University of California, Santa Barbara
Department of Electrical and Computer Engineering

Biology from an EE perspective

ECE 594R Spring 2007

Instructor: Prof. Rakesh Lal

Schedule:Tuesday Thursday, 4.00-5.50 pm, Phelps 1431

Course Information:

In this seminar course we will explore how concepts in areas such as circuits, networks, controls, signals & systems, finite automata and information theories can be used to model biological systems. Over the last hundred years, electrical & computer science and engineering have developed many tools and techniques which have been useful in teasing processes in biological systems or have been used for making systems that interface with the biological world. To date, electrical science has not been widely used to examine and model biological processes – the use of transmission line theory for modeling nerve conduction being a notable exception. This is surprising because EE & CS have generated a large suite of tools for modeling reality and designing systems that are very complex. And not so surprising, because the systems handled by biologists and electrical engineers are very different, though they might open map to very similar mathematical objects.

In the first half of the term, we give a broad overview of biological systems using standard texts and short case studies. The case studies we will use will depend on the composition of the class and what areas students would be interested in modeling.

In the second half of the term, students would present new ways of modeling biological systems using the tool sets they are most familiar with.

Topics covered would include: Biomolecules, cell organization, enzymes, basics of gene expression, cellular signaling and modeling of some organ systems.

Grading: Based on a midterm quiz (so that you do read and internalize some biology!), two open problems, participation and your seminar talk plus manuscript.

Texts: Molecular Cell Biology by Lodish et al. and Systems Biology in Practice by Klipp et al. (both would be in the reserve collection) plus material from monographs and papers.

Lectures:

Presentations used for the lectures are given below (almost all sketches and material are from the text's web site or wikipedia commons):
Lecture 1
Lecture 2
Lecture 3
Lecture 4
Lecture 5
Lecture 6
Lecture 7
Lecture 8
Lecture 9
Lecture 10

Suggested reading

Here's some recommended reading, mostly from Lodish et al.'s  Molecular Cell Biology. I suggest you do a quick read and then a more careful read of the ideas covered in the lecture. You should aim to understand the architecture of biological processes --  that enable an organism to respond to environmental stimuli -- at an intermediate level of detail. If one were to use the terminology of ECE, let's say at the gate level. In the first pass, I don't think we need to understand the processes at the bond or molecular orbital level nor should it be at the highest block level -- which you would have done in high school. The minimum reading that you should do is underlined. Unless mentioned otherwise, the chapters & sections suggested for reading are from Molecular Cell Biology, 5e.

Lectures 1 & 2 the links suggested in the lectures & Chapter 1  (Sec 1.1-1.5).
Lecture 3, these links (Sec 5.1-5.3, 6.1-6.2 -- 6.3-6.5 optional).
Lecture 4, Chapter 2 (Sec 2.1-2.4).
Lecture 5, Chapter 3 (Sec 3.1-3.5).
Lecture 6, Chapter 4 (Sec 4.1-4.6).
Lectures 7 & 8, Chapter 7 (Sec 7.1-7.7).
Lecture 9 Chapter 7, 13 & 14 (Sec 7.8, 13.1-13.6, 14.1-14.4, 14.7, 17.6)
Lecture 10 Chapter 11 & 12, Chapters 10 & 15 optional (Sec 11.1-11.6, 12.1-12.2)
 
In addition you should read the classic experiments from the book's reference site:
1. Bringing enzymes back to life
2. Cracking the genetic code



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Last Updated: May 9, 2007