課程資訊
課程名稱
生物系統模擬
Modeling and Simulation in Systems Biology 
開課學期
105-1 
授課對象
電機資訊學院  生醫電子與資訊學研究所  
授課教師
魏安祺 
課號
BEBI5009 
課程識別碼
945 U2990 
班次
 
學分
全/半年
半年 
必/選修
選修 
上課時間
星期四2,3,4(9:10~12:10) 
上課地點
電二101 
備註
總人數上限:30人 
Ceiba 課程網頁
http://ceiba.ntu.edu.tw/1051BEBI5009 
課程簡介影片
 
核心能力關聯
核心能力與課程規劃關聯圖
課程大綱
為確保您我的權利,請尊重智慧財產權及不得非法影印
課程概述

This class discusses current topics in systems biology focused on learning fundamental tools and modeling techniques to develop and apply quantitative models of cellular systems. Essential biological concepts and mathematical fundamentals will be reviewed. This class will require MATLAB programming. 

課程目標
Mathematical modelling is becoming an important tool for molecular and cell biology. This class aims to provide students an introduction to the key concepts that are needed for the construction and investigation of mathematical models in molecular systems biology. The class will cover the following topics:
1. Introduction of MATLAB
2. Modeling chemical reaction networks
3. Biochemical kinetics
4. Analysis of dynamic mathematical models
5. Metabolic networks
6. Signal transduction pathways
7. Gene regulatory networks
8. Electrophysiology
 
課程要求
Prerequisite: Calculus, General biology
Students should be comfortable with basic mathematical concepts of linear algebra, differential equations, probability and basic biochemistry & molecular biology. Prior experience with programming is recommended.
 
預期每週課後學習時數
 
Office Hours
 
指定閱讀
Mathematical Modeling in Systems Biology(2013), by Brian P. Ingalls 
參考書目
 
評量方式
(僅供參考)
 
No.
項目
百分比
說明
1. 
期中考 
30% 
 
2. 
期末報告 
30% 
 
3. 
作業 
40% 
會需要用MATLAB來寫作業 
 
課程進度
週次
日期
單元主題
第1週
9/22  Introduction  
第2週
9/29  Chemical reactions
Introduction to Matlab 
第3週
10/06  Systems of differential equations
Separation of Timescales
Enzyme kinetics 
第4週
10/13  Cooperativity
Compartmental modeling and transport 
第5週
10/20  Phase plane analysis
Stability 
第6週
10/27  Sensitivity analysis; Parameter fitting 
第7週
11/03  Review;
Homework;
Stochastic modeling 
第8週
11/10  Mid-Term 
第9週
11/17  Stochastic Modeling;
Metabolic network 
第10週
11/24  Constraint-based modeling 
第11週
12/01  Signal transduction pathways 
第12週
12/08  Gene regulatory networks 
第13週
12/15  Electrophysiology: membrane potential & ion channels, Morris-Lecar model, Hodgkin and Huxley model  
第14週
12/22  Cable theory
Physiological Modeling 
第15週
12/29  Systems pharmacology 
第16週
1/05  project presentation 
第17週
1/12  final exam week, project presentation