ESE680-003: Special topics on Electrical and Systems Engineering

Spring 2007

Systems Biology

Course info:

Schedule: Monday,Wednesday 9.30 - 11.00 at Towne 303.

Instructors: George Pappas (pappasg@seas),  Vijay Kumar (kumar@seas), Harvey Rubin (rubinh@mail.med), Agung Julius (agung@seas), Adam Halasz (halasz@seas)

Office hours: Agung Julius Tue 3-4pm (Levine 465), Adam Halasz Mon 11-12am (GRASP Lab)

Course description: Spectacular advances in experimental technology and computational tools are driving the fast emergence of a field of study at the intersection between traditional molecular biology, system theory, and physical sciences. Generally referred to as Systems Biology, it is the quantitative study of the functioning of living cells, based on the underlying molecular processes.

Systems biology has led to the development of quantitative models for the entire metabolism of several organisms, new understanding of the behavior of infectious disease pathogens, identification of new cancer drug targets, and the cheap synthesis of a new generation of drugs for malaria. Currently funded projects aim at novel approaches to treating cancer and the production of alternative fuels.

From a systems engineering perspective, the emergence of systems biology is especially exciting. The discovery of the DNA structure and the technology for obtaining large amounts of genetic information have resulted in a reductionist scientific program in biology, where the focus shifted from the level of organisms to the level of molecules. Researchers focused on thorough understanding of small biomolecular components (one stretch of DNA, one RNA, or one protein) without necessarily being interested in the global picture. The shift has brought about the notion of systems in biology, where functionalities in living organisms are seen as results of interaction between subsystems.

The goal of the course is to introduce the techniques used in modeling and computation in systems biology as well as an overview of the major directions of research, using both academic texts and current reserch literature, with a strong preference for the latter. Students are expected to gain a general understanding of the major techniques and applications, and choose a topic for more in-depth study for the final project.
 

Prerequisites: This course is meant for graduate students with some knowledge of calculus (functions, derivatives, integrals, ordinary differential equations) and linear algebra (vectors, matrices, linear transformations). Also, it is assumed that the students have working experience with a programming language, such as C or MATLAB. Some knowledge about cellular biology, differential equations and probability theory is an advantage. However, the course will provide a short review on the necessary background material.
Contact Agung Julius (agung@seas) or Adam Halasz (halasz@seas) for further information.

Grading: 20% class participation; 80% final project and presentation.

Course Outline (tentative):

We plan to have a number of introductory lectures covering major directions in system biology. The rest of the course will consist of sessions where we will have a brief introduction of the topic followed by one or two paper presentations of important papers by the students, followed by discussions. A list of relevant papers will be provided. The following is the (tentative) list of topics that will be covered in the course.
 

• Overview of systems biology
• Introductory notions of cellular biology
• Kinetic description of transcription, translation and gene regulation in genetic networks
• Metabolic network analysis
• Nonlinear dynamics in bio-molecular networks
• Stochastic modeling of biochemical reactions
• Signalling pathways
• Spatial dynamics
• Whole cell models
• Systems biology and control
• Hybrid systems modeling and analysis of biomolecular systems

Course Schedule: