Lab Schedule
The class meets 1–4 pm every Tuesday and Thursday in the basement of Kerckhoff, with a few exceptions. We will not meet in the event that Ditch Day falls on one of the scheduled class days, but we may schedule a make-up.
Below is a schedule of experiments, journal clubs, tutorials, office hours, and due dates. For several lab sessions, a prelab is due at the beginning of the lab period. All information for the prelabs, protocols, tutorials, and journal clubs can be found by clicking on the links below. This schedule will be closely followed, but is subject to change.
TA office hours are the only scheduled activities where attendance is not required. Office hours are Fridays and Mondays in the Kerckhoff basement (times TBA).
Prior to the start of class, you should compute the Setting up a Python Environment tutorial.
| Week | Date | Activity | Assignment Due |
|---|---|---|---|
| 1 | Tu 10/1 | Intro to Bi 1x | Safety | Lab basics | Restriction digest | |
| 1 | Th 10/3 | Intro to Python for scientific computing tutorial | |
| 2 | Tu 10/8 | Image processing tutorial (images) | JC: Nurse 2003 | |
| 2 | Th 10/10 | Intro to microscopy | |
| 2 | F 10/11 | -- | 1. Lab basics/Restriction digest |
| 3 | Tu 10/15 | Luria-Delbrück (simulation tutorial) | Seq. align. tutorial | Plotting univariate data tutorial (data set) | |
| 3 | Th 10/17 | Luria-Delbrück (plating) | JC: Baym, et al 2016 | |
| 2 | F 10/18 | -- | 2. Intro to microscopy |
| 4 | Tu 10/22 | Antibiotic resistance (plating) | Regression tutorial | |
| 4 | Th 10/24 | Luria-Delbrück (plating redo) | Data management tutorial | |
| 5 | Tu 10/29 | Antibiotic resistance (patch plates) | Luria-Delbrück (colony counting and PCR amplification) | |
| 5 | Th 10/31 | Antibiotic resistance (resistance/producer testing) | JC: Neidhardt 1999 | |
| 6 | Tu 11/5 | Antibiotic resistance (DNA extraction) | |
| 6 | Th 11/7 | Building a cell discussion | Readings: Monod growth paper, Monod Nobel lecture | |
| 6 | F 11/8 | -- | 3. Luria-Delbrück |
| 7 | Tu 11/12 | E. coli growth | |
| 7 | Th 11/14 | Discussion on data analysis for bacterial growth experiment | |
| 8 | Tu 11/19 | Discussion of efflux pump modeling | |
| 8 | Th 11/21 | Efflux experiment | |
| 8 | F 11/22 | -- | 4. E. coli growth |
| 9 | Tu 11/26 | Population genomics with QIIME2 tutorial | |
| 9 | Th 11/28 | No class; Thanksgiving Day | |
| 10 | Tu 12/3 | Work on write-ups | JC: Phillips Fig. 1 or Fig. 7? | |
| 10 | Th 12/5 | Course recap and wrap-up (in Kerckhoff 125) | |
| 10 | F 12/6 | -- | 5. Antibiotic resistance 6. Efflux pumps |