Introduction to Computational Biology
This project is maintained by EDS@UGA
Lecture and assignment schedules are subject to change without notice, because reasons.
Lecture videos and their materials are released (eLC for videos, this website for materials) on Tues & Thurs around 3:30pm.
Live mybinder integration with the published lecture material can be accessed here (may take several minutes to load if an image needs to be built).
Final exam will be Thursday, April 30, from 3:30 - 6:30pm. It will be on JupyterHub; it will be released at 3:30pm sharp and expected to be submitted by 6:30pm. Like the midterm, it will be open-everything, but keep the time limit in mind--you are responsible for making sure you submit on time. Please contact me in advance if you need to make different arrangements (e.g., longer testing interval, breaks during the exam, different day or time, etc); I'm more than happy to accommodate, I just need to know.
| Date | Topic | Links |
|---|---|---|
| 1/7 | Welcome to Computational Biology, pre-test | html pdf ipynb pretest |
| 1/9 | Introduction to the Command Line | html pdf ipynb |
| 1/9 | Assignment 1 Released | |
| 1/14 | Python syntax, variables, and operators | html pdf ipynb |
| 1/16 | Conditionals, loops, data structures | html pdf ipynb |
| 1/21 | numpy, modules, file I/O | html pdf ipynb |
| 1/23 | Molecular biology primer | html pdf ipynb |
| 1/23 | Assignment 1 Due 11:59pm ; Assignment 2 Released | |
| 1/28 | Sequence alignment | html pdf ipynb |
| 1/30 | Functions | html pdf ipynb |
| 2/4 | Dynamic programming | html pdf ipynb |
| 2/6 | Introduction to Probability | html pdf ipynb |
| 2/6 | Assignment 2 Due 11:59pm ; Assignment 3 Released | |
| 2/11 | Guest Lecture: Dr. Bodo Linz | pdf pptx |
| 2/13 | Hidden Markov Models | html pdf ipynb |
| 2/18 | Guest Lecture: Dr. Bodo Linz | pdf pptx |
| 2/20 | Computational modeling | html pdf ipynb |
| 2/20 | Assignment 3 Due 11:59pm | |
| 2/25 | MIDTERM LAB | MLC 368 computer lab |
| 2/27 | Midterm post-mortem review | |
| 3/3 | Visualization with matplotlib | html pdf ipynb |
| 3/5 | Structural biology | html pdf ipynb |
| 3/5 | Assignment 4 Released | |
| 3/9 - 3/13 | Spring Break | |
| 3/16 - 3/20 | Canceled | |
| 3/23 - 3/27 | Canceled | |
| Bonus | Molecular dynamics analysis with prody | html pdf ipynb |
| 3/31 | Parameter estimation | html pdf ipynb |
| 4/2 | Introduction to computer vision | html pdf ipynb |
| 4/2 | Assignment 4 Due 11:59pm ; Assignment 5 Released | |
| 4/2 | Final Project Proposals Due 11:59pm | |
| 4/7 | Bioimaging I with scikit-image | html pdf ipynb |
| 4/9 | Bioimaging II with opencv | html pdf ipynb |
| 4/14 | Clustering and machine learning with scikit-learn | html pdf ipynb |
| 4/16 | Open Science | html pdf ipynb |
| 4/16 | Assignment 5 Due 11:59pm | |
| Bonus | High Performance Computing (HPC) on the GACRC Sapelo2 Cluster | |
| 4/21 | Final Project Presentations |
Chenxiao Li Yulong Wang |
| 4/23 | Final Project Presentations |
Benjamin Hoffman Ryo Tamura Shivani Arbat |
| 4/30 | FINAL LAB | 3:30-6:30pm, JupyterHub |
| 4/30 | Final Project Deliverables Due 11:59pm | |