BENG 123 2009

Systems Biology and Bioengineering:

Lecture: Tu/Th 9:30 - 10:50 PM in PFBH 161
Section: W 2:00 - 2:50 PM in CENTER 220

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Course Information News
Instructor

Dr. Bernhard Ø. Palsson
Powell-Focht Bioengineering Hall
Room 417
bpalsson@bioeng.ucsd.edu
http://systemsbiology.ucsd.edu

Teaching Assistant

Jeff Orth
jorth@ucsd.edu
Office Hours: Th 11:00 AM - 12:00 PM in PFBH 4th Floor Lobby

Aarash Bordbar
aabordba@bioeng.ucsd.edu
Office Hours: F 3:00 - 4:00 PM in PFBH 226

Schedule
Syllabus
3/12: Jeff's finals week office hours: Wednesday (3/18) from 2:00 to 3:00 pm and Thursday (3/19) from 11:00 am to 12:00 pm.
3/9: Instead of class tomorrow, we will be having a question and answer session to go over the project at the normal class time in the normal room. Homework 7 is still due at the beginning of this session.
3/7: Here is an excel file that shows shadow prices calculated for the RBC model, which can be helpful in forming pools.
3/5: Here is an updated set of pools for the glycolysis simulator, including a short description of each pool.
3/3: Homework 7 has been posted. It is due 3/10 at the beginning of class. It is the last homework assignment. YES!!
3/2: Another project correction. The DPGEX reaction drains all of the phosphate out of the system so no ATP can be produced. Instead of using this reaction, you should simulate increased 23dpg use by increasing kDPGM. The project description document has been updated to correct the error.
2/24: The project document has been corrected again. Some of the SS fluxes and concentrations were rounded too much, making it impossible to calculate the correct rate constants. The project description document has been updated to correct the error.
2/23: There were two more typos in the project document. The G6PDH reaction should be "g6p + nadp -> gl6p + nadph" and the GSSGR reaction should be "nadph + gssg -> nadp + 2 gsh". The project description document has been updated to correct the error.
2/23: Homework 6 has been posted. It is due 3/3 at the beginning of class.
2/22: There was a small error in the project document. The DPGase reaction should include phosphate (phos) as a product. The project description document has been updated to correct the error.
2/18: The project has been posted on the Assignments page. It is due Friday 3/20 at 11:00 am.
2/17: Homework 5 has been posted. It is due 2/24 at the beginning of class.
2/9: The midterm is tomorrow at 9:30! No books or notes or computers allowed.
2/5: The glycolysis simulator has been posted: Solver and ODE. It is important to note that the after running the solver, an excel file is generated in the current directory which provides some important information about the system.
2/4: The review sheet for the midterm from section has been posted: MidtermNotes.doc
1/27: Homework 4 has been posted. It is due 2/3 at the beginning of class.
1/26: We now have a class discussion group where you can help each other with homework: BENG 123 WI09
1/23: There is a typo in problem 6.4 of homework 3. b1 should be changed to 0.045, 0.050, and 0.055 instead of 0.45, 0.50, and 0.55.
1/22: We have posted a paper that should help with homework 3 problem 5.1: Palsson1987.pdf
1/19: Homework 3 has been posted. It is due 1/27 at the beginning of class.
1/12: Homework 2 has been posted. It is due 1/20 at the beginning of class.
1/12: Homework 1 is due tomorrow at the beginning of class.
1/8: Special office hours tomorrow (1/9) at 4:00 PM in 4th floor lobby
1/5: To access the 2008 website - username: be123 password: lactate
12/27: The Winter 2009 BENG 123 course website is now up!

 

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

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