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):
- 9-10 am
- 1-2 pm
- 3-4 pm
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 access.caltech.edu) 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
- Course Ed page
- Course Zoom link
- Gather collaboration link (use Firefox or Google Chrome)
- Video recordings
- Shared data
Schedule
- < 03/31
- JupyterLab setup
- 03/31
- Welcome to Bi 1x
- Instructions for kombucha brewing
- Instructions for Luria-Delbrück starter culture
- Troubleshooting JupyterLab setup
- 04/04
- Start Luria-Delbrück culture (no class meeting)
- 04/05
- Check-in on kombucha brewing
- Check-in on Luria-Delbrück grow-ups
- Discussion on Luria-Delbrück experiment
- 04/07
- Luria-Delbrück plating
- Tutorial: Python for scientific computing (data set)
- 04/12
- Discussion of The Great Ideas of Biology by Paul Nurse
- 04/14
- Antibiotic resistance plating
- PCR/sequence alignment tutorial
- Tutorial: Plotting univariate data (data set)
- Tutorial: Simulating the Luria-Delbrück experiment
- 04/19
- Discussion of Antibiotic resistance
- 04/21
- Stressed out bacteria and antibiotic resistance:
Guest lecture by Lucas Meirelles and Elena Perry - Constructing your spectrophotometer
- 04/26
- Discussion of Obsession with dN/dt by Fred Neidhardt
- 04/28
- Modern approaches to detection of antibiotic resistance: lecture by Matt Cooper
- Calibrating your spectrophotometer
- Yeast growth
- 05/03
- Discussion of the yeast growth experiment
- 05/05
- The search for extraterrestrial life: Guest lecture by Haley Sapers
- Tutorial on regressions (data set)
- Continued work on yeast growth
- 05/10
- Discussion of enzyme catalysis experiment
- 05/12
- Enzyme catalysis
- 05/17
- Discussion of kombucha brewing experiment
- 05/19
- Tutorial on population genetics analysis using QIIME2 (QIIME2 setup, AWS usage, Getting started with analysis)
- 05/24
- Discussion of Figure 1 or Figure 7? by Rob Phillips
- 05/26
- Work on analysis of kombucha data
- 05/31
- Memorial Day, no class
- 06/02
- Course recap and wrap-up
- 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)
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.