Lectures Beng 123 Winter 2008

Systems Biology and Bioengineering:

Lecture: Tu/Th 9:30 - 10:50 PM in PFBH 191
Section: F 3:00 - 3:50 PM in PFBH 161

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2008 Schedule

Date Topic Lectures
1/8

1/10
1/11

1/15
1/17
1/18

1/22
1/24
1/25

1/29
1/31
2/1

2/5
2/7
2/8

2/12
2/14
2/15

2/19
2/21
2/22

2/26
2/28
3/1

3/4
3/6
3/7

3/11
3/13
3/14

Introduction/Basic Concepts/reconstruction (CH 1,2,3)

Reconstruction of Biochmical Reaction Networks (CH 4,5)
Discussion Section - review of linear algebra and MATLAB

The Stoichiometric Matrix (CH 6)
Fundamental Subspaces and SVD (CH 8)
Discussion Section - Examples of forming S and SVD

The (Right) Null Space (CH 9)
Modeling philosophy: dual causality (CH 12)
Discussion Section - computation of ExPas

Unbiased Sampling of Feasible Network States (CH 13)
Constraints of Network Functions, Optimal States (CH 14)
Discussion Section - Sampling Spaces

Optimal States (CH 14)
Kinetics-Based Concepts (SB2 CH 1-2)
Discussion Section - Optimization in MatLab

Midterm (covering lectures 1-9)
Dynamic Simulation (SB2 CH 3)
Discussion Section - Dynamic Simulation with Mathematica

Chemical Reactions and Enzyme Kinetics (SB2 CH 4-5)
Open Systems and Orders of Magnitude (SB2 CH 6-7)
Discussion Section -- Dynamic Simulation and Enzyme Kinetics

Open Systems and Orders of Magnitude (SB2 CH 6-7)
Stoichiometric Texture (SB2 CH 8)
Discussion Section - TBA

Regulation as Elementary Phenomena (SB2 CH 9)
Metabolic and Regulatory Pathways (SB2 CH 10-11)
Discussion Section - TBA

Metabolic and Regulatory Pathways (SB2 CH 10-11)
Course Review
Discussion Section - TBA

lec1.pdf
lec2.pdf
Past Years: 1, 2
brainexample.mat

lec3.pdf
lec4.pdf


lec5.pdf
lec6.pdf


lec7.pdf
lec8.pdf


lec9.pdf
lec10.pdf



lec11.pdf


lec12.pdf
lec13.pdf


lec14.pdf
Class Cancelled


lec16.pdf
lec17.pdf


lec18.pdf



 

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Location

417 Powell-Focht Bioengineering Hall

9500 Gilman Drive La Jolla, CA 92093-0412

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