BM2053: Mathematical Models & Systems Biology
BM2053: Mathematical Models & Systems Biology
Embedded Files
Course Details
Credits: 2
Segment: 3-6 of Aug-Nov '2024-25
Schedule: Slot-C (Mon 11:00-12:00, Wed 10:00-11:00, Thu 09:00-10:00) in BT118
Discussion hour: Tuesdays 1300-1400 (BM305)
Books
Nonlinear Dynamics and Chaos by Steven Strogatz
An Introduction to Systems Biology: Design Principles of Biological Circuits by Uri Alon
Mathematical Modeling in Systems Biology by Brian P. Ingalls
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
Handouts
Handouts
Exam 2 solution
Exam 3 solution
Repressilator (Elowitz and Leibler 2000, Nature)
Lab exam solution
Problem Sets
Problem Sets
Problem Set 2 - Write down Python programs to solve differential equations given in PS1 numerically.
Write down Python programs to solve equations appearing in PS3 numerically.
Problem Set 5
Course Policies
Course Policies
Leaves: Absence due to genuine reasons with proper documentation, such as a medical certificate from the IITH clinic, is permitted. The students missing any mid-semester exam will be awarded the average class marks (in a maximum of one exam) only after submitting a medical certificate from the institute health center.
If anyone misses more than one exam they must appear for a make-up examination within one week of the scheduled exam. The make-up examination will be given only after the submission of the medical certificate from the institute health center or any other (in case of non-medical emergencies) valid documentation.
Examinations: All the exams will be open notes and you can bring any handwritten material on paper. Any printed material, photocopies, soft copies, or books are not allowed.
If anyone misses the final exam due to genuine reasons they will have to write a make-up examination only after the submission of valid documentation (as mentioned above).
Course logistics
Course logistics
Assignments: The course has no assignments. Instead, practice problems will be given at regular intervals. Students are not expected to submit the answers to these problems.
Answers/solutions to the practice problems will not be provided. Students are encouraged to utilize the discussion hour to discuss the problems if they want to.
Mid-sem exams: Three mid-semester examinations (1 hour each) are planned for the course. They will take place during regular class at the end of each segment as per the following schedule
1st exam: Monday, 23 September 2024
2nd exam: Monday, 21 October 2024
3rd exam: Monday, 11 07 November 2024
Final exam: The final exam (2 hours) will cover all the topics covered in the course. It will take place on Friday 28 November 2024 from 1430-1630. The venue for the final exam will be announced later in the semester.
Lab exams: There will also be 2 lab exams in the course. Dates and the nature of these will be announced as the semester progresses.
Some suggestions
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.
Since there are no assignments in the course. You are advised to take the practice problems seriously and solve them at a regular interval. This will also make it easier for you take help during discussion hour. Solving all of them the night before the exam will not be very fruitful.
There will be one discussion hour each week for clarification of doubts and practice problems. Take advantage of that.
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