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Prepare4Bioinformatics.md

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Curriculum to Prepare for Computation in Bioinformatics

Become familiar with Unix/Linux

  1. Gain access to a Unix/Linux computer

    1. Existing server
      If there is a server available, ask the systems administrator to create a user account for you. You will likely need to use secure shell (ssh) to access the server.

    2. Virtual instance of Linux (Ubuntu) on VirtualBox
      VirtualBox is a virtualization server from Oracle. Please follow the instructions here

    3. MacOS – terminal

      1. The underlying operating system of MacOS is a variant of Unix derived from the NEXT OS (built as a variant of UNIX without the proprietary UNIX constraints, not unlike Linux).
      2. One can try to follow the Bash exercises in the Mac terminal (bash is usually the default shell). If you experience problems, type “echo $0” and record the name of the shell. If it is not bash, it might be best to install VirtualBox and Ubuntu.

  2. Practice using commands in the Bash shell

    1. There are some resources below. Please try to work through examples and exercises in these resources. Try typing the commands if there is an example output. Some important commands are:

      1. cd – change directory
      2. ls – list directory contents
      3. pwd – present working directory (where am I?)
      4. echo – usually “echo $varname”, prints the content of the variable varname.
      5. date – prints the current date (and time) to the screen
      6. cat – concatenate. cat filename will print the contents of the file. cat can also be used to append files together.
      7. tree – not always installed by default. Displays directory in a text-based tree structure
      8. mv – move a file, also acts to rename a file
      9. mkdir – create a directory
      10. rm – remove a file
      11. rmdir – remove a directory (if empty)
      12. touch – create a file (if name doesn’t exist) or update the file to the current time. Also create a file with a specific date and time.
      13. exit – leave the current shell (closes shell and terminal window)

Bash Resources

Elementary Bash:

Bash for beginners (start here) Intro to Bash syntax and tools

Bash guide for beginners

Bash Guide for Beginners (find on the page: different formats available)

Bash FAQ (Greg’s Wiki) (see appropriate tab)

Bash Guide (Greg’s Wiki) (see appropriate tab)

Bash Reference manual:

GNU Bash Reference

Bash Scripting:

Introduction to bash scripting

Ryan’s Bash Scripting Tutorial

Bash scripting cheatsheet

Advanced Bash Scripting Guide (find on the page: different formats available)

Learn R

  1. Download and install R (https://cran.r-project.org/)

  2. Download and install RStudio (https://posit.co/downloads/)

  3. Install the tidyverse set of packages (https://www.tidyverse.org/packages/) in your R. Note that on Windows, it is often easiest to install everything as a personal installation, i.e., in your userspace. If you install R, RStudio and the packages for everyone on the computer, you need to run the RGUI as administrator.

  4. Some beginning resources (free):

    1. https://www.rpubs.com/meldataaa/BeginnersGuidetoR

    2. https://rpubs.com/jbaumann3/994268

    3. https://rpubs.com/acolumbus/how-to-get-started-with-r

    4. https://rpubs.com/ShaniahA/946625

    5. https://rpubs.com/JianKuang/132393

    6. https://bookdown.org/rwnahhas/IntroToR/ (NOTE: You can look around bookdown.org for more books on R)

  5. The R for Data Scientists book (https://r4ds.had.co.nz/) FREE ONLINE

  6. Handy “cheat sheets” (2-page summaries) for Rstudio and tidyverse packages: https://posit.co/resources/cheatsheets/

Learn Python

This is not required but can be useful

  1. Download python and install https://www.python.org/downloads/

  2. Download an integrated development environment (IDE):

    1. PyCharm (https://www.jetbrains.com/pycharm/download/)

    2. PyDev (plugin for eclipse; https://www.pydev.org/)

    3. Visual Studio (https://visualstudio.microsoft.com/vs/community/; https://visualstudio.microsoft.com/vs/features/python/)

    4. Spyder (https://www.spyder-ide.org/)

  3. Learning Resources

    1. Tutorialspoint (https://www.tutorialspoint.com/python/index.htm)

    2. Python Tutorial (https://www.pythontutorial.net/)

    3. Other websites: https://medium.com/javarevisited/10-free-python-tutorials-and-courses-from-google-microsoft-and-coursera-for-beginners-96b9ad20b4e6