CS5984 Computational Cell Biology
Instructor: Dr. Yang Cao, ycao@cs.vt.edu, Office Hours: TR, 10:00-11:00am.
Office Location: 2160D Torgersen Hall
Class Location: McBryde 233
Class time: TR, 12:30-13:45
Web page: www.cs.vt.edu/~ycao/cs5984
Reference book:
Computational Cell Biology, Christopher Fall et al., Springer, 2005
Essential Cell Biology: An Introduction to the Molecular Biology of the Cell, BRUCE ALBERTS et al., Garland Publishing Inc., 1997
and a list of journal papers
Reference: Computational systems biology, H. Kitano, Nature, 420, 206-210, Nov. 14, 2002 (It is a review paper on Nature. Do Not worry if you do not understand its content, just read it like a newspaper or scientific fiction. Later you may want to read it again. )
Reference (They are books. Read them only if you are really interested. ):
· Ernst Hairer, Syvert P. Norsett, Gerhard Wanner, Solving Ordinary Differential Equations I : Nonstiff Problems
· U. M. Ascher, Linda R. Petzold, Computer Methods for Ordinary Differential Equations and Differential-Algebraic Equations
Lecture Notes and other related materials are available through blackboard system.
Topics to be covered
•Basic knowledge of the process of modeling and simulation
•Related topics in Mathematics (Very basic)
–ODEs
–Probability Theory
•Software: Matlab and SBML
•Typical Model
–Basic Enzyme Kinetics model
–Gene Expression Model
–basic positive and negative feedback gene circuits
–toggle switch model
–gene oscillator model
–Cell Cycle Model
–noise in a single cell
other related biological model that you are interested
What you are required to do in this class:
Participation (listen, think and ask)
Presentation about a published work (somebody else's work)
A small project (that you feel interested) and the corresponding presentation
Final: Submit two review papers
One is for the paper you read (a general review)
One is for the project you did (a detailed review)
Grading policy:
My philosophy of graduate-level teaching is to offer help for students to study advanced topics. Score is a recognition of your hard work. Since we will cover a broad area across: biology, physics, chemistry, mathematics, statistics, control theory and computational science, I do not expect everybody to understand everything in this class (if you do, that's great!). Thus there is no final exam. The grade will be based on class participation (50%), presentation (30%) and the small project (20%). Basically if you finish all the required work, you will get a decent score.
Warning: You will fail if you are involved in the following behaviors:
1. Cheating; 2. Miss too many classes; 3. Fail to submit two review papers