BM2053: Mathematical Models and Systems Biology

Course contents

This undergraduate course is to familiarise students with the mathematical modeling in biology. The course will introduce the importance of the system level approach to the study of the biological systems and the relevant mathematical methods. We will look at examples of the application of mathematical modeling in systems biology and medicine. The modeling and computational methods covered in the course will also be demonstrated in the lab part of the course. The tentative course contents are

• Introduction to mathematical modeling and systems biology
• Analysis of dynamic mathematical models- phase plane analysis, stability analysis, bifurcation analysis, oscillations
• Modeling of enzyme kinetics, biochemical reaction networks, gene regulatory networks, biological oscillators, switches
• Modeling of physiological systems, examples from systems medicine
• Pattern formation, reaction-diffusion systems
• Applications of modeling in biomedical engineering

References

• Nonlinear Dynamics and Chaos by Steven Strogatz
• An Introduction to Systems Biology: Design Principles of Biological Circuits by Uri Alon

Course logistics and policies

• Assignments: This course does not have graded assignments. Instead, practice problems will be provided at regular intervals. Students are not required to submit solutions.
• Answers/solutions to the practice problems will not be provided. Students are encouraged to utilise the discussion hour to discuss the problems if they want to.
• Exams: There are four exams scheduled (roughly) at the end of each segment. See above for dates.
• All exams will be closed-book and closed-notes, unless announced otherwise.


• Attendance: Attendance will be marked in each class but it will not contribute to the evaluation.
• Missing exams: On missing an exam due to a medical emergency you will be allowed to write a make-up exam on producing a medical certificate from the institute health center. Missing an exam due to any other reason (including being away for any extra-curricular activities) will result in no marks.
• The use of unfair means, including but not limited to plagiarism or copying, is strictly prohibited. Any violation will result in strict disciplinary action, including zero marks and/or reporting to academic authorities as per institute policy.

Some suggestions

• The best way to follow the course is to work out the details of the topics discussed in each class by yourself after the class.
• There will be one discussion hour each week for clarification of doubts and practice problems. Take advantage of that.
• You have to take the practice problems seriously and solve them on your own. In case you are facing difficulty, you can come and meet the instructor during the discussion hour