Lectures BENG 212 Winter 2008

Systems Biology and Bioengineering II:

Network Reconstruction & Functional States
Lecture: Tu/Th 3:30 - 4:50 PM in PFBH 161

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2008 Schedule

Date Topic Part Lecturer Material
1/8
1/10
other

1/15
1/17
other

1/22
1/24
other

1/29

1/31

other

2/5
2/7
other

2/12
2/14
other

2/19

2/21

2/26
2/28

3/4

3/6

3/11
3/13

3/16
3/21

Course introduction– educational values in SB (CH 1-3)
The S-Matrix (CH 6)
Review of Linear Algebra, Matlab, Nat Protocols

The S matrix / topological properties (CH 7)
The S matrix / SVD and fundamental subspaces (CH 8)
HW #1: Reconstruct PPS and TCA/combine with glycolysis

SVD / funamental subspaces / tiling
SVD finish / the null space of S (CH 9)
HW #2: Compute properties of S from HW1 and core E. coli

No class today

Left null space / column and row spaces (CH 10-11)

HW #3: Calculate extreme pathways

Modeling philosophy: dual causality (CH 12)
Properties of solution spaces (CH 13)
HW #4: FBA with core E. coli

E. coli core model and COBRA Toolbox
Sampling (CH 14)
HW #5 shadow prices and reduced costs

FBA 1: basics (CH 15)

FBA 2: exploration and shadow prices (CH 15)

FBA 3: growth solutions/alternative optima/FVA/FCF (CH 15-16)
FBA 4: genetic perturbations/MOMA/ROOM (CH 15-16)

FBA 5: sensitivity analysis: robustness and PPh (CH 15-16)

FBA 6: advanced topics (CH 15-16)

Final Presentations
Metabolic engineering

Takehome exams due
Project writeups due

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Location

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9500 Gilman Drive La Jolla, CA 92093-0412

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