ls ~
ls ~/Downloads

Two full stops .. indicates the parent folder. The folder one level above :

ls ..
ls ../..

Further Examples using cd

You can also use .. with the cd command:

cd Year1/P5computing
pwd
cd ..
pwd
cd /usr
pwd

The cd command on its own take you back to your home:

cd
pwd

Now make another new directory inside P5Computing using the command mkdir.

cd ~/Year1/P5computing
mkdir NewFolder

There are many more commands that you can use.

For a list of OS commands, see http://ss64.com/bash
For a comprehensive introduction to shell, see this self-paced online course.

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