Description
BE 150: Quantitative studies of cellular and developmental systems in biology, including the architecture of specific genetic circuits controlling microbial behaviors and multicellular development in model organisms. Specific topics include chemotaxis, multistability and differentiation, biological oscillations, stochastic effects in circuit operation, as well as higher-level circuit properties such as robustness. Organization of transcriptional and protein-protein interaction networks at the genomic scale. Topics are approached from experimental, theoretical and computational perspectives.
Bi 250b: The class will focus on quantitative studies of cellular and developmental systems in biology. It will examine the architecture of specific genetic circuits controlling microbial behaviors and multicellular development in model organisms. The course will approach most topics from both experimental and theoretical/computational perspectives. Specific topics include chemotaxis, multistability and differentiation, biological oscillations, stochastic effects in circuit operation, as well as higher-level circuit properties such as robustness. The course will also consider the organization of transcriptional and protein-protein interaction networks at the genomic scale.
General Information
[Alon] U. Alon, An Introduction to Systems Biology: Design Principles of Biological Circuits, CRC Press, 2006.
Students in BE 150 should also obtain the following notes (freely downloadable from the web):
[BFS] D. Del Vecchio and R. M. Murray, Biomolecular Feedback Systems
The following additional texts and notes may be useful for some students:
[Klipp] Edda Klipp, Wolfram Liebermeister, Christoph Wierling, Axel Kowald, Hans Lehrach, Ralf Herwig, Systems biology: A textbook. Wiley, 2009.
[Strogatz] Steven Strogatz, Nonlinear Dynamics And Chaos: With Applications To Physics, Biology, Chemistry, And Engineering. Westview Press, 2001.
Announcements
Hi class,
There will be no recitation this Friday. Also, the homework is not due until Monday (5/19).
Hi all,
Vipul and I will both be out of town next Wed-Friday so we won't be around to collect homeworks. Therefore, we are extending the due date of HW5 to the following Monday (5/19).
However, we will also not be available to answer questions online from Wed-Friday, so please plan accordingly.
HW5 has been posted on the class wiki.
It will be due two weeks from today (May 15th).
Hello class,
After grading all of your homework sets for four weeks now, Vipul and I have noticed some recurring trends.
I realize it's pretty late in the game to be giving homework submission advice, but this is advice that will be helpful to you and your TAs in other classes.
- Page headers: Always, always, always, include your name on every page, especially if you are sending it via email. And also the title of the course. We grade Bi250 and BE150 sets separately.
- GRAPHS. I have a lot of thoughts about graphs.
- Axes: When you make a graph, you should think to yourself: "What is the purpose of this graph?" The answer should NOT be "Because the TAs love to look at vague graphs." The answer should be "Oh I want to illustrate the time-dependent behavior of X, therefore, I should size the axes appropriately and include labels." If you are trying to point out something that is happening at time 10s and it's a spike that goes from 0 to 1, your axes should be x = [ 0 to 20s ] and y = [-1 to 2]. Your axes should NOT be x = [0 to 1000s] and y = [0 1000]. Matlab will choose scales that show ALL of your data, but you need to make intelligent choices about what you want to show us.
- Descriptions: After you make the graph, please write (in words) a description of the graph. What does the graph show? Why do you think we asked you make this graph? Usually we ask you to make a graph because it allows you to visualize, and then better understand, the system. We don't know if you really understand it if you just submit an entire homework set of unexplained graphs with no words.
- Organization: When TAs grade homework, we are looking for specific things to check off and give you points for. You can help us by boxing your final answer or making it pretty obvious. The last thing you want is points off because we can't find your final answer in a mountain of derivations.
- Read what the question is asking. Make sure you are solving for the right variable. Make sure you are answering the specific question that we ask.
Hi everyone,
We've added a couple extra lines to the homework. Please redownload it or just look at the rest of this message.
Part 3(a)
-Assume Ctot = 3.4 µM and k = 0.116 h-1
-Run simulations for 200 h
Part 3(b)
- Run simulations for 200 h
Hi everyone,
HW4 has been posted on the class wiki.
Since we're posting it a day late it will be due a day later as well (Next Thursday 5/1 at 5pm)
Hi all,
We are still working on putting together HW4, so it's not yet posted on the wiki.
Don't worry though, it will be due a week from whenever we post it.
Hi everyone,
It is time to start thinking about your final projects! They are worth 25% of your overall grade.
Here's what we want you to do:
1. Pick an interesting biological system.
2. Propose analysis using tools that we used in this class.
3. Either make your own teams (2-3 people), or propose an idea individually and we will group by interest
4. Send an email to be150-tas@caltech.edu by Friday ( April 25th 2014 ). The email should include all the information from items 1-3 (the system, the analysis, anyone you're teaming up with).