Course schedule

Following is the tentative schedule.

Every Wednesday at 1 pm PST, we will have class meetings. The content of these meetings will very from week to week. Activities include but are not limited to instruction on how to perform an experiment or analysis, guest lectures, and discussions. Relevant parts of the Wednesday meetings will be recorded and posted.

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.

Every Thursday from 4:30–6:30 pm we have TA-led discussions and homework help. These are not recorded.

Note that to 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 to have access to the videos via Google Drive.

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.

Important links


< 03/31
JupyterLab setup

Welcome to Bi 1x
Instructions for kombucha brewing
Instructions for Luria-Delbrück starter culture
Troubleshooting JupyterLab setup

Start Luria-Delbrück culture (no class meeting)
Check-in on kombucha brewing
Check-in on Luria-Delbrück grow-ups
Discussion on Luria-Delbrück experiment

Luria-Delbrück plating
Tutorial: Python for scientific computing (data set)

Discussion of The Great Ideas of Biology by Paul Nurse

Antibiotic resistance plating
PCR/sequence alignment tutorial
Tutorial: Plotting univariate data (data set)
Tutorial: Simulating the Luria-Delbrück experiment

Discussion of Antibiotic resistance

Stressed out bacteria and antibiotic resistance:
Guest lecture by Lucas Meirelles and Elena Perry
Constructing your spectrophotometer

Discussion of Obsession with dN/dt by Fred Neidhardt

Modern approaches to detection of antibiotic resistance: lecture by Matt Cooper
Calibrating your spectrophotometer
Yeast growth

Discussion of the yeast growth experiment

The search for extraterrestrial life: Guest lecture by Haley Sapers
Tutorial on regressions (data set)
Continued work on yeast growth

Discussion of enzyme catalysis experiment

Enzyme catalysis

Discussion of kombucha brewing experiment

Tutorial on population genetics analysis using QIIME2 (QIIME2 setup, AWS usage, Getting started with analysis)

Discussion of Figure 1 or Figure 7? by Rob Phillips

Work on analysis of kombucha data

Memorial Day, no class

Course recap and wrap-up

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.

M 04/12
Enter colony counts for the Luria-Delbrück experiment
F 04/23
1. Luria-Delbrück
F 04/30
1. Luria-Delbrück sequencing problem
F 05/07
2. Antibiotic resistance
F 05/14
3. Growth curves (spectrophotometer instructions)
F 05/21
4. Enzyme catalysis (spectrophotometer instructions)
W 06/02
Extra credit assignments (poetry slam)
F 06/04
5. Kombucha populations (QIIME2 setup, AWS usage, Getting started with analysis)