Python for Biologists is freely available online and designed for complete beginners. It’s a practical introduction to Python because it uses biological examples. Advanced Python for Biologists is a book that dives deeper by discussing techniques for building larger programs, including recursion and trees, complex data structures, object-oriented Python, functional Python, comprehensions, and exceptions.

Biopython is a set of freely available tools for biological computation written in Python by an international team of developers.

Python debugger (import pdb) intro videos: ~ 6 min and ~ 15 min

In class, we will solve some introductory problems using ROSALIND, but the resource includes many advanced problems that get more challenging as you move down each topic list. Check out those of interest to you and build your skills. You may get ideas for your group project by doing these exercises.

Software carpentry and Data Carpentry have many lessons designed for research computing in Python, R, Git, Unix Shell, etc.

Resources for statistical computing in R.

A straight-forward GitHub tutorial written by a computational biologist that will get you started.

A ~20 minute YouTube videos introducing GitHub from LearnCode.academy.

Instructor office hours will be held Tuesdays from 12:30 - 2:30PM in LSB 324. To meet at a time other than this, you must email me at hwheeler1@luc.edu to schedule a day and time in advance; I cannot meet with students that just “drop by”. Another route to get assistance is to ask questions via email. I will do my best to respond to emails within 24 hours. For programming help, tutoring hours are also available from the Computer Science Department. When you encounter a problem, error message, etc., google it first!