Note: This schedule is only a rough plan for the course. We will generally cover the topics in the order listed, but not always in the given amount of time.
I will add material as the course progresses and correct dates if we get too far ahead or behind. Thus, it is a good idea to recheck this page from time to time.Python: I will be doing all of the in-class coding in Python. It's not required that you use Python for the projects, but unless there's another language that
you are very familar with, using Python is highly recommended. There are some very good on-line Python tutorials:
www.learnpython.org - interactive tutorial, great for trying things out.
www.youtube.com/watch?v=N4mEzFDjqtA - one hour overview of Python, useful as a refresher.
www.tutorialspoint.com/python - step-by-step Python tutorial.
Occasionally we will discuss papers and topics not directly covered in the text.
| Week | Dates | Topic | Reading | Assignment | Comments and Topics |
|---|---|---|---|---|---|
| 1 | 1/9-1/13 | Introduciton to the course | Python tutorials as needed (a few options are listed above) | Classes start Wednesday, Jan. 11th. About the course, Python review; boxcar2d - evolve cars, picbreeder | |
| 2 | 1/16-1/20 | Python, Genetic Algorithms | en.wikipedia.org/wiki/Genetic_algorithm, www.doc.ic.ac.uk/~nd/surprise_96/journal/vol1/hmw/article1.html | No class Monday, Jan. 16th. Genetic algorithms: populations, selection, mutation. Python review: general syntax, lists, classes pet.py, pet2.py | |
| 3 | 1/23-1/27 | GA in Python | Writing a genetic algorithm in Python tamagotchi.py, tamagotchiPlus.py GA1.py, | ||
| 4 | 1/30-2/3 | Encoding | Project 1 | DNA to integers in Python GA2.py, GA3.py (Now with Crossover!), | |
| 5 | 2/6-2/10 | Pairwise Sequence Alignment | Ch. 2 | Sequence alignment using generated data GA4.py , decode1.py (put in the same folder as GA4 to "decode" "DNA", | |
| 6 | 2/13-2/17 | Pairwise Sequence Alignment | Ch. 2 | Sequence alignment using database data scoringMatrix.py, globalAlignment.py, globalAlignment.py (more general), | |
| 7 | 2/20-2/24 | Hidden Markov Models | Ch. 3 | No class Monday, Feb. 20. Introduction to HMM. How to program. repeatsAlignmentGeneral.py, Two files that are more interesting with the repeat alignment: seq1repeat.txt, seq2repeat.txt | |
| 8 | 2/27-3/3 | Hidden Markov Models | Ch. 3 | Using HMM mm.py, Project 2, | |
| 9 | 3/6-3/10 | Pairwise alignment with HMMs | Ch. 4 | ||
| 10 | 3/13-3/17 | Spring Break | |||
| 11 | 3/20-3/24 | Ch. 4 | viterbi.py, forward.py, | ||
| 12 | 3/27-3/31 | HMMs, Optimizaiton | Ch. 4 | ||
| 13 | 4/3-4/7 | HMMs | Progressive approaches and HMM. | ||
| 14 | 10/4-14/4 | Profile HMMs | Ch. 5 | Project 3, CS515 Project, | HiddenMMV1.py, HiddenMMV2.py, Ungapped, gapped, non-global HMMs |
| 15 | 4/17-4/21 | No Class | |||
| 16 | 4/24-4/28 | Multiple Sequence Alignment | Ch. 6 | ||
| 17 | 5/1-5/5 | Building Phylogenetic trees | Ch. 7 | ||
| 18 | 5/8-5/12 | Final exams |