**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

**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

· **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. 9 ^{th}.
**

**Feb 14 topic: Gene Expression and Gene Regulation
Network**

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