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.
Group A Schedule
| Week | Date | Group A Activity | Assignment Due |
|---|---|---|---|
| 1 | Tu 4/1 | Intro to Bi 1x (in Chen 130) | Intro to Python for scientific computing tutorial | |
| 1 | Th 4/3 | Safety | Lab basics | Restriction digest | |
| 2 | Tu 4/8 | Image processing tutorial I (images) | JC: Nurse 2003 | |
| 2 | Th 4/10 | Intro to microscopy | |
| 5 | F 4/11 | -- | 1. Lab basics/Restriction digest |
| 3 | Tu 4/15 | Luria-Delbrück (simulation tutorial) | Seq. align. tutorial | Plotting univariate data tutorial (data set) | |
| 3 | Th 4/17 | Luria-Delbrück (plating) | JC: Baym, et al 2016 | |
| 3 | F 4/18 | -- | 2. Intro to microscopy |
| 4 | Tu 4/22 | Luria-Delbrück (colony counting and PCR amplification) | Regression tutorial | |
| 4 | Th 4/24 | Antibiotic resistance (plating) | |
| 5 | Tu 4/29 | Antibiotic resistance (patch plates) | Data wrangling tutorial | |
| 5 | Th 5/1 | JC: Neidhardt 1999 | Antibiotic resistance (resistance/producer testing) | |
| 5 | F 5/2 | -- | 3. Luria-Delbrück |
| 6 | Tu 5/6 | Building a cell discussion | Readings: Monod growth paper, Monod Nobel lecture | |
| 6 | Th 5/8 | Antibiotic resistance (DNA extraction) | |
| 7 | Tu 5/13 | Bacterial growth discussion (data set) | |
| 7 | Th 5/15 | E. coli growth | |
| 8 | Tu 5/20 | JC: Phillips Fig. 1 or Fig. 7? | Work on E. coli growth write up | |
| 8 | Th 5/22 | Population genomics with QIIME2 tutorial | |
| 8 | F 5/23 | -- | 4. E. coli growth |
| 9 | Tu 5/27 | Discussion on modeling efflux experiment | |
| 9 | Th 5/29 | Efflux experiment | |
| 9 | F 5/30 | -- | 5. Antibiotic resistance |
| 10 | Tu 6/3 | Work on write-ups | |
| 10 | Th 6/5 | Course recap and wrap-up (in Chen 130) | |
| 10 | F 6/6 | -- | 6. Efflux pumps |
Group B Schedule
| Week | Date | Group B Activity | Assignment Due |
|---|---|---|---|
| 1 | Tu 4/1 | Intro to Bi 1x (in Chen 130) | Safety | Lab basics and restriction digest | |
| 1 | Th 4/3 | Intro to Python for scientific computing tutorial | |
| 2 | Tu 4/8 | Intro to microscopy | |
| 2 | Th 4/10 | Image processing tutorial I (images) | JC: Nurse 2003 | |
| 5 | F 4/11 | -- | 1. Lab basics/Restriction digest |
| 3 | Tu 4/15 | Luria-Delbrück (plating) | JC: Baym, et al 2016 | |
| 3 | Th 4/17 | Luria-Delbrück (simulation tutorial) | Seq. align. tutorial | Plotting univariate data tutorial (data set) | |
| 3 | F 4/18 | -- | 2. Intro to microscopy |
| 4 | Tu 4/22 | Antibiotic resistance (plating) | |
| 4 | Th 4/24 | Luria-Delbrück (colony counting and PCR amplification) | Regression tutorial | |
| 5 | Tu 4/29 | Data wrangling tutorial | Antibiotic resistance (patch plates) | |
| 5 | Th 5/1 | Antibiotic resistance (resistance/producer testing) | JC: Neidhardt 1999 | |
| 5 | F 5/2 | -- | 3. Luria-Delbrück |
| 6 | Tu 5/6 | Antibiotic resistance (DNA extraction) | |
| 6 | Th 5/8 | Building a cell discussion | Readings: Monod growth paper, Monod Nobel lecture | |
| 7 | Tu 5/13 | E. coli growth | |
| 7 | Th 5/15 | Bacterial growth discussion (data set) | |
| 8 | Tu 5/20 | Work on E. coli growth write up | JC: Phillips Fig. 1 or Fig. 7? | |
| 8 | Th 5/22 | Population genomics with QIIME2 tutorial | |
| 8 | F 5/23 | -- | 4. E. coli growth |
| 9 | Tu 5/27 | Efflux experiment | |
| 9 | Th 5/29 | Discussion on modeling efflux experiment | |
| 9 | F 5/30 | -- | 5. Antibiotic resistance |
| 10 | Tu 6/3 | Work on write-ups | |
| 10 | Th 6/5 | Course recap and wrap-up (in Chen 130) | |
| 10 | F 6/6 | -- | 6. Efflux pumps |