Course

Wednesday & Friday 10:10 - 12:00 Classroom: Room 123, IMB, AS Register for the course! 

Mathematical Modeling in Biology for Fall 2025

Organizer: Dr. Wei-Hsiang Lin &Dr. Jian-Geng Chiou

Prerequisite: Calculus (undergraduate level)

This course focuses on concepts and techniques in systems biology and applied mathematics. We will introduce basic ODE and PDE models in biology, and analyze them in equation or with numerical simulation (Python codes will be provided, but students are welcome to use any programming languages for projects).

This course has problem sets every week. Problem sets will not be graded, but answers will be provided. There will be office hours every two weeks.

Grading is based on Midterm (50%), and Final exam or Final project (50%). Student can decide to participate either final exam, final project, or both. If student participate both, higher grade will be used.

Midterm and Final exam are based on the problem sets. Exams are open book but no electronic devices.

Student can choose to do Final project (50%, optional) for the class. The topic can be original research or extension of some papers. For master or PhD students, you are welcome to develop your own thesis research in the Final project.

Reference books (optional): 1. Ordinary differential equation (?). 2. Nonlinear dynamics and chaos (Strogatz). 3. Mathematical biology (?)

Reference videos (linear algebra, etc): https://biocircuits.github.io/

	Date	Topic	Lecturer
1	09/03, 09/05	Introduction to quantitative model (1)	Jian-Geng Chiou
2	09/10, 09/12	Introduction to quantitative model (2)	Wei-Hsiang Lin
3	09/17, 09/19	Introduction to ODE, 1D stability analysis	Wei-Hsiang Lin
4	09/24,09/26	Linear transformation. Eigensystems.	Wei-Hsiang Lin
5	10/01,10/03	2D stability analysis in ODE.	Wei-Hsiang Lin
6	10/08	Topics: bifurcation	Jian-Geng Chiou
7	10/15,10/17	Topics: Multi-stability, oscillatory dynamics	Jian-Geng Chiou
8	10/22	ODE examples in biology (1)	Wei-Hsiang Lin
9	10/29,10/31	ODE examples in biology (2)	Wei-Hsiang Lin
10	11/05,11/07	Midterm, Introduction to PDE, transport and age model	Jian-Geng Chiou, Wei-Hsiang Lin
11	11/12,11/14	Introduction to PDE, boundary condition	Jian-Geng Chiou
12	11/19,11/21	Diffusion and random walks	Jian-Geng Chiou
13	11/26,11/28	Topics: Reaction diffusion, Turing system, pattern formation	Jian-Geng Chiou
14	12/03,12/05	Research Topic: biofilm, electrochemical wave	Jian-Geng Chiou
15	12/10,12/12	Research Topic: chemical/mechanical wave Final project presentation	Wei-Hsiang Lin
16	12/17, 12/19	Final project presentationMbr>Final exam	Jian-Geng Chiou & Wei-Hsiang Lin