BENG 123 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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Course Information News

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

Teaching Assistant

Nathan Lewis
Office Hours: W 4:00 - 6:00 PM
4th floor PFBH (by the elevators)

Frederick Lo
Office Hours: T 11:00 -1:00 PM PFBH 442

3/14: Here's a review sheet for the final.

3/8: Homework 9 is up.

3/4: If you didn't get the final project emailed to you, here it is: Beng123FinalProject.pdf.
3/4: Grades have been updated.

2/21: Today's BENG 123 lecture was moved to PFBH 161 (computer lab) today. The time will remain the same 9:30am-10:50am. Also as a reminder there is another conflict on Feb 26 that has been worked out and the class has been moved to Rm 1202 CSE building EBU3B 9:30am-10:50am.
2/21: HW7 is up.
2/20: HW6, will be due friday by the start of the discussion section. Also, HW6 should be turned in on paper, and your code shuold be emailed to In addition, if your simulation is taking too long, feel free to multiply each rate constant by 100 (but be sure to plot the time frame of 0 to .01 seconds) or change the tspan. Just be sure to document what you did. One last thing... make sure thatfor the question that says "Can you generalize...", be sure to defend your answer (don't just put yes or no).
2/20: for 3.5 on hw6, only plot the phase portraits for x1 vs. x2 and x1 vs. x5.
2/19: A few examples for executing dynamic simulations in Mathematica can be found on the resources page.
2/19: Nate's office hours on Wednesday will be held from 1:30-3:30 this week.
2/13: As a Valentine's day eve surprise, here's your exam (and homework) grades! They're ordered by the last 6 digits of your ucsd ID.
2/9: Nate's office hours this week will M 4-5pm and W 5-6pm.
2/8: Here's a brief midterm review sheet.
2/7: By popular demand, the midterm exam review will be in WLH 2113 on Sat. from 10:00am-11:00am!
2/7: A new version Homework 5 is up. For your assignment you must use at least 5 COBRA functions from the toolbox. Enjoy!
2/7: If you plan on using any ACS computers for hw #5, you'll need to use an alternate method to install the software (this has only been tested on the PFBH 161 computers):
1. Download this file (
2. Open "My Computer" and go to C:\
3. In the address bar, replace C:\ with H:\MATLAB\
4. Copy all of the files in into H:\MATLAB\ (you must use ctrl+C and crtl+V since it won't let you drag and drop)
5. make sure the address bar in MATLAB says H:\MATLAB\ and all of your assignment files are copied into that directory
6. type in MATLAB CobraLPSolver = 'glpk'; solverOK = changeCobraSolver(CobraLPSolver);
1/29: A new version Homework 4 is up. A few corrections were made on the examples. In addition, the spreadsheet and network picture were updated. It's important that you use the updated versions or your simulations will not work. Enjoy!
1/22: Homework 3 is up! Enjoy!
1/21: Nate's office hours this week will be W 2-3pm and 5-6pm. (He'll be in a meeting from 4-5pm... sorry)
1/17: A new version of HW2 (and the ecoli_core_model.xls file) has been posted... make sure to do all of the questions on the new version (one part of question 3 has been removed)
1/11: There is a typo on Homework 1. In the problem description for the Matlab exercise, Problem 9, it should read "do not do Problem 9 by hand." It currently reads "do not do Problem 8 by hand." Please do #8 by hand!
1/10: Homeworks 1, 2 and 4 are now up... 3 and 5 should also be up this coming week. If the homework pdf is scrambled when you download it, right click on the link and click "save link as" to get an unscrambled version
1/8: Welcome to Systems Biology and Bioengineering! Feel free to give yourself a self-guided tour of the website.
12/14: The Winter 2008 BENG 123 course website is now up!




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