Wk/Date |
|
Topic |
|
Reading |
|
Resources |
|
Remarks / Due / Exam |
|
|
|
|
|
|
|
|
|
1
1/10, Mon |
|
Introduction to bioinformatics
Perl programming |
|
Lesk, Ch. 1
Pierce, Perl, Ch. 1 |
|
== self ==
:: my old Perl page ::
:: Notepad ++ :: |
|
You need to take notes for all algorithm-related topics ! |
|
|
|
|
|
|
|
|
|
2
1/17 |
|
Introduction to bioinformatics
Perl programming |
|
Lesk, Ch. 1, slides
Pierce, Perl, Ch. 2 |
|
Week 1 & 2 slides (Blackboard) |
|
1/17, Mon: Dr. Martin Luther King Jr. Holiday |
|
|
|
|
|
|
|
|
|
3
1/24 |
|
Exhaustive Search
Perl programming |
|
Jones, Ch. 4
Pierce, Perl, Ch. 3, 4+ |
|
|
|
Note: Submission dates to be confirmed during class |
|
|
|
|
|
|
|
|
|
4
1/31 |
|
Genome organization and evolution
Perl programming |
|
Lesek, Ch. 2, slides
Pierce, Perl, Ch. 5 |
|
|
|
Assignment 1 Due 1/31 Mon
(Blackboard "Assignments")
|
|
|
|
|
|
|
|
|
|
5
2/7 |
|
Greedy Algorithms
Perl programming |
|
Jones, Ch. 5
Pierce, Perl, Ch 6, 7 |
|
|
|
Assignment 2 Due 2/7 Mon
(Blackboard "Assignments") |
|
|
|
|
|
|
|
|
|
6
2/14 |
|
Scientific publications and archives
Archives and information retrieval
Perl programming |
|
Lesk, Ch. 3
Lesk, Ch. 4, slides
Pierce, Perl, Ch 8, 9, 10 |
|
|
|
Assignment 3 Due 2/14 Mon |
|
|
|
|
|
|
|
|
|
7
2/21 |
|
Protein Secondary Structure Prediction
Perl programming
|
|
Leong, RT-RICO
|
|
|
|
Note: Exam I - 2/21 Mon |
|
|
|
|
|
|
|
|
|
8
2/28 |
|
Protein Secondary Structure Prediction
Perl programming
|
|
Leong, RT-RICO
Pierce, Perl, Ch 10, 14, 18
|
|
|
|
3/5 Sat: Instruction ends for Spring Break 1pm
Assignment 4 Due 3/2 Wed |
|
|
|
|
|
|
|
|
|
9
3/7 |
|
|
|
|
|
|
|
Spring Break |
|
|
|
|
|
|
|
|
|
10
3/14 |
|
Project topic selection
Perl programming
|
|
Project specification
Pierce, Perl, Ch 20+, LWP & others
|
|
|
|
3/14, Mon: Classes resume after Spring Break 8am
|
|
|
|
|
|
|
|
|
|
11
3/21 |
|
Alignments and phylogenetic trees (skip)
Dynamic Programming Algorithms
Project discussion
|
|
Lesk, Ch 5
Jones, Ch. 6
|
|
Protein with SS from PDB
ncbi BLAST URL API user's guide (html) (pdf) |
|
Assignment 5 Due 3/21 Mon |
|
|
|
|
|
|
|
|
|
12
3/28 |
|
Project discussion |
|
|
|
|
|
Project part I Due 3/30 Wed |
|
|
|
|
|
|
|
|
|
13
4/4 |
|
Proteomics and systems biology
Project discussion
|
|
Lesk, Ch 7
|
|
|
|
Note: Exam II - 4/4 Mon |
|
|
|
|
|
|
|
|
|
14
4/11 |
|
Project presentation |
|
|
|
|
|
Project part II Due 4/11 Mon |
|
|
|
|
|
|
|
|
|
15
4/18 |
|
Project presentation |
|
|
|
|
|
4/22, Fri: Spring Holiday |
|
|
|
|
|
|
|
|
|
16
4/25 |
|
Project presentation |
|
|
|
|
|
4/26, Tue: Follows Friday Schedule; last day of classes |
|
|
|
|
|
|
|
|
|
16, 17
Exam |
|
Final Exam - Wed, May 4, 3:30-6:30 P.M. - Project report submission + presentation |
|
4/28-30, 5/2-4: Final Exams
Note: Project report |
|
|
|
|
|
|
|
|
|