Schedule

Course schedule

Following is the tentative schedule. It is subject to change. The date listed is the Monday of the week. The lecture and tutorial material may be watched on your own time (links will be provided as that content is recorded).


Every Wednesday at 1 pm PST, we will have a discussion on "Why we do the things we do." The idea here is that we discuss ideas about experimentation and why certain choices are made. We have specific questions we will discuss each time, but we are intentionally not sharing them ahead of time. We want the discussions to be free form, featuring on-the-fly thinking and discussion. These discussions will be recorded and made available in the event that you miss one of the Wednesday sessions or want to review the discussion (or even share with your family).


Every Monday, we will have a discussion, either about a paper we have read ahead of time, or about the particulars of one of the experiments we will be working with. For discussions involving a paper, you should read the paper ahead of time. The discussion times are (all Pacific Standard Time):

You will sign up for one discussion time, and that will be your discussion time for the term. In the event that you have a one-off conflict, you may join another discussion. These discussions are not recorded.


Note that access to videos by clicking the links on the course schedule, you need to enter credentials twice. First, you will need to enter the username and password for the Bi 1x class, which was sent to you via email. Then, you will need to enter your Caltech credentials (those you use for access.caltech.edu) to have access to the videos via Google Drive. You may have trouble streaming videos using Safari. I found that Firefox and Chrome work.


Before class starts, you should get a working Python environment for scientific computing set up on your computer. To do so, follow the instructions in the Setting up a Python environment tutorial.


Zoom links


Schedule

04/06
Welcome to Bi 1x lecture (JB)
Python for scientific computing tutorial [video] (JB)
Discussion of The Great Ideas of Biology (JB)
Why we do the things we do
Readings

04/13
Luria-Delbrück lecture (SW)
PCR/sequence alignment tutorial (JB) [DNA polymerase video]
Discussion of Luria-Delbrück experiment [skeleton notebook] (SW)
Why we do the things we do
Readings

04/20
E. coli growth lecture (LT)
Image processing I tutorial (images) [video] (JB)
Discussion of E. coli growth (LT)
Why we do the things we do and homework help
Readings
04/27
Microbiology lecture (LT)
Image processing II tutorial (images) [video] (JB)
Discussion of Obsession with dN/dt by Fred Neidhardt (JB)
Why we do the things we do and homework help
Readings
05/04
Statistical mechanics of gene expression (MM)
Discussion of the LacI experiment and Figure 1 or Figure 7? (MM)
Why we do the things we do and homework help
Thursday homework help video
Readings
05/11
Lecture on synthetic biology (LM)
Delay differential equations tutorial [video] (JB)
Image processing III tutorial (images) [video] (JB)
Discussion of the delay oscillator experiment (LM)
Why we do the things we do and homework help
Readings

05/18
Lecture on developmental biology (SP)
Reaction-diffusion modeling tutorial (JB)
Discussion of the Drosophila patterning experiment (SP)
Why we do the things we do and homework help
Readings

05/25
No class Monday (Memorial Day)
Hacker stats tutorial (SW) [video]
Lecture on optogenetics and model organisms (Ravi Nath and Claire Bedrook), live on Wednesday
Thursday homework help video
Readings

06/01
Discussion of Markus Meister's blog posts about science fiction (Monday 1 pm session should go to one of the others)
TA research talks and reflections on Bi 1x
Thursday homework help video
Readings

Due dates

Homeworks are posted below next to their respective due dates. All homeworks are due at 5pm PST.


All data sets necessary to do the assignments may be downloaded here.


Th 04/23
Luria-Delbrück
Fr 05/08
E. coli growth
Fr 05/15
LacI titration
Fr 05/22
Delay oscillator segmentation results
Fr 05/29
Delay oscillator assignment
Fr 05/29
Drosophila embryogenesis
Fr 06/05
C. elegans optogenetics