Introduction to Computational Biology
This project is maintained by EDS@UGA
Each assignment is two weeks.
Lectures are Tues & Thurs, 9:30 - 10:45am at Robert C. Pharmacy 238.
Final exam will be Tuesday, May 2, from 8:00 - 11:00am in our usual lecture location.
| Date | Topic | Links |
|---|---|---|
| 1/5 | Course Introduction and pre-test | slides pretest |
| 1/10 | Command line basics | slides bash |
| 1/12 | Python syntax, variables, and operators | slides |
| 1/12 | Assignment 1 Released | |
| 1/17 | Control flow, loops, and data structures | slides |
| 1/19 | File I/O and Importing Modules | slides |
| 1/24 | Molecular Biology Primer | slides |
| 1/26 | Sequence Alignment | slides |
| 1/26 | Assignment 1 Due 11:59pm; Assignment 2 Released | |
| 1/31 | Advanced data structures with NumPy | slides |
| 2/2 | Dynamic Programming | slides |
| 2/7 | Dr. Alex Bucksch on developing DIRT with Python | slides |
| 2/9 | Dr. Shan-ho Tsai on high-performance scientific computing with the GACRC | slides |
| 2/9 | Assignment 2 Due 11:59pm; Assignment 3 Released | |
| 2/14 | Functions | slides |
| 2/16 | Introduction to Probability | slides |
| 2/21 | Hidden Markov Models | slides |
| 2/23 | Using Biopython | slides |
| 2/23 | Assignment 3 Due 11:59pm | |
| 2/28 | Dr. Bodo Linz on analyzing clades of Bordetella species | slides |
| 3/2 | MIDTERM EXAM | |
| 3/5 - 3/12 | Spring Break | |
| 3/14 | Midterm Exam Postmortem Review | |
| 3/16 | No Lecture | project |
| 3/21 | Dr. Liming Cai on profile HMMs for multiple sequence alignment | |
| 3/23 | Computational Modeling | slides |
| 3/28 | Computational Structural Biology | slides |
| 3/30 | Molecular Dynamics | slides pymol |
| 4/4 | Introduction to Computer Vision | slides |
| 4/6 | Bioimaging | slides |
| 4/7 | Final Project Proposals Due 11:59pm | |
| 4/11 | Visualization with matplotlib | slides |
| 4/13 | Dr. Rene Ranzinger on open source projects in biological research | slides |
| 4/17 | Assignment 456 Released | |
| 4/18 | Clustering and machine learning with scikit-learn | slides |
| 4/20 | Multitasking with multiprocessing and joblib, and process control with subprocess | slides |
| 4/25 | Final Project Presentations | materials |
| 4/26 | Assignment 456 Due 11:59pm | |
| 5/2 | FINAL EXAM | |
| 5/2 | Final Project Deliverables Due 11:59pm | |