BIOS 477/877 Bioinformatics and Molecular Evolution (3 credits)

[Last updated: January 12, 2025]

Unix/Linux/Programming Tutorials:

• Unix/Linux/Shell scripting tutorials
  • Ryan's Tutorials: a collection of introductory technology tutorials (including Linux, Bash scripting, HTML, Regular expression, and more) by Ryan Chadwick
  • The Linux Command Line (Internet Edition) by William Shotts (free PDF version downloadable)
  • Learning the Shell
  • Unix Tutorial by Kevin Heard (UC Berkeley)
  • Linux tutorial at javatpoint
  • Linux Beginner Tutorials at Linux.org
  • Linux Intermediate Tutorials at Linux.org
  • Linux Advanced Tutorials at Linux.org
    
    
  • learnshell.org interactive Shell Programming tutorial
  
  
• Programming tutorials (see also links listed above)
  
  • Software carpentry: teaching basic lab skills for research computing (including shell, python, R, Matlab, SQL and more)
  • Data carpentry: building communities teaching universal data literacy (domain specific, including genomics curriculum)
  
  [Python]
  
  • Python for beginngers @ phython.org
  • LearnPython.org interactive Python tutorial
  • The Python (v3.8.1) Tutorial at python.org
  • The Python (v2.7.17) Tutorial at python.org
  • Python Tutorial - GeeksforGeeks
  • Real Python Tutorials
  
  
  • Biopython.org
  • Biopython - basics @ Duke
  
  [Perl]
  
  • Unix and Perl Primer for Biologists GitHub by Keith Bradnam & Ian Korf (UC Davis)
  • Unix and Perl Primer for Biologists (PDF version)
    
    
  • Perldoc Tutorials at perldoc.perl.org
  • Perl Tutorial - Learn Perl With Examples - GeeksforGeeks
  • PerlMonks Tutorials
  • Perl Maven tutorial
  • Perl Tutorial
  • Modern Perl
  • Learn Perl: a free interactive Perl tutorial
  • Minimum Viable Perl
  
  
  • A Beginner's Introduction to Perl 5.10 (Part 1) by Doug Sheppard at perl.com
  • A Beginner's Introduction to Perl 5.10 (Part 2, Files and Strings) at perl.com
  
  [Ruby,Julia, etc.]
  
  • Ruby Documentation at ruby-lang.org
  • learnrubyonline.org free interactive Ruby tutorial
    (Many other tutorials for PHP, Java, HTML, etc. are also available from the above page)
  
  
  • A blog for learning Julia (a high-level, high-performance programming language for technical computing)
  • Tutorials at julialang.org
  
  [R]
  
  • The R Manuals at cran.r-project.org
  • Beginner's guide to R at Computerworld
  • R language for programmers
  • Tutorials for learning R at R-bloggers
  
  [MySQL]
  
  • MySQL tutorial at mysql.com
  • MySQL Tutorial at mysqltutorial.org
  
  [HTML, CSS, JavaScript]
  
  • Getting Started wiht the Web @ Mozilla Developer Network (MDN) Web Docs
  • HTML & CSS tutorial at learn-html.org
  • HTML tutorial at w3schools.com
  • HTML for Beginnigers The Easy Way: Start Learning HTML & CSS Today