CMSC423: Bioinformatic Algorithms, Databases, and Tools (Fall
Treangen (treangen at cs) x5-7395
Office hours: Tuesdays
12:30-2pm or by appointment
Office address: AVW
Alternate office (by appointment): 3120B
Sciences Building (bldg #296).
Building is usually locked.
Call me from the intercom and I'll buzz you in.
Milad Gholami (mgholami at cs)
TA office hours: Mondays and Wednesdays 9-11am
office: AVW 1112
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 learn 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.
also learn new algorithms that can apply to other areas of computer
science, not just bioinformatics: clustering, string matching, basic
machine learning, etc.
This course is designed to complement
BSCI 348S, Comparative Bioinformatics.
CMSC 351 or permission of instructor (Note: CMSC 351 will
not be waived for CS students). Programming expertise is a must. No
background in biology is required. If you are uncertain about
meeting these requirements please contact me.
Neil C. Jones and Pavel A. Pevzner
Richard Durbin, Sean R. Eddy , and Anders Krogh
The course will cover the following main areas. A
detailed lecture schedule is provided here.
Introduction to molecular biology
Sequence alignment: exact and
inexact string matching, multiple sequence alignments
Phylogenetic tree construction
Gene prediction and annotation
Genome Sequencing and Assembly.
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 a programming project.
The final grades
will be a combination of the grades for the homework, project,
midterm and final exam. 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 %
Projects - 30
Midterm - 25%
Final - 35%
otherwise indicated in class, most assignments will be given out on
Thursdays of each week and will be expected in by the beginning of
the Tuesday class. Remember, the TA office hours are on Mondays and Wednesdays so
stop by to see Milad if you have any questions about your
Assignments submitted late will not be accepted!
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. The University of Maryland, College Park has a
nationally recognized Code of Academic Integrity, administered by the
Student Honor Council. This Code sets standards for academic
integrity at Maryland for all undergraduate and graduate students. As
a student you are responsible for upholding these standards for this
course. It is very important for you to be aware of the consequences
of cheating, fabrication, facilitation, and plagiarism. For more
information on the Code of Academic Integrity or the Student Honor
Council, please visit http://www.shc.umd.edu.
To further exhibit your commitment to academic integrity, remember
to sign the Honor Pledge on all examinations and assignments: "I
pledge on my honor that I have not given or received any unauthorized
assistance on this examination (assignment)."