Lab Schedule
The class meets every Tuesday from 7-10pm and every Wednesday from 1-4pm in Braun B115, with a few exceptions. We also have one required Thursday meeting on 4/4 from 7-10pm. 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 each lab session, with the exception of week 1, 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. Unless otherwise specified, they are on Saturday afternoons, 2-5pm, in the Braun B115 conference room. Instructor office hours are by appointment.
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 4/2 | Intro to Bi 1x | Safety | Lab basics | |
| 1 | W 4/3 | Intro to Python for scientific computing tutorial | Restriction digestion | |
| 1 | Th 4/4 | No class | |
| 1 | Sa 4/6 | No office hours | |
| 2 | Tu 4/9 | Image processing tutorial I (images) | JC: Nurse 2003 | |
| 2 | W 4/10 | Intro to microscopy | |
| 2 | Sa 4/13 | Lab basics/Restriction digestion and Intro to microscopy office hours | |
| 3 | Tu 4/16 | Luria-Delbrück (plating) | 1. Lab basics/Restriction digestion 2. Intro to microscopy |
| 3 | W 4/17 | Luria-Delbrück simulation tutorial | |
| 3 | Sa 4/20 | No office hours | |
| 4 | Tu 4/23 | Bioinformatics tutorial I | JC: Neidhardt, 1999 | |
| 4 | W 4/24 | Luria-Delbrück (colony counting and PCR amplification) | Discussion about synthetic biology | |
| 4 | Sa 4/27 | Luria-Delbrück office hours | |
| 5 | Tu 4/30 | E. coli growth (bulk) | 3. Luria-Delbrück |
| 5 | W 5/1 | E. coli growth (movies) | |
| 5 | Sa 5/4 | E. coli growth office hours | |
| 6 | Tu 5/7 | LacI titration | |
| 6 | W 5/8 | Image processing tutorial II (images) | Stat mech of gene expression | |
| 6 | Sa 5/11 | E. coli growth | LacI titration office hours | |
| 7 | Tu 5/14 | <Image processing tutorial III (images) | DDE tutorial | Kombucha brewing | 4. E. coli growth |
| 7 | W 5/15 | Delay oscillator | |
| 7 | Sa 5/18 | LacI titration | Delay oscillator office hours | |
| 8 | Tu 5/21 | Kombucha DNA extraction | 5. LacI titration |
| 8 | W 5/22 | Bioinformatics tutorial II | JC: microbial ecology | |
| 8 | Sa 5/25 | Delay oscillator office hours | |
| 9 | Tu 5/28 | Hacker stats tutorial | 6. Delay oscillator |
| 9 | W 5/29 | C. elegans optogenetics | |
| 9 | Sa 6/1 | C. elegans optogenetics | Kombucha office hours | |
| 10 | Tu 6/4 | Work on write-ups | |
| 10 | W 6/5 | Course recap and wrap-up | |
| 10 | F 6/7 | -- | 7. C. elegans optogenetics 8. Kombucha |
Group B Schedule
| Week | Date | Group B Activity | Assignment Due |
|---|---|---|---|
| 1 | Tu 4/2 | Intro to Bi 1x | Safety | |
| 1 | W 4/3 | Lab basics | Intro to Python for scientific computing tutorial | |
| 1 | Th 4/4 | Restriction digestion | |
| 1 | Sa 4/6 | No office hours | |
| 2 | Tu 4/9 | Intro to microscopy | |
| 2 | W 4/10 | Image processing tutorial I (images) | JC: Nurse 2003 | |
| 2 | Sa 4/13 | Lab basics/Restriction digestion and Intro to microscopy office hours | |
| 3 | Tu 4/16 | Luria-Delbrück simulation tutorial | 1. Lab basics/Restriction digestion 2. Intro to microscopy |
| 3 | W 4/17 | Luria-Delbrück (plating) | |
| 3 | Sa 4/20 | No office hours | |
| 4 | Tu 4/23 | Luria-Delbrück (colony counting and PCR amplification) | Discussion about synthetic biology | |
| 4 | W 4/24 | Bioinformatics tutorial I | JC: Neidhardt, 1999 | |
| 4 | Sa 4/27 | Luria-Delbrück office hours | |
| 5 | Tu 4/30 | E. coli growth (movies) | 3. Luria-Delbrück |
| 5 | W 5/1 | E. coli growth (bulk) | |
| 5 | Sa 5/4 | E. coli growth office hours | |
| 6 | Tu 5/7 | Image processing tutorial II (images) | Stat mech of gene expression | |
| 6 | W 5/8 | LacI titration | |
| 6 | Sa 5/11 | E. coli growth | LacI titration office hours | |
| 7 | Tu 5/14 | Delay oscillator | 4. E. coli growth |
| 7 | W 5/15 | Image processing tutorial III (images) | DDE tutorial | Kombucha brewing | |
| 7 | Sa 5/18 | LacI titration | Delay oscillator office hours | |
| 8 | Tu 5/21 | Bioinformatics tutorial II | JC: microbial ecology | 5. LacI titration |
| 8 | W 5/22 | Kombucha DNA extraction | |
| 8 | Sa 5/25 | Delay oscillator office hours | |
| 9 | Tu 5/28 | C. elegans optogenetics | 6. Delay oscillator |
| 9 | W 5/29 | Hacker stats tutorial | |
| 9 | Sa 6/1 | C. elegans optogenetics | Kombucha office hours | |
| 10 | Tu 6/4 | Work on write-ups | |
| 10 | W 6/5 | Course recap and wrap-up | |
| 10 | F 6/7 | -- | 7. C. elegans optogenetics 8. Kombucha |