General principles in life are encoded in its dynamics! Let's try to quantify them!
Introduction
This cross-disciplinary course aims to give an introductory and an updated view of quantitative biology (Q-Bio). The philosophy, concepts, significance and current progresses in Q-Bio will be introduced and discussed. Design principles underlying functional biological dynamics will be explained using biological oscillators, switches and trigger waves as examples. To illustrate the links between design principles and biological dynamics, I will show how mathematical modeling and computer simulations are useful tools (prior programming experience and mathematical trainings are NOT required). Current applications of Q-Bio (genetic circuit design, cell fate control, cancer therapy, etc.) will also be introduced. This course also plans to leverage the growing Q-Bio community in Taiwan by inviting Q-Bio scientists (listed below) of different expertises to introduce different concepts and biological systems to broaden students’ views on Q-Bio. In addition to lectures, we will also divide students into groups to do Q-Bio projects (see below for example projects) to gain hands-on research experience.
Goals
- Introduce the Q-Bio field to junior (1st and 2nd year) students.
- Basic concepts of mathematical modeling for biological systems.
- Familiarize students with the concepts, tools and research approaches in Q-Bio.
- Prepare students for taking advanced Q-Bio courses (e.g., Synthetic Biology and Mathematical Modeling in Biology)
Lectures
1. Q-Bio --- why?
2. Emergent biological dynamics (oscillations, digital switches, trigger waves, and biological patterns)
3. Design principles in biology (python intro)
4. Formalizing conceptual models via mathematics (assign group)
5. Design principles underlying biological dynamics (ultra-sensitivity)
6. Design principles underlying biological dynamics (biological switches and trigger waves) + Project introduction
7. Tool-building in biology based on design principles
8. Q-bio topic: understanding gene transcription via thermodynamics, co-lecture with Dr. 周信宏
9. Q-bio topic: quantitative imaging analysis, co-lecture with Dr. 趙本秀 (Project proposal)
10. Q-bio topic: diffusion and random walk, co-lecture with Dr. 林耿慧
11. Q-bio topic: ecological dynamics, co-lecture with Dr. 柯柏如
12. Q-bio topic: modeling cell growth rate, co-lecture with Dr. 林暐翔
13. Q-Bio: generative AI in biology, co-lecture with Dr. 吳亘承 and Dr. 陳映嘉
14. Q-bio topic: pattern formation via reaction-diffusion, co-lecture with Dr. 邱澗庚
15. Project presentation
Q-Bio scientists involved in 2024 course
Example Q-Bio projects
Lovely 2024 Q-Bio class!
