Lab Schedule
The class meets every Tuesday from 7-10 pm and every Wednesday from 1-4 pm 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 will schedule a make-up.
Below is a schedule of experiments, journal clubs, tutorials, office hours, and due dates. Prior to many 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 Mondays and Tuesdays 7-8 pm in the Kerckhoff basement.
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 3/29 | Intro to Bi 1x (in Broad 100) | Safety | Lab basics and restriction digest | |
| 1 | W 3/30 | Intro to Python for scientific computing tutorial | |
| 2 | Tu 4/5 | Intro to microscopy | |
| 2 | W 4/6 | JC: Nurse 2003 | Image processing tutorial I (images) | |
| 3 | Tu 4/12 | Luria-Delbrück (plating) | Luria-Delbrück (simulation tutorial) | 1. Lab basics/Restriction digest |
| 3 | W 4/13 | Guest lecture by Matt Cooper (in Broad 100) | Plotting univariate data tutorial (data set) | |
| 4 | Tu 4/19 | JC: Baym, et al 2016 | Luria-Delbrück (colony counting and PCR amplification) | 2. Intro to microscopy |
| 4 | W 4/20 | Antibiotic resistance (plating) | Regression tutorial | |
| 5 | Tu 4/26 | Spectrophotometer construction and calibration | 3. Luria-Delbrück (except sequencing) |
| 5 | W 4/27 | Antibiotic resistance (DNA extraction) | |
| 6 | Tu 5/3 | Antibiotic resistance (patch plate and resistance/producer testing) | JC: Neidhardt 1999 | |
| 6 | W 5/4 | Image processing tutorial II (images) | Enzyme kinetics | |
| 7 | Tu 5/10 | Practice with C. elegans | Hacker stats tutorial | |
| 7 | W 5/11 | C. elegans optogenetics | Sequence alignment tutorial | |
| 8 | Tu 5/17 | E. coli growth (bulk) | 4. Enzyme kinetics |
| 8 | W 5/18 | E. coli growth (movies) | |
| 9 | Tu 5/24 | JC: Phillips Fig. 1 or Fig. 7? | Work on E. coli growth write-up | 5. C. elegans optogenetics |
| 9 | W 5/25 | Guest lecture from Charles Kollmer | Population genomics with QIIME2 tutorial (part 1, part 2, part 3) (in BBB B180) | |
| 10 | Tu 5/31 | Work on write-ups (in Chen 130) | |
| 10 | W 6/1 | Course recap and wrap-up (in Broad 100) | |
| 10 | F 6/3 | -- | 3. Luria-Delbrück (sequencing) 6. Antibiotic resistance 7. E. coli growth |
Group B Schedule
| Week | Date | Group B Activity | Assignment Due |
|---|---|---|---|
| 1 | Tu 3/29 | Intro to Bi 1x (in Broad 100) | Intro to Python for scientific computing tutorial | |
| 1 | W 3/30 | Safety | Lab basics | Restriction digest | |
| 2 | Tu 4/5 | JC: Nurse 2003 | Image processing tutorial I (images) | |
| 2 | W 4/6 | Intro to microscopy | |
| 3 | Tu 4/12 | Luria-Delbrück (simulation tutorial) | Luria-Delbrück (plating) | 1. Lab basics/Restriction digest |
| 3 | W 4/13 | Guest lecture by Matt Cooper (in Broad 100) | Plotting univariate data tutorial (data set) | |
| 4 | Tu 4/19 | Luria-Delbrück (colony counting and PCR amplification) | JC: Baym, et al 2016 | 2. Intro to microscopy |
| 4 | W 4/20 | Regression tutorial | Antibiotic resistance (plating) | |
| 5 | Tu 4/26 | Antibiotic resistance (DNA extraction) | 3. Luria-Delbrück (except sequencing) |
| 5 | W 4/27 | Spectrophotometer construction and calibration | |
| 6 | Tu 5/3 | Image processing tutorial II (images) | Enzyme kinetics | |
| 6 | W 5/4 | Antibiotic resistance (patch plate and resistance/producer testing) | JC: Neidhardt 1999 | |
| 7 | Tu 5/10 | Hacker stats tutorial | Practice with C. elegans | |
| 7 | W 5/11 | Sequence alignment tutorial | C. elegans optogenetics | |
| 8 | Tu 5/17 | E. coli growth (movies) | 4. Enzyme kinetics |
| 8 | W 5/18 | E. coli growth (bulk) | |
| 9 | Tu 5/24 | Work on E. coli growth write-up | JC: Phillips Fig. 1 or Fig. 7? | 5. C. elegans optogenetics |
| 9 | W 5/25 | Guest lecture from Charles Kollmer | Population genomics with QIIME2 tutorial (part 1, part 2, part 3) (in BBB B180) | |
| 10 | Tu 5/31 | Work on write-ups (in Chen 130) | |
| 10 | W 6/1 | Course recap and wrap-up (in Broad 100) | |
| 10 | F 6/3 | -- | 3. Luria-Delbrück (sequencing) 6. Antibiotic resistance 7. E. coli growth |