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:: Spring 2011 :: CSC 526, Spring 2011 :: Spring 2011 :: Assignments :: Spring 2011 :: Instructor: :::: Best viewed with Firefox |
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| 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") |
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| 5 2/7 |
Greedy Algorithms Perl programming |
Jones, Ch. 5 Pierce, Perl, Ch 6, 7 |
Assignment 2 Due 2/7 Mon (Blackboard "Assignments") |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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