Welcome to Introduction to Python!
Welcome to the Introduction to Python course, offered by UT Austin's CCBB as part of the 2nd annual Big Data in Biology Summer School!
Stephanie Spielman will be the lead instructor for this course. She is a 4th year Ph.D. student in the Ecology, Evolution, and Behavior program in Claus Wilke's lab. Check out her website here. Eleisha Jackson will be the TA for this course. Eleisha is a 3rd year Ph.D. student in the EEB program, also in Claus Wilke's lab.
Before class starts, it is absolutely essential that you get your computer up-and-running for programming! The necessary steps to take depend on what kind of computer you're using (Mac or PC; if you're using Linux, you should already be good to go). Follow the instructions, linked below, that match your computer.
PC/Windows Instructions (Note: PC setup can take 1-3 hours, so set aside enough time!). Here is a link for getting set-up with a popular text editor, gedit: https://help.ubuntu.com/community/gedit.
The Unix Tutorial for Beginners (http://www.ee.surrey.ac.uk/Teaching/Unix/) is a great resource and starting point for getting comfortable with the command-line environment
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 and Rosalind are excellent for learning and practicing python and bioinformatics skills. UT has an account with Rosalind, so if you're a UT student, simply log in with your standard UT credentials.
The book Practical Computing for Biologists (website: http://practicalcomputing.org) 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.
UT Biocomputing Google Group:
Post any questions and join in the conversation in the UT Biocomputing google group: https://groups.google.com/forum/#!forum/utbiocomputing
Day One: UNIX and Python Variables Day One Slides
Day One Exercises
Day One Cheatsheet
Day One UNIX Exercise Solutions and Day One Python Exercise Solutions
Day Two: Control Flow in Python Day Two Slides
Day Two Exercises
Day Two Cheatsheet
Day Two Exercise Solutions
Day Three: Functions Day Three Slides
Day Three Exercises
Day Three Exercise Solutions
Day Four: File Input/Output and Python Modules Day Four Slides
Day Four Exercises
Day Four Cheatsheet
Reference: Interpreting Error Messages
Reference: File Input/Output
Day Four Exercise Solutions
Supplement: BioPython BioPython Slides