Introduction to Scientific Computing Workshop at Botany 2017

Website: https://tlawrence3.github.io/Introduction-to-Scientific-Computing/

Workshop Program

• Introduction to the workshop - Slides - Download

• Introduction to linux

  1. Introduction to directory structures and command line
     • Slides
     • Worksheet
     • Commands covered: cd, mv, cp, rm, mkdir, less, ls
     • Concepts covered
       • Using the terminal
       • Directory structure
       • Absolute vs. Relative path
       • $PATH and where programs live
  2. Installing Software from package managers and source code
     • Slides
     • Worksheet
     • Concepts covered
       • Working with package managers
       • Compiling software
       • Using GitHub
  3. Manipulating text data on command line
     • Slides
     • Worksheet 1
     • Worksheet 2
     • Commands covered: wc,cut,paste,grep,head,tail,sort,uniq,tr
     • Concepts covered
       • File structure
       • Wildcards
       • Piping commands
  4. FAST and sequence data manipulation
     • Slides
     • Worksheet
     • Concepts covered
       • FAST(A/Q) data structure
       • FAST utilities
  5. Using a cluter
     • [Slides]
     • [Worksheet]
     • Concepts covered
  6. Wrap-up and introduction to documentation
     • Slides
     • Concepts covered
       • Documentation of computional workflow for manuscripts

• Introduction to Python

  1. Introduction to Python
     • Slides
     • Worksheet
     • Concepts covered
       • Variables
       • Printing
       • Slices
  2. Python: Loops, Lists, Files, and Modules
     • Slides
     • Worksheet
     • Concepts covered
       • Loops
       • List data structure
       • Reading files
       • Loading modules
  3. Python: Flow Control, Conditional Statements, and Dictionaries
     • Sildes
     • Worksheet
     • Concepts covered
       • If statements
       • Logical operators
       • Dictionary data structure