CS6404 Modeling and Simulation in Systems Biology

Open your mind. Your world could be different

Instructor: Dr. Yang Cao, ycao@vt.edu, Office Hours: TR, 10:30-11:30am.

Office Location: 2160D Torgersen Hall

Class Location: 2050 Torgersen Hall/607 McBryde Hall

Class time: Tuesday, 2:00-5:00pm

New! Class Schedule is available

Web page: courses.cs.vt.edu/~cs6404

Course Announcement: Download the Flyer

Syllabus: To be determined in the first few weeks

Reference book:

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

Possible Project List

Jan 18 topic title: Introduction to this class

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. )

Jan 20 topic title: Introduction to Modeling and Simulation

Jan 23 topic title: From randomness to chemical reaction

Reference:

1.     GILLESPIE DT, EXACT STOCHASTIC SIMULATION OF COUPLED CHEMICAL-REACTIONS 
JOURNAL OF PHYSICAL CHEMISTRY 81 (25): 2340-2361 1977. Pdf file can be download from   10.1021/j100540a008

2.     GILLESPIE DT, GENERAL METHOD FOR NUMERICALLY SIMULATING STOCHASTIC TIME EVOLUTION OF COUPLED CHEMICAL-REACTIONS 
JOURNAL OF COMPUTATIONAL PHYSICS 22 (4): 403-434 1976. You cannot download an e-file for this paper online. For a limited time, you can download the pdf file here.

Interestingly, please compare the above two papers with the following one:

1.     Morton-Firth CJ, Bray D Predicting temporal fluctuations in an intracellular signalling pathway JOURNAL OF THEORETICAL BIOLOGY 192 (1): 117-128 MAY 7 1998    

According to Tongli’s suggestion, I add the following two papers for interested students. The first one contains the original idea and the second one used a modified model as a test example.

·       SHNERB NM The importance of being discrete: Life always wins on the surface PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 97 : 10322 2000

·       Cao Y, Li H, Petzold L Efficient formulation of the stochastic simulation algorithm for chemically reacting systems JOURNAL OF CHEMICAL PHYSICS 121 (9): 4059-4067 SEP 1 2004 (only need to read Section VI, B, Spatially Inhomogeneous System).

Jan 25 topic title: Simulation methods for nonstiff ordinary differential equation

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

Jan 31 topic title: Stochastic simulation algorithms for biochemical systems

Reference: the two papers listed for Jan 23’s topic, and the following book

·       Markov Processes : An Introduction for Physical Scientists by Daniel T. Gillespie (Hardcover - October 8, 1991)

Feb 7 topic title: (continue) Stochastic simulation algorithms for biochemical systems

Note: Welcome to my GBCB talk at VBI conference room on Thursday, Feb. 9th.

Feb 14 topic: Gene Expression and Gene Regulation Network

Feb 21 topic: Randomness in the Cell: Data from Experiments