Schedule for Biology Students
| Dates | Tuesday | Thursday | Readings |
|---|---|---|---|
| Jan 4, 6 | What is bioinformatics? Intro to some useful web sites: Pubmed, Expasy, BLAST |
What computers can and cannot do; The problem of search |
Skim Chap 1 [Dum], Chap 2 [Dum] |
| Jan 11, 13 | Modular programming; getting to know the Python interpreter |
variables and types functions Assign Project 1 |
Chaps 1-2 [Python] |
| Jan 18, 20 | other people's functions assignment, substrings |
conditionals Assign Project 2 Project 1 due |
Chaps 3.6-3.9, 4.1-4.8 [Python] |
| Jan 25, 27 | conditionals | iteration Assign Project 3 Project 2 due |
Chaps 6.1-6.2, 7.1-7.9 [Python] |
| Feb 1, 3 | iteration | Midterm | Chap 7 [Dum] |
| Feb 8, 10 | How BLAST works scoring matrices Project 3 due Assign Group Project 1 |
more on BLAST FASTA and FASTX |
Chap 9 [Dum] Chap 8 [Python] |
| Feb 15, 17 | Multiple Sequence Alignment PCR and making primers ClustalW |
how ClustalW works similarity matrices |
Chap 13 [Dum] |
| Feb 22, 24 | phylogenetic trees Group Project 1 due Assign Final group project |
phylogenetic trees UPGMA |
Chap 13 [Dum] |
| Mar 1, 3 | Gene prediction | Gene prediction | Chap 5, pp. 145-153 Steve's extra reading |
| Mar 8, 10 | Gene prediction | data mining review for final Group Project 2 due |
extra reading |
| Exam Week | Final exam: Thurs, March 17, 8:30-10:30 in Butterfield 106 | ||