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   <td>Vetrans Day</td>
   <td>Vetrans Day</td>
   <td>[ Molecular Programming]</td>
   <td>[ Molecular Programming]</td>
   <td>[ Adleman's Paper]. [ Qian and Winfree's Paper]</td>
   <td>[ Adleman's Paper]. [ Qian and Winfree's Paper]</td>

Revision as of 18:27, 14 November 2012

Introduction to Synthetic Biology : Fall 2012

  • BioE 423/523, CSE 486/586, EE 423/523
  • Instructor: Prof. Eric Klavins
    • Office Hours: Tu, Th 8:30AM - 10:20AM, CSE 236
      • Office hours on 11/13 are 10am - noon.
  • Teaching Assistant: Kevin Oishi
    • Office Hours: Mo, Fr, 10:00AM - 11:20AM, Sieg 128
  • MWF 11:30-12:20
  • Grading (Undergrads): Homework : 30%, Midterm : 30%, Final : 30%, Project : 10%
  • Grading (Grads): Homework : 30%, Midterm : 25%, Final : 25%, Project : 10%, Review : 10%
  • Homework policies: The lowest homework grade will be dropped. Extra credit will be recorded and used subjectively when determining letter grades. Homework must be turned in on time. Late homeworks are not accepted except for prearranged travel or unexpected illness.


Date Topic Readings and Other Materials Assignment Solution
1 9/24 History A variety of optional readings are listed below. A1, due 10/1 A1 Solution
9/26 Synthetic Biology Special Issue of Science on Synthetic Biology
and optional overviews of synthetic biology.
9/28 Gene Expression Find a tutorial that speaks to you
2 10/1 Chemical Kinetics
ODEs in Matlab
For more on chemical reactions, check out Lecture 2 of Feinberg's notes. The notation is a bit different, but the ideas are the same. A2, due 10/8 A2 Solution
10/3 Introduction to gro Read the paper on gro. A few other papers are listed below.
10/5 iGEM! Check out UW's iGEM wiki page and also read about other teams.
3 10/8 Gene Regulation

Rewiring cells: synthetic biology as a tool to interrogate the organizational principles of living systems. Optional readings are listed below.

A3, due 10/15 A3 Solution
10/10 Modeling Gene Regulation Boolean networks
10/12 Synthetic Gene Networks A Yobust and tunable gene oscillator
4 10/15 Signaling

Check out Bonnie Bassler's TED Talk on quorum sensing .

0.gro,1.gro,2.gro,3.gro. Optional readings are listed below.
A4, due 10/22 A4 Solution
10/17 Pattern Formation

This paper demonstrates some of the impossibility ideas we discussed. More papers are listed below.

10/19 Extra Pattern Formation Slides le_example.gro,midpoint.gro
5 10/22 Noise Stochastic Gene Expression. Other noise papers listed below. A5, due 10/29 A5 Solution
10/24 Modeling Noise Nothing required, but you might want to check out the list below of books on probability.
10/26 Noise in Gene Expression You can read my 2009 course notes on stochasticity. Links to other resources are below.
6 10/29 Review
11/1 Bioweapons, biosecurity, and ethics Look at the PBS Documentary on the Living Weapon.
7 11/5 Midterm Results and Solutions
11/7 Example of the moment equation method (no notes). Other examples here. A6, due 11/14
11/9 Computation See my notes and also the paper by Soloveichik et al.
8 11/12 Vetrans Day Molecular Programming Adleman's Paper. Qian and Winfree's Paper
9 11/19
11/21 Guest Lecture: Rob Carlson
11/23 Thanksgiving
10 11/26 Guest Lecture: Georg Seelig
11/28 Guest Lecture: James Carothers
11/30 Grad Presentations
11 12/3 Grad Presentations
12/5 Grad Presentations
12/7 FINAL
12/12 FINAL MEETING : Simulation presentations!


1 History

2 Synthetic Biology Overviews

3 Biology Reviews

4 Chemical Kinetics

5 gro

6 iGEM

7 Gene Regulation

8 Gene Regulation

  • A more recent paper on identifying gene networks based on expression patterns using boolean networks.

9 Synthetic Gene Networks

10 Signaling

11 Pattern Formation

13 Noise

14 Modeling Noise

15 Noise in Gene Expression

16 Ethics, Biosafety, Biowarfare