BENG 212 2009

Systems Biology and Bioengineering II:

Network Reconstruction & Functional States
Lecture: Tu/Th 2:00 - 3:30 PM in PFBH 161

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Course Information News

Dr. Bernhard Ø. Palsson
Powell-Focht Bioengineering Hall
Room 417

Teaching Assistant

Roger Chang
Powell-Focht Bioengineering Hall
Room 417


Project Ideas

Preliminary Project Report Requirements

* Office Hours: Fri 1:00 - 2:00 PM in PFBH 417 *
3/12: Assignments: Final Exam posted, due by Mon. 3/16 by 6:00pm by email to Roger
3/12: Lectures: lecture slides for 3/12 posted
3/10: Lectures: lecture slides for 3/10 posted
3/6: Resources: Applebee 2009 chapter on adaptive evolution posted (please review before lecture on 3/10)
3/5: Lectures: lecture slides for 3/5 posted
3/3: Lectures: lecture slides for 3/3 posted
2/26: Lectures: lecture slides for 2/26 posted
2/26: Assignments: HW6 posted, due by Thurs. 3/5 by midnight by email to Roger
2/24: Assignments: HW5 re-posted, due by Fri. 2/27 by midnight PLEASE NOTE NEW OBJECTIVE OF PROBLEM 2
2/24: Lectures: lecture slides for 2/24 posted
2/20: Assignments: HW5 posted, due by Fri. 2/27 by midnight by email to Roger
2/19: Lectures: lecture slides for 2/19 posted
2/17: Lectures: lecture slides for 2/17 posted
2/16: Lectures: lecture slides for all previous lectures updated to current versions
2/12: Assignments: current core E.coli model (w/ Nitrogen metabolism) posted
2/12: Assignments: HW4 posted, due by Thurs. 2/19 by midnight by email to Roger
2/12: Lectures: lecture slides for 2/12 posted
2/5: Lectures: lecture slides for 2/5 posted
2/4: Lectures: syllabus changed
2/3: Lectures: lecture slides for 2/10 posted
2/3: Lectures: lecture slides for 2/3 posted
2/2: Assignments: HW3 reposted with final slight modification (7:00pm)
1/30: Assignments: HW3 reposted with another slight modification (2:20pm)
1/29: Lectures: lecture slides for 1/29 posted
1/29: Assignments: HW3 reposted with a slight modification (1:45pm)
1/29: Assignments: HW3 posted, due by Thurs. 2/5 by midnight by email to Roger
1/28: Assignments: change in due date for preliminary reports to 2/12 by midnight
1/27: Home: outline for preliminary reports posted
1/27: Lectures: lecture slides for 1/27 updated
1/25: Lectures: lecture slides for 1/27 posted
1/25: Resources: Wiback 2002 and Price 2003 articles on RBC metabolism posted
1/24: Assignments: corrected HW2 posted (no need for biomass rxn and typo for binary S matrix corrected)
1/22: Resources: Papin 2003 article posted
1/22: Lectures: lecture slides for 1/22 posted
1/22: Resources: Famili 2003 article posted on SVD
1/22: Assignments: HW2 posted, due by Thurs. 1/29 by midnight by email to Roger
1/20: Lectures: lecture slides for 1/20 posted
1/15: Notice: preliminary project reports will be due on Feb. 5th by midnight by email to Roger
1/15: Project Presentations will be on Friday, March 13th 3:15-6:15pm, Fung Auditorium
1/15: Lectures: lecture slides for 1/15 posted
1/14: Assignments: HW1 posted, due by Thurs. 1/22 by midnight by email to Roger
1/13: Lectures: lecture slides and term project slides for 1/13 posted
1/12: Lectures: more lecture slides for 1/8 posted
1/12: Lectures: Book Chapter 6 posted
1/12: Resources: 3 articles posted on human metabolic network/modeling
1/12: Project Ideas: revised description of topic #7
1/9: Office Hours: TA office hours will be Friday 1-2pm in PFBH 417
1/8: Resources: posted iAF1260 (genome-scale E. coli model)
1/8: Notice: Please email TA with your preference of office hours Tu 12-1, Th 1-2, or Fri 1-2
1/8: Resources: posted A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information - Feist 2007
1/8: Lectures: lecture slides for 1/8 posted
1/5: Home: List of project ideas posted on front page
1/5: Home: Syllabus and 2009 schedule are posted
1/5: Updated website for 2009




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9500 Gilman Drive La Jolla, CA 92093-0412

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