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This is an applied course in computation for Bioinformatics. We will cover the UNIX environment and philosophy, including using the shell and command line tools effectively. We will learn about using version control effectively to both for provenance of our own work and for working collaboratively. We will cover good programming practices such as automated builds and testing. We will learn to program in Python, and learn good design principles of both functional and object oriented programming. We will learn to store and query data in databases. We will learn efficient approaches to work with large amounts of numerical data. Finally, we will apply these skills in a collaborative data intensive bioinformatics project.
Instructors : James Taylor (james.taylor at emory.edu) and Tim Read (tread at emory.edu)
Meeting Location : 1133 O. Wayne Rollins Building
Meeting Time : Thursdays, 3:15 PM
Week 1: The Unix Shell; Preliminaries, Hey, I want to do this on my Mac, Part 1
Week 2: Version control with Git and Github; Part 1 and Part 2
Week 3: Python basics, Data structures in Python
Week 4: Strings and IO, Flow Control, Functions and Modules
Week 5: Object oriented programming, Debugging, Testing
Week 6: The Python standard library and PyPI, Numerical programming with Numpy, Plotting with Matplotlib
Week 7: First Exercise
Week 8: First Exercise continued
Week 9: Second Exercise
Week 10: Third Exercise
Week 11: Fourth Exercise
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Week N: Databases and SQLite
Week N+1: SciPy, Scikits, and Pandas
Week N+2: BioPython
...