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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.

Using SSH protocol to connect to a remote Linux machine

Using SCP protocol to transfer files

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

Mastering Linux command line and coreutils

Suggested tutorials/courses

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://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

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

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