BIOINFORMATICS LAB Episode I - Unix · 2019-04-08 · /etc UNIX system configuration and...

BIOINFORMATICS LAB

Episode I - Unix

Federico M. Giorgi, PhD

Department of Pharmacy and Biotechnology

First Cycle Degree in Genomics

2/60

Course Layout

CFUs: 4

Hours: 60

Lessons: 15

Part I (~Days 1-8): Bioinformatics on UNIX

Part II (~Days 9-15): Bioinformatics on R

TA: Chiara Cabrelle

3/60

Type:

• Oral

• Pick a tool from a list I will give you (try not to bring all the same one ☺ )

– Make a short presentation (one to ten slides) about it

• Questions on what we did in the Lab

• Material on IOL and/or here: https://giorgilab.org/lessons/

• Final Score: 1/3 this course, 2/3 Prof. Ferre’s course

Dates:

• June 26th 2019

• July 18th 2019

Exam

4/60

Resources

https://giorgilab.org/lessons/

• Final slides (Lessons + Exercises): https://iol.unibo.it

• Ongoing (Lessons +Exercises):

https://giorgilab.org/lessons/

https://iol.unibo.it/

5/60

• Dr. Antonio Colaprico

– University of Miami, FL, USA

– Bioinformatics Tools to understand

molecular changes

– 18th April (Thursday)

• Dr. Andrew Holding

– CRUK, University of Cambridge, UK

– ChIP-Seq data analysis

– 13-17th May

Guest Teachers

6/60

• What did Theory Course say?

• Definition is not clear

• My definition

– Doing Biological Research with computational tools

– Make sense of the huge vastity of Biological Data

– Problem Solving

What is Bioinformatics?

7/60

Purpose of this course

To turn you into hardcore hands-on Bioinformaticians

Biologists give you a task that requires computational skills? You

can solve it.

You will learn cutting edge tools that are used today in every

Bioinformatics Lab in the World

8/60

Purpose of this course

Search for

“Bioinformatics”

found 950 jobs

To turn you into hardcore hands-on Bioinformaticians

Biologists give you a task that requires computational skills? You

can solve it.

You will learn cutting edge tools that are used today in every

Bioinformatics Lab in the World

10/60

Why is Unix important for Bioinformatics?

• Work on huge (>1GB) files

• peek at them (head, tail, less, wc)

• modify them (sed, vim)

• mangle them (sort, cut)

• Build simple and complex pipelines ( | )

• Repeat custom analysis with one click

• Most everyday bioinfo programs run only on Unix (samtools, hisat, blast)

• Free

Unix

11/60

• Invented in 1969 by the Bell Labs research center

• It comes from “Unics”

Uniplexed Information and Computing Service

• Unix invented

• Multi-tasking

• Multi-Users

• Hierarchical file system (directories)

• Multi-platform

• Linux is Unix

• Linux is a modified highly successful Unix developed by Linus Torvalds

• Several Unix distributions:

Some History on Unix

12/60




• Unix invented

• Multi-tasking

• Multi-Users


• Multi-platform

• Linux is Unix




13/60




• Unix invented

• Multi-tasking

• Multi-Users


• Multi-platform

• Linux is Unix




14/60




• Unix invented

• Multi-tasking

• Multi-Users


• Multi-platform

• Linux is Unix




15/60

Some ways to run Unix:

• Install it on your PC or server (hardcore)

• Install it on your PC alongside Windows (dual-boot)

• Mac-OS X is a Unix-like system, most commands will work in its terminal

• Install it inside Windows (Microsoft Store introduced it in 2018)

• Virtualization (VMWare, VirtualBox)

Let’s try Unix

16/60

• Click on Oracle VM VirtualBox Manager

• Start it!

• Ignore warnings!

• You should see this:

Let’s turn Unix On

17/60

Welcome to Unix!

18/60

Your Unix Environment

You can break it, but please don’t

Tech Guru Info• Xubuntu 18.04.1 with Guest Additions

running onVirtualBox 6.4.0• userid student• password 4genomics4

The whole file system

19/60




Your personal space,

the Home File System

20/60




The Course Folder

21/60

Your Unix File System

/

bin sbin hometmp lib usretc

Directory

Typical Contents

/ The "root" directory

/bin Essential system programs

/sbin Superuser system utilities (for performing system administration tasks)

/etc UNIX system configuration and information files

/tmp Temporary file storage space (can be used by any user)

/libProgram libraries (collections of system calls that can be included in programs by a compiler) for low-level system utilities

/usr Higher level user programs

/homeUser home directories containing personal file space for each user. Each directory is named after the login of the user.

/dev Hardware devices

/media Removable hardware devices

/proc A pseudo-filesystem for each active program

“root”

22/60


/ “root”


Directory

Typical Contents












student~

“tilde”, an alias

for your home

23/60


/ “root”


Directory Typical Contents












student

DesktopDownloads Pictures Programsgenomics2019hg38

annotation assembly ngs seqs presentations

24/60




Tools we will use in

the next days

25/60




The Terminal

The Terminal is a Unix shell

• Command-line environment

• Not a Graphical User Interface Environment

• Double click on it!

26/60

UNIX Terminal Exercises(Open exercises_01_unix.pdf)

27/60

• Please turn it off nicely

Turn Unix off CORRECTLY

Click on the mouse

28/60



Click Again

29/60



Last Click

www.giorgilab.org

Federico M. Giorgi, PhD

Department of Pharmacy and Biotechnology

[email protected]

BIOINFORMATICS LAB Episode I - Unix · 2019-04-08 · /etc UNIX system configuration and...

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