CS 618
- Professor:
- TA Office Hours:
[Click for TA hours]
- Text: "System Modeling in Cellular Biology: From Concepts to Nuts and Bolts", by Zoltan Szallasi and Articles from current literature
- Laboratory: Open Lab machines, supercomputer
- Prerequisites: CS 252, CS 312
- Class:
- Section 1: TTh 9:30-10:45 2208 TMCB
- Web Page: http://dna.cs.byu.edu/CS618/
Overview:
With the completion of the sequencing project for the human genome researchers
have a large corpus of data to use in understanding biological systems.
Unfortunately, there are a number of significant Computer Science problems that have to be solved before this data can be used to develop drugs and treat
genetic diseases.
Systems biology is the data-centric quantitative modeling of biological processes and systems.
It requires an understanding of chemistry, biology and a lot of programming expertise. In this class we assume that you have little or no biology or chemistry background and will cover these topics briefly to give you the background you need to write code.
We will be developing computational models of the biological systems that interact in the human body.
Down syndrome or trisomy 21 is a genetic disorder caused by the presence of all or part of an extra 21st chromosome. About 1 in 800 births have some form of Down syndrome. This condition is interesting from a systems biology perspective because we know exactly which genes are replicated in order to cause the physical symptoms. We will be developing tools to model Down syndrome in this class.
- Lectures
Most of the class time will be spent reviewing material from the book and
from articles relevant to the laboratories. You are expected to read the
material before you come to class.
- Reading Summary
You will be expected to turn in a 2-3 paragraph summary of the reading assignment at the start of class.
- Paper Presentations A student will present a paper each Thursday that is related to the material we are talking about. You will be given feedback to help you to improve your presentation skills.
- Laboratories - You will
be expected to write significant pieces of code to implement algorithms we talk about in class. You will also
critique papers from the current literature as part your laboratory writeups.
- Project You will select a project near the beginning of the class
and will work on it throughout the semester. We will tailor classroom materials
and discussions towards helping you with your project.
Grading:
Reading Summary
|
10%
|
Paper Presentation
|
10%
|
|
Project Proposal
|
20%
|
|
Laboratories
|
20%
|
|
Project Oral Presentation
|
10%
|
|
Final Project Writeup
|
30%
|
|
A
|
93.3-100%
|
B-
|
80.0-83.3%
|
D+
|
66.7-70.0%
|
|
A-
|
90.0-93.3%
|
C+
|
76.7-80.0%
|
D
|
63.3-66.7%
|
|
B+
|
86.7-90.0%
|
C
|
73.3-76.7%
|
D-
|
60.0-63.3%
|
|
B
|
83.3-86.7%
|
C-
|
70.0-73.3%
|
E
|
00.0-60.0%
|
Policies On Harassment and Disabilities from The EEO Office, 28
October 2002
-
PREVENTING SEXUAL HARASSMENT -
Title IX of the Education Amendments of 1972 prohibits sex discrimination against any participant in an educational program or activity that receives federal funds. The act is intended to eliminate sex discrimination in education and pertains to admissions, academic and athletic programs, and university-sponsored activities. Title IX also prohibits sexual harassment of students by university employees, other students, and visitors to campus. If you encounter sexual harassment or gender-based discrimination, please talk to your professor; contact the Equal Employment Office at 801-422-5895 or 1-888-238-1062 (24-hours), or http://www.ethicspoint.com; or contact the Honor Code Office at 801-422-2847.
- Students with Disabilities Brigham Young University is committed
to providing a working and learning atmosphere that reasonably
accommodates qualified persons with disabilities. If you have any
disability that may impair your ability to complete this course
successfully, please contact the University Accessibility Center
(422-2767). Reasonable academic accommodations are reviewed for all
students who have qualified documented disabilities. Services are
coordinated with the student and instructor by the UAC. If you need
assistance or if you feel you have been unlawfully discriminated
against
on the basis of disability, you may seek resolution through established
grievance policy and procedures. You may contact the Equal Employment
Office at 422-5895, D-282 ASB.
