Crash course on IT for IntBio students

Mastering Linux & Command Line

Getting access to a Linux Machine

You'll need an acceess to a Linux machine.

Option 1: Install Ubuntu as a Virtual Machine https://www.virtualbox.org
Option 2: Live Ubuntu USB stick https://www.howtogeek.com/howto/linux/create-a-bootable-ubuntu-usb-flash-drive-the-easy-way/
Option 3: Connect remotely to a server using SSH protocol. Server address, username and password will be provided. Alternatively, you can launch a server in Amazon cloud, see here https://youtu.be/GQCIKXwLudg (is free for the first year, but requires a credit card for registration).

Using SSH protocol to connect to a remote Linux machine

To connect to a Linux machine you'll need its address, username, password or security key.
On Windows install PuTTy https://www.putty.org , https://youtu.be/1wQ8wQfa7lw
Mac and Linux have built in SSH client ssh username@server_address
Forwarding graphics.
- On Linux/Mac just add -X option to ssh command. Mac install XQuartz beforehand https://www.xquartz.org .
- On Windows - install X server https://sourceforge.net/projects/xming/ , launch, in PuTTy enable X11 forwarding.
  Type xclock in terminal to check if it works.

Using SCP protocol to transfer files

Windows: Install WinSCP https://winscp.net/eng/download.php
Linux/Mac: use scp command or Mindnight Commander https://midnight-commander.org .

Using SSH key authentication

Here is an exmaple public key in Linux SSH format.
Converting Linux SSH key format to PuTTy format can be done using PuTTYgen Explained here
Generating your own SSH keys: Windows - PuTTYgen, Linux/Mac - use ssh-keygen command.
Connect using SSH key instead of a password:
- Linux/Mac ssh -i samplekey.pem username@server_address , set correct permission before chmod 400 samplekey.pem
- PuTTy - see here last image.

Using X2GO

Using X2Go to conntect to a Linux machince that has X2Go installed. Video (in Russian) on using x2Go.

Mastering Linux command line and coreutils

List of notions and commands to be familiar with. Study yourself or use tutorials below.

Suggested tutorials/courses

Into to basic terminal commands here.
Mastering Linux Shell http://swcarpentry.github.io/shell-novice/
Introduction to Linux - this course by Bioinformatics Institute will make you familiar with basics of Linux.

Package management systems

apt-get tutorial here
For enabling the universe repository see here. It contains many community maintained programs.

Useful programs to be familiar with

GNUplot
ffmpeg
ImageMagick

Some examples and problems for solving

A bash script to count and plot the number of baby names here.

Quiz

Check that you are familiar with all the commands here.

Introduction to Git/ GitHub

http://github.com

http://swcarpentry.github.io/git-novice/

Youtube tutorials

GitHub

GitHub Learning Lab - the Learning Lab bot

Making your lab web-page via GitHub, here are instructions (in Russian).

Git Cheat Sheet

Literature management

Literature searching
Literature reference managers

Introduction to Python

https://github.com/intbio/PythonIntro
Basic Python / Jupiter notebooks http://www.intbio.org/CBsem/19Feb2018_IT.html

http://swcarpentry.github.io/python-novice-inflammation/

http://swcarpentry.github.io/python-novice-gapminder/

Data analysis and plotting

Introduction to R

Introduction to LaTeX

Introduction to Web technologies