CS6824 Computation in Biochemical Systems
Fall 2010 

Instructor Yang Cao

The goal of this course is to provide a survey of simulation algorithms widely used for 
both deterministic and stochastic biochemical systems. We will start with deterministic reaction 
rate equations and teach numerical theory and techniques for solving ordinary differential 
equations. Biochemical systems such as the predator and prey model, Brusselator and cell cycle model 
will be used as examples. After students are familiar with the numerical theory and techniques for ODEs. 
We will discuss progress in stochastic simulation over the last ten years.  Many ideas 
developed for the numerical solution of ODEs can be generalized to stochastic simulation. 
Students will pick a course project to practice what they learn in the class. The skills learned 
in this class will be valuable not just for people working in computational systems biology, but 
also for researchers working on general engineering problems. 

All students in science and engineering background are welcome to enroll in this course. 
Students are expected to have interest in scientific computing and have some background in
numerical methods.