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Designing Your Course
Sample Syllabus
MAT 487 / BIO 310 Computational Biology
Instructor:
Dr. Laurie Heyer
Chambers 131
E-mail: laheyer@davidson.edu
Course description: Computational biology is an interdisciplinary
course that explores mathematical, statistical and computational
techniques useful in the study of genomes and proteomes.
Text: Beginning Perl for Bioinformatics
by James Tisdall, 2001, O'Reilly.
Course goals: (1) To understand and apply various algorithms
and statistical tests for analyzing DNA, RNA and protein sequences,
microarray data, and gene circuits. (2) To gain practical experience
with Perl, a programming language widely used in molecular biology.
The following assessments of your progress toward these goals will
be used.
Homework. Weekly assignment of programming exercises
will help solidify your working knowledge of Perl.
Quizzes. Approximately every two weeks, there will be
a take-home quiz on the algorithmic and statistical aspects of the
course.
Projects. Two projects that involve building interactive
web sites will be assigned to interdisciplinary teams of approximately
four students. Each team will unveil their project web site by demonstrating,
in class, its use on a real-world problem. The instructor and the
class will evaluate projects for content, design, and clarity of
the in-class demonstrations. The first project, on Kyte-Doolittle
hydrophobicity profiles, will be unveiled Feb. 28. The second project,
on hierarchical clustering, will be unveiled May 2.
Final Exam. The final will be a take-home mini-project
that will ask you to solve a problem using methods you have learned
in the course.
Use of software: Perl for the PC is freely available.
It is installed on all lab computers. You are encouraged to install
it on your own computer, as well.
Office Hours: I have office hours specifically dedicated
to meeting with students, Mon-Thurs, 2:00-3:30 p.m. However, you
will often find me available in my office at other times, and you
are encouraged to make appointments to meet with me.
Grading: Course grades will be based on a percentage
of 700 total possible points, allocated among the components of
the course as follows:
Homework 200 points Projects 200 points Quizzes 200 points Final
100 points
Approximate schedule:
| Date |
Topic |
Assignment Made |
Assignment Due |
| Jan 15 |
Intro to Computational Biology |
|
|
| 17 |
Sequence alignment |
|
|
| 22 |
Ch. 4 |
Program 1 |
|
| 24 |
Sequence alignment |
|
|
| 29 |
Ch 5 |
Quiz 1; Program 2 |
Program 1 |
| 31 |
Sequence alignment |
|
Quiz 1 |
| Feb 5 |
Ch 5, cont |
Program 3 |
Program 2 |
| 7 |
BLAST, BLAST statistics |
Project 1 |
|
| 12 |
Project related topics from Ch 6 and 8 |
Program 4 |
Program 3 |
| 14 |
Project related topics |
Quiz 2 |
|
| 19 |
Perl Miscellany |
|
Program 4 |
| 21 |
Gene prediction, promoter analysis |
|
Quiz 2 |
| 26 |
Project work day |
|
|
| 28 |
Project 1 Unveiling |
|
Project 1 |
| Mar 12 |
Ch 7 |
Program 5 |
|
| 14 |
Structure prediction |
Quiz 3 |
|
| 19 |
Lab: structure |
Program 6 |
Program 5 |
| 21 |
Microarray data analysis |
|
Quiz 3 |
| 26 |
Lab: microarray data |
Program 7 |
Program 6 |
| 28 |
Hierarchical clustering |
Quiz 4 |
|
| Apr 4 |
K-means, SOM clustering |
|
Program 7 |
| 9 |
Lab: clustering |
Program 8 |
Quiz 4 |
| 11 |
Comparing clusterings |
Quiz 5; Project 2 |
|
| 16 |
Lab: clustering |
Program 9 |
Program 8 |
| 18 |
Analyzing gene circuits |
|
Quiz 5 |
| 23 |
Phylogenetic trees |
Quiz 6 |
Program 9 |
| 25 |
Sequencing and SNPs |
|
Quiz 6 |
| 30 |
Project work day |
|
|
| May 2 |
Project 2 Unveiling |
|
Project 2 |
| 7 |
Wrap up, course evaluations |
Final Exam |
|
| 13 |
(Seniors) |
|
Final Exam |
| 15 |
(Others) |
|
Final Exam |
|
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