About
NOTE: This site will be moving soon! Please update your bookmarks to https://sjspielman.github.io/bdib2018_python/.
Welcome to the Introduction to Python course, offered by UT Austin's CCBB as part of the 5th annual Big Data in Biology Summer School! Stephanie Spielman will be the course instructor. She is currently a postdoc at Temple University and will be joining Rowan University's Department of Biological Sciences as Assistant Professor in Fall 2018. The TA for this course will be Dariya Sydykova, who is currently a PhD candidate in the Wilke lab here at UT.
In this course, we will learn basic concepts in scientific computing through the lens of the Python programming language, specifically using the version Python3. You will be introduced to the following concepts:
- Run Python code from the console
- Create and run Python scripts
- Control flow with if/else statements and for-loops
- Writing custom functions
- Reading and writing text files
- Regular expressions and text parsing
Materials
Resources
- Google is easily the most valuable resource for figuring things out. If you encounter an issue, chances are somebody else has also encountered it and has asked about it. Googling your error messages is one of the best debugging strategies there is. In particular, try to find links to the website http://www.stackoverflow.com. This forum-based website has all the answers, possibly literally (but they might be super snarky).
- The popular websites Code Academy, Rosalind, and Lynda are excellent for learning and practicing python and bioinformatics skills. UT has an account with Rosalind and Lynda, so if you're a UT student, simply log in with your standard UT credentials.
- This paper, An Introduction to Programming for Bioscientists: A Python-based Primer, provides a great resource for beginning Python programming.
- The book Practical Computing for Biologists by Haddock and Dunn provides a really thorough, entry-level overview of introductory computing concepts, including (but not limited to!) Unix and Python. The book's accompanying website is also regularly updated with important tips, examples, and errata.
- If you want to go past just Python programming, this UNIX Tutorial for Beginners is a great resource and starting point for getting comfortable with the command-line environment.