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Main Groups Schedule Literature Links Vendors

Note: Homeworks are due on Mondays by midnight. Most homework will be posted on the wiki on you group page.

Each week will have approximately the following schedule. On Monday the lecture will introduce the lab for that week. On Wednesday and Friday the lecture will cover the molecular biology, mathematical modeling, and design. There will be homeworks, primarily on modeling, due on Mondays.

Week Lecture Topic Homework Lab Description
3/26: Brief Introduction, Lab Safety and Scheduling ppt (read DS 317--320)
3/28: Detailed overview of the course ppt (try reading the repressilator paper -- we'll get back to this later)
3/30: All about e. coli ppt (read DS 130--140)
- Lab Safety, Pipetting (read DS 317--330)
4/2: Bacterial cultures ppt (read DS 331--350)
4/4: Important Molecules ppt (read SBiP ch. 2)
4/6: Transcription and Translation ppt (read DS ch. 2)
HW1 --

due 4/2

Bacterial Cultures (read DS 331--350)
4/9: Restriction enzymes and gels ppt (read DS pp. 351--374)
4/11: Regulation ppt
4/13: Introduction to kinetics pdf (read Feinberg ch. 1-2).
HW2 --

due 4/9

Restriction Analysis

4/16: Examples of reactions networks pdf
4/18: Qualitative Behavior of Reaction Networks pdf. Here are my notes on dynamical systems: (1), (2), (3)
4/20: Protein and nucleotide assays ppt (Ranjana Mehta)
HW3 --

due 4/16

Rapid Colony Transformation
4/23: Possibilities of Genetically Engineered Devices ppt + Group Project Ideas
4/25: Enzyme Kinetics, pdf
4/27: No Class: Engineering Open House
HW4 --

due 4/23

Antiobiotic Resistance Assay
4/30: Recombination, ppt
5/2: BioBricks ppt
5/4: Finding Parameters from Data pdf
HW5 --

due 4/30

Recombination of Antibiotic Resistance Genes
5/7: Stochastic Chemical Reactions pdf
5/9: The Stochastic Simulation Algorithm pdf (read Gillespie-71).
5/11: Stochastic Phenomena in cells ppt. Read this and this.
HW6 --

due 5/7

Transformation with Antibiotic Resistance Plasmids
5/14: The Finite State Projection Method pdf Read this paper.
5/16: Guest speaker: Jennifer Nemhauser: Arabidopsis signaling pathways. Read this paper. Mathematical model due. Meetings on 5/17.
5/18: Model reduction pdf.
HW7 --

due 5/21

Replica Plating
5/21: No class
5/23: Guest Speaker:Nitin Baglia: Systems Biology. Read this paper. Simulation output due.
5/25: Discussion of final projects and in vitro transcriptional circuits. Read this and this.
-- Purification and Identification of Plasmids
5/28: Memorial Day
5/30: Discussion
6/1: Poster Session!
-- An In Vitro Circuit
6/6: Wiki page will be graded.
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