Introduction to Synthetic Biology, Fall 2010

Time and place: M/W/F 11.30-12.20 in Anderson Hall 010.

Instructor: Georg Seelig gseelig*at*u.washington.edu

TA: Yuan-Jyue Chen yuan08*at*uw.edu
Office hours and location: TBA

Grading: The grade will be based on homework (3/4) and class project (1/4). There are no exams.

Homework: New homework will be handed out on Wed and is due the following Wed by the end of class. Late homework will not be graded.

Undergrads: Class projects are based on reading papers from the reasearch literature and summarizing them in an essay. The essay should contain (i) an introduction that situates the main papers in the wider literature; (ii) a summary of the technical contributions these papers make; (iii) a more detailed technical analysis of a specific system from the paper (this includes a simulation of system behavior).

Grads: Same as ugrads but the essay also needs to contain a suggestion on how to continue the research discussed in the papers you read. Graduate students will present their projects in class at the end of the term.

'''Date''' '''Topic''' '''HW''' '''Solutions'''
9/29 Introduction
10/1 Chemical kinetics and differential equations class notes HW1 available HW1 solutions
10/4 Chemical kinetics and differential equations class notes
10/6 Transcription and translation class notes HW1 due, HW2 available
10/8 Gene regulation class notes
10/11 Lac operon: Combinatorial gene regulation class notes
10/13 Synthetic transcriptional networks: bistable switches paper class notes HW3 available HW3 solutions
10/15 Robert Egbert talk: Building a bi-stable switch and other topics
10/18 Synthetic transcriptional networks: oscillators paper class notes
10/20 Posttranscriptional gene regulation: Small bacterial RNA paper class notes HW3 due tomorrow, HW4 available
10/22 Posttranscriptional gene regulation: Small bacterial RNA modeling paper class notes
Review paper on small bacterial RNA
10/25 Posttranscriptional gene regulation: Eukaryotic microRNA and RNAi class notes
 Review paper on microRNA and siRNA
10/27 Posttranscriptional gene regulation: Eukaryotic microRNA and RNAi class notes No HW this week
10/29 Posttranscriptional gene regulation: Eukaryotic microRNA and RNAi class notes
11/1 Posttranscriptional gene regulation: Two-component systems and MAP Kinases
11/3 Guest speaker Larry Ruzzo (UW CSE) on computational prediction of sRNA slides (Larry Ruzzo) HW5 available
11/5 Posttranscriptional gene regulation: Two-component systems and MAP Kinases class notes
11/8 Guest speaker Aaron Chevalier (UW BioE) on "bacterial photography"
11/10 Engineering MAPK pathways, modeling phosphorelay circuits class notes HW5 due, HW6 available
11/12 DNA Nanotechnology class notes
11/15 DNA Nanotechnology class notes
11/17 DNA Nanotechnology class notes HW6 due, HW7 available
11/19 DNA Nanotechnology class notes
11/22 Noise, robustness and stochastic chemical reactions class notes
11/24 Noise, robustness and stochastic chemical reactions
11/26 Thanksgiving
11/29 Noise, robustness and stochastic chemical reactions class notes HW7 due, HW8 available
12/1 Guest lecture Herbert Sauro
12/3 Noise, robustness and stochastic chemical reactions class notes
12/6 Noise, robustness and stochastic chemical reactions class notes
12/8 Guest lecture Jennifer Nemhauser and Eric Klavins
12/10 Pattern formation
12/13 Finals week
12/15 Finals week
12/17 Finals week