纲要
本课程目的为使学生对于遗传及生化网络上的生物性功能有计量上的了解。也将会提供学生建构网络组件的必须数学工具，如生物开关、震荡仪、过滤器、放大器等。成功利用系统生物学处理的一系列生物问题范例，将由探讨近期相关文献的方式加以介绍。本课程潜在的挑战是学生们多半来自不同的背景。必要时请自行研读相关的生物或数学资料。熟读课程中的问题讨论可以帮助你填补不足的知识空缺，以及帮助你准备相关作业。
本课程共分成三大部分：
- I 系统为生物学（14堂）将细胞视成一个完全搅拌反应器
- II系统细胞生物学（8堂）将细胞视成一个既有浓度梯度的分隔系统
- III系统发育生物学（3堂）在社会脉络中细胞间的信息沟通
教科书
以课程讲义 为主。以下推荐两本优良生物参考书：
Bruce Alberts等著，《细胞分子生物学》，第四版，New York：Garland Science，2002。
Harvey Lodish 等著，《分子细胞生物学》，第五版，New York：W. H. Freeman and Company, 2004。
（译注：以上两本皆有中译本。）
作业、考试及成绩
本课程会时常使用MATLAB® 作为必需解题工具。请确定你已经明白或学会如何使用。
本课程共有五个习题集，期末习题集发放自行带回去做。分数分配如下：
| 习题集一 |
15% |
| 习题集二 |
15% |
| 习题集三 |
15% |
| 习题集四 |
15% |
| 习题集五 |
15% |
| 期末考 |
25% |
Overview
The goal of this course is to help students develop a quantitative understanding of the biological function of genetic and biochemical networks. Students will be provided with the essential mathematical tools needed to model network modules, such as biological switches, oscillators, filters, amplifiers, etc. An array of example biological problems that can be successfully tackled with a systems biology approach will be introduced by discussing recent papers on the subject. The intrinsic challenge of this class is that students are coming in with wildly different backgrounds. Read up on your biology or math if needed. Use time in the recitations to help close some of the knowledge gaps and to help you prepare for the homework.
There are three levels of complexity to Systems Biology:
- I Systems Microbiology (14 Lectures) 'The cell as a well-stirred biochemical reactor'
- II Systems Cell Biology (8 Lectures) 'The cell as a compartmentalized system with concentration gradients'
- III Systems Developmental Biology (3 Lectures) 'The cell in a social context communicating with neighboring cells'
Text
The course notes serve as the text. For good biology reference texts, see:
Alberts, Bruce, et. al. Molecular Biology of the Cell. 4th ed. New York: Garland Science, 2002. ISBN: 0815332181.
Lodish, Harvey, et al. Molecular Cell Biology. 5th ed. New York: W. H. Freeman and Company, 2004. ISBN: 0716743663.
Assignments, Exams, and Grading
MATLAB® will be used intensively during the course. Make sure you know or learn how to use it as it is necessary for the problem sets.
There are 5 problem sets and one take home final for the course. The grading breakdown is as follows:
| Problem set 1 |
15% |
| Problem set 2 |
15% |
| Problem set 3 |
15% |
| Problem set 4 |
15% |
| Problem set 5 |
15% |
| Final |
25% |
