Course Details

Semester1 2009/10

Pre-Requisites: A background in Science/Engineering/Computing ; good  comfort levels with mathematical modeling and analysis techniques.

Lecturer:      Prof. P.S. Thiagarajan

                      thiagu@comp.nus.edu.sg

                      Tel. 6516 7998                                       

Lectures: Mondays  4:00 PM -  6:00 PM;  Venue :  COM1/209(SR9) New!

Labs: TBA

Note: Most of the links from this course web page will be activated soon.

Course Description 

This course provides an introduction to computational approaches to systems biology.  A systemic approach to biology is not new but it has recently gained significant momentum due to emerging experimental technologies accompanied by computational  tools. In this context,  there is increasing consensus that it is both feasible and necessary to formulate computer-aided mathematical  models of biochemical networks. This will enable researchers to make testable quantitative predictions and validate such predictions. However, formidable barriers remain to be surmounted before this vision of systems biology can be realized.

Our goal will be to display -a part of- the current state of the field from a computer science perspective. We shall focus on the dynamical aspects of biochemical networks but with an emphasis on signaling networks and the means for modeling, simulating and analyzing such networks. We shall present core material in the form of lectures as well as snippets of ongoing research through invited presentations.  Self-study,  two tool-based modeling assignments, a term project accompanied by a report and a seminar will be key components of the work expected from the participants. The course will be largely self-contained and students with diverse backgrounds are expected/welcome  to sign up for the course.  Here is a  broad description of the course contents:   

Course Material

• Selected parts of the text book: 

               Systems Biology in Practice:

               Authors: E. Klipp, R. Herwig, A. Kowald, C. Wierling, H. Lehrach

               Publisher: Wiley-VCH (2005)

• Selected Review Papers from the literature.

• Lecture Slides

Course Structure:    We will focus on the following three broad themes.

• Foundations: A quick look at Cell biology, mathematical modeling and experimental techniques.

• The biological processes that are currently being studied and the computational techniques being used/developed to study these processes.

• Computer-aided tools that are currently available and their relative strengths and weaknesses.

In addition, there will be invited presentations dealing with current research. Finally, and most importantly, there will also be presentations by the course participants based on their term projects.

 Grading

There will be no mid-term or final examinations. The grading will be based on lab assignments , reading assignments, the term project and the seminar presentation. The lab asssignments will deal with the modeling and simulation of selected biological processes and it will be based on tools such as the Cell Illustrator, COPASI and the MATLAB packet, SimBio.