Resources

  • 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.

  • 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 couple of ~20 minute YouTube videos introducing GitHub: one from LearnCode.academy and one from GEEKBLOGTV.

  • Instructor office hours will be held Tuesdays from 9:30 - 11:15AM in Doyle 304. 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. You may also email the TA, Thomas Hatzopoulos thatzopoulos@luc.edu, with questions. For programming help, tutoring hours are also available from the Computer Science Department, I recommend attending Abdul Zakkar’s sessions. When you encounter a problem, error message, etc., google it first!