Date |
Topic |
Assigned |
Due |
Jan 15 |
Bioinformatics overview; Syllabus; Unix, Perl and Editors
|
System Setup Read Ch. 1-2 |
|
17 |
String Manipulation (Chapter 3) |
|
|
22 |
Regular Expressions (Chapter 4) |
HW 1 |
|
24 |
Regex (Chapter 4), continued (plus some from Chapter 12) |
HW 2 |
|
29 |
Calculations and Randomness (Chapters 5 and 13) |
|
|
31 |
Control Structures (Chapter 6) |
HW 3 |
|
Feb 5 |
Control Structures, cont., and Subroutines (Chapter 7) |
HW 4 |
|
7 |
Reading Files (Chapter 8) and Arrays (Chapter 9) |
HW 5 |
|
12 |
Arrays, cont. |
|
|
14 |
Sequence analysis with EMBOSS (use dottup for dot plots) |
Review 1 |
|
19 |
|
||
21 |
|
|
|
26 |
Project Work Day |
|
|
28 |
Project Presentations |
Project 1 |
|
Mar 1-9 |
SPRING BREAK |
||
Mar 11 |
Genes and promoters |
|
|
13 |
Genes and promoters PWM Math Minute |
HW 6 |
|
18 |
Sequence evolution models |
|
HW 6 |
20 |
Phylogenetic trees |
|
|
25 |
HOLIDAY |
||
27 |
Phylogenetic trees, cont. |
|
HW 7 |
April 1 |
Comparative genomics |
|
|
3 |
Comparative genomics GRIMM |
|
|
8 |
Microarray data analysis
|
|
|
10 |
Microarray data analysis, cont. |
|
Review 2 |
15 |
Protein structure informatics
|
|
|
17 |
RNA structure prediction |
|
|
22 |
Project Work Day (no class) |
|
|
24 |
Project Work Day (no class) |
|
|
29 |
Project Presentations |
|
Project 2 |
May 1 |
Wrap up, course evaluations |
|
|
6 |
No Class |
Final Exam |
|
12 |
Exam due at 5:00 p.m. |
|
Final Exam |