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(Introduction to Synthetic Biology : Fall 2012)
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(Schedule)
 
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* Instructor: Prof. Eric [[User:Klavins|Klavins]]
* Instructor: Prof. Eric [[User:Klavins|Klavins]]
** Office Hours: Tu, Th 8:30AM - 10:20AM, CSE 236
** Office Hours: Tu, Th 8:30AM - 10:20AM, CSE 236
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*** No office hours on 10/23. They have been reschedule to 8:30-10:20 on 10/24
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*** Office hours on 11/13 are 10am - noon.
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*** Office hours on 10/25 are as usual.
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* Teaching Assistant: Kevin [[User:Oishi|Oishi]]
* Teaching Assistant: Kevin [[User:Oishi|Oishi]]
** Office Hours: Mo, Fr, 10:00AM - 11:20AM, Sieg 128
** Office Hours: Mo, Fr, 10:00AM - 11:20AM, Sieg 128
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</td>
</td>
   <td>[[SBF12_A3|A3]], due 10/15</td>
   <td>[[SBF12_A3|A3]], due 10/15</td>
-
   <td></td>
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   <td>[http://depts.washington.edu/soslab/sbf12/sbf12_a3-sol.pdf A3 Solution]</td>
   <td></td>
   <td></td>
</tr>
</tr>
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   <td>10/12</td>
   <td>10/12</td>
   <td>[http://depts.washington.edu/soslab/sbf12/9-Synthetic-Gene-Networks.pdf Synthetic Gene Networks]</td>
   <td>[http://depts.washington.edu/soslab/sbf12/9-Synthetic-Gene-Networks.pdf Synthetic Gene Networks]</td>
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   <td>A [http://www.nature.com/nature/journal/v456/n7221/full/nature07389.html Yobust and tunable gene oscillator]</td>
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   <td>A [http://www.nature.com/nature/journal/v456/n7221/full/nature07389.html Robust and tunable gene oscillator]</td>
   <td></td>
   <td></td>
   <td></td>
   <td></td>
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[http://depts.washington.edu/soslab/sbf12/lec_10_0.gro 0.gro],[http://depts.washington.edu/soslab/sbf12/lec_10_1.gro 1.gro],[http://depts.washington.edu/soslab/sbf12/lec_10_2.gro 2.gro],[http://depts.washington.edu/soslab/sbf12/lec_10_3.gro 3.gro]. Optional readings are listed below.</td>
[http://depts.washington.edu/soslab/sbf12/lec_10_0.gro 0.gro],[http://depts.washington.edu/soslab/sbf12/lec_10_1.gro 1.gro],[http://depts.washington.edu/soslab/sbf12/lec_10_2.gro 2.gro],[http://depts.washington.edu/soslab/sbf12/lec_10_3.gro 3.gro]. Optional readings are listed below.</td>
   <td>[[SBF12_A4|A4]], due 10/22</td>
   <td>[[SBF12_A4|A4]], due 10/22</td>
-
   <td></td>
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   <td>[[:Image:Sbf12_a4-sol.pdf|A4 Solution]]</td>
   <td></td>
   <td></td>
</tr>
</tr>
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   <td>[http://www.sciencemag.org/content/297/5584/1183.full Stochastic Gene Expression]. Other noise papers listed below.</td>
   <td>[http://www.sciencemag.org/content/297/5584/1183.full Stochastic Gene Expression]. Other noise papers listed below.</td>
   <td>[[SBF12_A5|A5]], due 10/29</td>
   <td>[[SBF12_A5|A5]], due 10/29</td>
-
   <td></td>
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   <td>[[:Image:Sbf12_a5-sol.pdf|A5 Solution]]</td>
   <td></td>
   <td></td>
</tr>
</tr>
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<tr>
<tr>
   <td>11/1</td>
   <td>11/1</td>
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   <td>Bioweapons, biosecurity, and ethics</td>
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   <td>[http://depts.washington.edu/soslab/sbf12/16-Ethics.pdf Bioweapons, biosecurity, and ethics]</td>
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   <td></td>
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   <td>Look at the [http://www.pbs.org/wgbh/americanexperience/features/timeline/weapon-timeline/ PBS Documentary on the Living Weapon].</td>
   <td></td>
   <td></td>
