Lectures BENG 212 Winter 2010

Systems Biology and Bioengineering II:

Network Reconstruction & Functional States
Lecture: Tu/Th 9:30 - 10:50 AM in PFBH 161

Home | Lectures | Assignments | Resources



Part 1: Reconstruction of networks (BIGG data bases)

Part 2: Properties of reconstructions

Part 3: Methods to determine functional states of networks

Part 4: Applications of Genome scale Models

2010 Schedule

Date Topic Part Lecturer Material Reading Material
1/5
1/7
Other

1/12
1/14
Other

1/19
1/21
Other

1/26
1/28
Other

2/2
2/2
2/4
Other

2/9
2/11
Other

2/16

2/18
Other

2/23
2/25
2/23
Other

3/2
3/4

3/9
3/11
3/12

Course introduction: Logistics and SB intro
Educational Values in Systems Biology
Review of Linear Algebra, MatLab, Nat Protocols

Reconstructions : Overview & Details
The E. coli & Human Reconstructions
COBRA Tutorial/Project Prep

Other Networks
The S matrix
HW #1: Reconstruct PPS and TCA, combine with glycolysis

Topological Properties and SVD
SVD and Fundmental subspaces
HW#2: compute propertes of S from HW1 and core E. coli

Phase 1 Project reports due
Extreme Pathways and Left Null Space
Finding Functional States/ Dual Causality
HW #3: ExPa

Tutorial: FBA Primer and Core Model
Exploring capabilites/equivalent solutions
HW #4: COBRA basics, functional states of core E.coli

Biological Objective Functions

COBRA Methods Overview
HW #5: FBA and shadow prices

Environmental Perturbations
Genetic Parameters
Phase 2 Project reports due.
HW #6: Environemntal and genetic perturbations

Omics Data and Metabolic Models
Model-driven Design/ Metabolic Engineering

Model Based Understanding - Adaptive Evolution
Model Driven Discovery / Gap-Filling
Project Presentations 3:15-6:15pm, Fung Auditorium

1
1


1
1


1
2


2
2


2
3


3
3


3

3


3
3



4
4

4
4
4


BOP
BOP
HN

BOP
BOP
HN/AB

JL/DRH
BOP
HN

BOP
BOP
HN

BOP
BOP
HN

JO
BOP
HN

AMF

BOP
HN

HN
BOP
HN
HN

DRH
JO

BOP
JO
class


pdf, pdf
pdf


pdf, pdf
pdf, pdf
pdf

pdf, pdf
pdf


pdf, pdf
pdf


pdf
pdf, pdf


pdf
ppt


pdf

pdf


pdf
pdf



pdf
pdf

pdf
pdf







pdf
pdff
pdf













pdf



pdf,pdf
pdf
pdf, pdf
pdf














Finals Week
3/15
3/19

Take-home exams due by Noon
Project writeups due by Noon




class
class



 

Location

Location

417 Powell-Focht Bioengineering Hall

9500 Gilman Drive La Jolla, CA 92093-0412

Contact Us

Contact Us

In Silico Lab:  858-822-1144

Wet Lab:  858-246-1625

FAX:   858-822-3120

Website Concerns: sbrgit@ucsd.edu

User Login