Schedule - Advanced Programming & Database Management for Biologists

Week 1 The Shell

• Introducing the Shell
• Files and Directories
• Creating Things
• Pipes and Filters
• Loops
• Shell Scripts

Assignment 1

Week 2: Version Control

• Introduction
• Collaborating
• Conflicts

Assignment 2

Week 3: Programming Basics in Python

• Introduction
• Modularization & Documentation
• First Class Functions

The above is a fairly rapid overview. If you’d like a little more detail take a look at:

• Intro to Python: Analyzing Patient Data
• Intro to Python: Creating Functions
• Intro to Python: Repeating Actions with Loops
• Intro to Python: Making Choices

Assignment 3

Week 4: Scientific Programming in Python

• Numpy
• Pandas
• Matplotlib

Assignment 4

Week 5: Data Structures

• Intro
• Tuples
• Storage
• Dictionaries
• Aliasing

Assignment 5

Week 6 Databases using SQL - Queries

• Selecting Data
• Sorting and Removing Duplicates
• Filtering
• Calculating New Values
• Missing Data
• Aggregation
• Combining Data

Assignment 6

Week 7 Databases using SQL - Interfacing w/Python, Creating and Modifying, Database structure

• Python + SQLite
• Programming with Databases
• Creating and Modifying Data

Assignment 6

Week 8: More Version Control & Working with Servers

• Version Control: Branching
• Version Control: GitHub Flow
• Secure Shell
• Job Control

Week 9: Defensive Programming and Debugging

• Debugger
• Why you need to test
• Testing (including Exception Handling)

Assignment 7

Week 10: Oriented Programming

• Classes & Objects: Introduction
• Classes & Objects: Basics
• Classes & Objects: Interfaces
• Classes & Objects: Inheritance

Assignment 8

Week 11: Program Design & Regular Expressions

• Regular Expressions: Introduction
• Regular Expressions: Operators
• Regular Expressions: Mechanics
• Regular Expressions: Patterns
• Regular Expressions: More Tools
• Code Like Pythonista (W)

Assignment 8

Weeks 12: Project

• Project

Weeks 13: Project

• Project

Week 14: Project No class Wednesday or Friday - Thanksgiving

• Project

Week 15: Project Projects Due on Friday

• Project

Optional topics to introduce during weeks 12-15

• Concurrency (multiprocessing)
• Scientific Python: Numpy, Scipy, Matplotlib
• Biopython
• R in Python
• Packaging (setuptools, py2exe)