Programming For Biology 2025

programmingforbiology.org

Instructors
Simon Prochnik
Sofia Robb
Eric Ross
Jessen Bredeson

• Big Picture
  • Why?
  • Helpful Tips
• Unix 1
  • Unix Overview
    • What is the Command Line?
  • The Basics
    • Logging into Your Workstation
    • Bringing up the command line
    • OK. I've Logged in. What Now?
    • Command Line Prompt
    • Issuing Commands
    • Command Line Editing
    • Wildcards
  • Directories and how they are organized
    • Home Sweet Home (your home directory ~)
    • Changing to a New Directory
    • Absolute and relative paths
  • Essential Unix Commands
    • Getting Information About Commands
    • Finding Out What Commands are on Your Computer
    • Arguments and Command Line Switches
    • Spaces, tabs and newline Characters
  • Useful Commands
    • Manipulating Directories
    • Reading files
    • Analyzing, processing files
    • Editing files
    • Connecting to other computers
    • Standard I/O and Redirection
    • A Simple Example
    • Redirection Meta-Characters
    • Filters, Filenames, and Standard Input
    • Standard I/O and Pipes
    • More Pipe Idioms
  • Permissions
  • More Unix
  • Link to Unix 1 Problem Set
• Unix 2
  • Text Editors
  • Introduction to vi
    • Getting Started with vi
    • Creating, Writing, And Saving a File Walk through
    • Common Activities and vi Commands
    • Other Useful Tips
    • Mug of vi
  • Visual Studio Code
    • What is VSCode
    • VSCode interface
    • How Does VSCode Work
    • Documentation
  • Git for Beginners
    • The Big Picture
      • Collaboration
      • Storing Versions
      • Restoring Previous Versions
      • Backup
      • The Details
    • The Basics
    • SSH Keys
    • Adding a new SSH key to your GitHub account
    • Generating a new SSH KEY
      • Adding your SSH key to the ssh-agent
    • Adding a new SSH key to your GitHub account
    • Paste into your GitHub account
    • Do this to ensure that you do not encounter errors by attempting to add files that are too large
    • One-time Git setup
    • Creating a new repository
      • Keeping track of differences between local and remote repositories
      • Deleting and moving files
    • Get a copy of file on your remote
      • Tips
    • Cloning a Repository
      • Bringing Changes in from the Remote Repository to your Local Repository
    • Links to slightly less basic topics
    • Link To Unix 2 Problem Set
• Python 1
  • Official Python Documentation
  • Python Overview
  • Running Python
    • Interactive Interpreter
    • Python Scripts are Text Files
    • Running Python Scripts
    • A quicker/better way to run python scripts
  • Syntax
    • Python Variable Names
    • Naming conventions for Python Variable Names
    • Reserved Words
    • Lines and Indentation
    • Comments
    • Blank Lines
  • Data Types and Variables
    • Numbers and Strings
    • Lists
    • Tuples
    • Dictionaries
    • Command line parameters: A Special Built-in List
    • What kind of object am I working with?
  • Link to Python 1 Problem Set
• Python 2
  • Operators
    • Arithmetic Operators
    • Assignment Operators
    • Comparison Operators
    • Logical Operators
    • Membership Operators
    • Operator Precedence
  • Truth
    • Use bool() to test for truth
  • Logic: Control Statements
    • If Statement
    • if/elif
  • Numbers
    • integer
    • floating point number
    • complex number
    • Conversion functions
    • Numeric Functions
  • Comparing two numbers
  • Link to Python 2 Problem Set
• Python 3
  • Sequences
  • What object-specific functions or "methods" go with my object?
  • Strings
    • Quotation Marks
    • Strings and the print() function
    • Special/Escape Characters
    • Concatenation
    • The difference between string + and integer +
    • Determine the length of a string
    • Changing String Case
    • Find and Count
    • Replace one string with another
    • Extracting a Substring, or Slicing
    • Reverse a string or a list
    • Other String Methods
  • String Formatting
    • The f-string mini-language
    • Summary of special formatting symbols so far