   <td></td>
   <td></td>
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   <td rowspan=3 class="big">7</td>
   <td rowspan=3 class="big">7</td>
   <td>11/5</td>
   <td>11/5</td>
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   <td></td>
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   <td>Midterm Results and Solutions</td>
   <td></td>
   <td></td>
   <td></td>
   <td></td>
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<tr>
<tr>
   <td>11/7</td>
   <td>11/7</td>
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   <td></td>
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   <td>Example of the moment equation method (no notes).</td>
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   <td></td>
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   <td>Other examples  [http://faculty.washington.edu/klavins/ssb/ssb_Part9.pdf here]. </td>
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   <td></td>
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   <td>[[SBF12_A6|A6]], due 11/14</td>
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   <td></td>
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   <td>[[:Image:Sbf12_a6-sol.pdf|A6 Solution]]</td>
</tr>
</tr>
<tr>
<tr>
   <td>11/9</td>
   <td>11/9</td>
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   <td></td>
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   <td>[http://depts.washington.edu/soslab/sbf12/17-Computation.pdf Computation]</td>
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   <td></td>
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   <td>See [http://faculty.washington.edu/klavins/ssb/ssb_Part9.pdf my notes] and also the paper by [http://www.springerlink.com/content/n77hw26844982521/fulltext.pdf Soloveichik et al.]</td>
   <td></td>
   <td></td>
   <td></td>
   <td></td>
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<tr>
<tr>
   <td>11/14</td>
   <td>11/14</td>
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   <td></td>
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   <td>[http://depts.washington.edu/soslab/sbf12/18-Molecular-Programming.pdf Molecular Programming]</td>
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   <td></td>
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   <td>[http://www.cs.duke.edu/courses/cps296.4/spring04/papers/Adleman94.pdf Adleman's Paper]. [http://www.qianlab.caltech.edu/seesaw_digital_circuits2011.pdf Qian and Winfree's Paper]</td>
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   <td></td>
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   <td>[[SBF12_A7|A7]], due 11/21</td>
   <td></td>
   <td></td>
</tr>
</tr>
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<tr>
<tr>
   <td>11/16</td>
   <td>11/16</td>
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   <td></td>
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   <td>[http://depts.washington.edu/soslab/sbf12/19-Chemotaxis.pdf Chemotaxis and Reaction/Diffusion]</td>
   <td></td>
   <td></td>
   <td></td>
   <td></td>
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<tr>
<tr>
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  <td>11/30</td>
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<td>11/30</td>
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  <td>Grad Presentations</td>
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<td>
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  <td></td>
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Olson<br>
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   <td></td>
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Rao<br>
 +
Amimeur<br>
 +
Vines
 +
</td>
 +
<td>
 +
[http://www.nature.com/msb/journal/v7/n1/full/msb201121.html Engineering microbial biofuel tolerance and export using efflux pumps]<br>
 +
[http://www.nature.com/nature/journal/v467/n7312/abs/nature09333.html Fundamental limits on the suppression of molecular fluctuations]<br>
 +
[http://www.pnas.org/content/102/10/3581.short Ultrasensitivity and noise propagation in a synthetic transcriptional cascade]<br>
