CMSC423: Bioinformatic Algorithms, Databases, and Tools (Spring 2007)
Time: Monday & Wednesday, 3:30 - 4:45
Location: CSIC 3120
Instructor: Mihai Pop
Office hours: Tuesdays 1-2pm
3120F Biomolecular Sciences Building (bldg #296). Building is
usually locked. Call me from the intercom and I'll buzz you
TA: Behjat Siddiquie (behjat at cs)
TA office hours: Wednesdays 11am - 12pm
TA office: AVW 1112 (the TA room)
Computers have revolutionized modern biological research, by providing
biologists with the means to manage and analyze the large amounts of
data generated through high-throughput experiments. This course
provides a practical introduction to the main
algorithms, databases, and tools used in bioinformatics, at the same
time providing insight into the biological problems being addressed.
The course will cover public databases such as Genbank and PDB,
software tools such as
BLAST, and their underlying theory and algorithms. Students will
to perform a number of useful tasks
in analyzing sequence data and managing bioinformatic databases, with a
focus on problems of current relevance in biological research.
This course is designed to complement BSCI 348S, Comparative Bioinformatics.
CMSC 351 or permission of instructor. Programming expertise is a
must. No background in biology is required. If you
uncertain about meeting these requirements please contact me.
An Introduction to Bioinformatics Algorithms (Computational Molecular Biology)
Neil C. Jones and Pavel A. Pevzner
MIT Press, 2004
The course will cover the following main areas. A detailed syllabus is
- Introduction to molecular biology
- Bioinformatic databases
- Sequence alignment: exact and inexact string matching,
- Phylogenetic tree construction
- Gene prediction and annotation, microarrays and gene expression
- Protein and RNA structure prediction, proteomics.
Coursework and grading
Regular homework assignments will consist of a combination of one or
more of the following: (i) exercises from the textbook; (ii)
small programming assignments; (iii) "discovery" exercises using
publicly available bioinformatics tools. In addition, all
students must complete two programming projects, the first selected by
the instructor and the second chosen by the students in consultation
with the instructor.
The final grades will be a combination of the grades for the homework,
project, and mid-term and final exams. In addition,
participation in the class will be taken into account for extra credit.
The breakdown of you final grade is shown below.
Homework - 10 %
Project 1 - 15 %
Project 2 - 15 %
Midterm - 25%
Final - 35%
Unless otherwise indicated in class, most assignments will be given out
on Wednesdays of each week and will be expected in by the beginning of
the Monday class. Remember, the office hours are on Tuesdays so
come by if you have any questions about your assignments.
Assignments submitted late will
be graded as follows: up to 1 day late - 10 points will be deducted
from the grade, up to 2 days late - 20 points will be deducted.
Your assignment will not be graded beyond the second day past the
deadline. If for reasons outside your control you will not be
able to submit an assignment on time, see me as soon as possible to discuss an alternate deadline.
This course follows the University's
attendance policy. In short, if you will miss class
for any reason you should let me know in advance, unless this
is not possible (e.g. sudden illness). In any case, please
let me know as soon as you are aware that will not be able to attend a
class (e-mail is OK). I will work with you to help you catch
up on homework or exams if you have to miss any of the lectures.
I expect that the students taking this class fully adhere to the Code of Academic
Integrity. Please read this document in full if you
have not already done so. In addition, the University
requires that you sign the Honor Pledge on every examination you turn in. Please read the relevant excerpt from
the Code of Academic Integrity (reproduced below).