Below is the lecture schedule. Some lectures have required readings that must be done before lecture. PDFs of the reading material is linked to in the schedule.
Scheduled office hours for the TAs to help you with your homework are 3-4:30 pm on Wednesdays in SPL 102.
Due dates
- Th, 10/23: Homework 1 (rational design) due
- nupack_utils.py
- na_design.py
- rmexe (Windows only)
- NUPACK Setup Primer
- Th, 11/06: Homework 2 (directed evolution) due
- Tu, 11/11: pre-proposal due
- Th, 11/20: HW3 (rational design) due
- Th, 12/04: Homework 4 (directed evolution) due
- Fr, 12/12: proposal due at 5 PM
Lecture/reading schedule
- L1: Tu 09/30, Arnold (download all readings)
- L2: Th 10/02, Bois
- L3: Tu 10/07, Bois
- L4: Th 10/09, Bois
- Eddy 2004
- Dirks and Pierce 2003 (optional, useful for homework)
- L5: Tu 10/14, Bois
- L6: Th 10/16, Bois
- Interlude: Review papers to inspire rational design projects (download all readings)
- Zhang and Seelig 2011
- Zhang, et al. 2014
- Jung and Ellington 2014
- Geary, et al. 2014 (not a review, but interesting new result)
- L7: Tu 10/21, Arnold
- L8: Th 10/23, Arnold
- L9: Tu 10/28, Arnold
- L10: Th 10/30, Arnold
- L11: Tu 11/04, Bois
- L12: Th 11/06, Bois
- Wolfe and Pierce, 2014 (optional)
- Gillespie 1976 (optional)
- Gillespie 1977 (optional)
- L13: Tu 11/11, Bois
- L14: Th 11/13, Bois
- L15: Tu 11/18, Arnold
- L16: Th 11/20, Arnold
- L17: Tu 11/25, Arnold
- Th 11/27: Thanksgiving, no class
- L18: Tu 12/02, Arnold
- L19: Th 12/04, Arnold and Bois