    • What's the point?
  • Link to Python 3 Problem Set
• Python 4
  • Lists and Tuples
    • Lists
    • Tuples
    • Back to Lists
    • Accessing Values in Lists
    • Changing Values in a List
    • Extracting a Subset of a List, or Slicing
    • List Operators
    • List Functions
    • List Methods
    • Building a List one Value at a Time
  • Loops
    • While loop
    • While Loop Syntax
    • Infinite Loops
    • For Loops
    • For Loop Syntax
    • PCR Program Loop Example
    • Loop Control
    • Loop Control: Break
    • Loop Control: Continue
    • List Comprehension
  • Link to Python 4 Problem Set
• Python 5
  • Dictionaries
    • Creating a Dictionary
    • Accessing Values in Dictionaries
    • Changing Values in a Dictionary
    • Accessing Each Dictionary Key/Value
    • Building a Dictionary one Key/Value at a Time
    • Checking That Dictionary Keys Exist
    • Dictionary Operators
    • Building a Dictionary one Key/Value at a Time using a loop
    • Sorting Dictionary Keys
    • Dictionary Functions
    • Dictionary Methods
    • Sorting a Dictionary by values in a for loop
  • Sets
    • Set Operators
    • Set Functions
    • Set Methods
    • Build a dictionary of NT counts using a set and loops
  • Link to Python 5 Problem Set
• Python 6
  • I/O and Files
    • Writing to the Screen
    • Reading input from the keyboard
    • Reading from a File
    • Open a File
    • Reading the contents of a file
    • Opening a file with with open() as fh:
    • Writing to a File
    • Building a Dictionary from a File
  • Link to Python 6 Problem Set
• Python 7
  • Regular Expressions
    • Individual Characters
    • Character Classes
    • Anchors
    • Quantifiers
    • Variables and Patterns
    • Either Or
    • Subpatterns
    • Using Subpatterns Inside the Regular Expression Match
    • Using Subpatterns Outside the Regular Expression
    • Get position of the subpattern with finditer()
    • Subpatterns and Greediness
    • Practical Example: Codons
    • Truth and Regular Expression Matches
    • Using Regular expressions in substitutions
    • Using subpatterns in the replacement
    • Regular Expression Option Modifiers
  • Helpful Regex tools
  • Link to Python 7 Problem Set
• Python 8
  • Data Structures
    • List of lists
    • Lists of dictionaries
    • Dictionaries of lists
    • Dictionaries of dictionaries
    • Building Complex Datastructures
  • Link to Python 8 Problem Set
• Python 9
  • Exceptions
    • try/except/else/finally
    • Getting more information about an exception
    • Raising an Exception
    • Creating Custom Exceptions
  • Link to Python 9 Problem Set
• Python 10
  • Functions
    • Defining a Function that calculates GC Content
    • Using your function to calculate GC content
    • The details
    • Naming Arguments
    • Keyword Arguments
    • Default Values for Arguments
    • Lambda expressions
  • Scope
    • Local Variables
    • Global
  • Modules
    • Getting information about modules with pydoc
    • os.path
    • os.system
    • subprocess
      • Capturing output from a shell pipeline
      • Capturing output the long way (for a single command)
      • Check the exit status of a command
      • Run a command that redirects stdout to a file using python subprocess
    • sys
    • re
    • collections
    • copy
    • math
    • random
    • statistics
    • glob
    • argparse
  • Many more modules that do many things
  • Your own modules
  • Link to Python 10 Problem Set
• Python 11
  • Classes
    • You have been using classes to create objects
    • attributes and methods
    • Creating a Class
    • Creating a DNARecord Object
    • Retrieving attribute values
    • Using class methods
    • Getting data into a new instance of our class
      • init
  • Link to Python 11 Problem Set
• Workshops and Overviews
  • Pipelines -- Simon Prochnik
  • Package Managers -- Jessen Bredeson
  • BioPython -- Sofia Robb
  • Pytest Testing -- Jessen Bredeson
  • Ethics and Responsibility in Bioinformatics -- Simon Prochnik
  • Coding with AI -- Simon
  • RNAseq -- Brian Haas
  • Protein Homology -- Bill Pearson