 +
[http://www.sciencedirect.com/science/article/pii/S0022283605013380 EnvironmentallyControlled Invasion of Cancer Cells by Engineered Bacteria]
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</td>
 +
   <td>[[SBF12_A8|A8]], due 12/12</td>
   <td></td>
   <td></td>
</tr>
</tr>
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   <td rowspan=3 class="big">11</td>
   <td rowspan=3 class="big">11</td>
   <td>12/3</td>
   <td>12/3</td>
-
  <td>Grad Presentations</td>
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<td>
-
  <td></td>
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Rose<br>
 +
Kooiman<br>
 +
Bolten<br>
 +
Younger
 +
</td>
 +
<td>
 +
[http://www.ncbi.nlm.nih.gov/pubmed/23039994 Designing synthetic regulatory networks capable of self-organizing cell polarization]<br>
 +
[http://stke.sciencemag.org/cgi/content/abstract/sci;319/5862/482 The Frequency Dependence of Osmo-Adaptation in Saccharomyces cerevisiae]<br>
 +
[http://www.nature.com/nbt/journal/v30/n11/full/nbt.2401.html Ribozyme-based insulator parts buffer synthetic circuits from genetic context]<br>
 +
[http://stke.sciencemag.org/cgi/content/abstract/sci;301/5630/213 A B Cell-Based Sensor for Rapid Identification of Pathogens]
 +
</td>
   <td></td>
   <td></td>
   <td></td>
   <td></td>
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<tr>
<tr>
   <td>12/5</td>
   <td>12/5</td>
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  <td>Grad Presentations</td>
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<td>
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  <td></td>
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Brettner<br>
 +
Stevens<br>
 +
Pfeuffer<br>
 +
Parks
 +
</td>
 +
<td>
 +
[asd asd]<br>
 +
[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002579 Modular Design of Artificial Tissue Homeostasis: Robust Control through Synthetic Cellular Heterogeneity]<br>
 +
[http://www.nature.com/msb/journal/v8/n1/full/msb201252.html Sequestration-based bistability enables tuning of the switching boundaries and design of a latch]<br>
 +
[http://jcs.biologists.org/content/123/4/537.abstract A design principle underlying the synchronization of oscillations in cellular systems]
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</td>
   <td></td>
   <td></td>
   <td></td>
   <td></td>
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* Stephen Wolfram, [http://www.wolframscience.com/ A New Kind of Science], 2002.
* Stephen Wolfram, [http://www.wolframscience.com/ A New Kind of Science], 2002.
* Daniel Yamins, Radhika Nagpal, [http://www.eecs.harvard.edu/ssr/papers/aamas08-yamins.pdf Automated Global-to-Local Programming in 1-D Spatial Multi-Agent Systems], AAMAS, 2008.
* Daniel Yamins, Radhika Nagpal, [http://www.eecs.harvard.edu/ssr/papers/aamas08-yamins.pdf Automated Global-to-Local Programming in 1-D Spatial Multi-Agent Systems], AAMAS, 2008.
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== 12 More on Pattern Formation==
 
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== 13 Noise ==
== 13 Noise ==
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* Klavins, [http://faculty.washington.edu/klavins/ssb/ssb_Part9.pdf 2009 Course Notes on Stochasticity], 2009.
* Klavins, [http://faculty.washington.edu/klavins/ssb/ssb_Part9.pdf 2009 Course Notes on Stochasticity], 2009.
* Ozbudak, Thattai, Kurtser, Grossman and van Oudenaarden, [http://web.mit.edu/biophysics/papers/NATURE2002.pdf Regulation of noise in the expression of a single gene], ''Nature Genetics'' 2002.
* Ozbudak, Thattai, Kurtser, Grossman and van Oudenaarden, [http://web.mit.edu/biophysics/papers/NATURE2002.pdf Regulation of noise in the expression of a single gene], ''Nature Genetics'' 2002.
 +
 +
== 16 Ethics, Biosafety, Biowarfare ==
 +
 +
* American experience material on biowarfare: http://www.pbs.org/wgbh/americanexperience/features/timeline/weapon-timeline/
 +
* Video on polio reconstruction: http://www.youtube.com/watch_popup?v=hfElVabRh2Y&vq=medium#t=31.
 +
* The CDC's biosafety guidlines: http://www.cdc.gov/biosafety/publications/bmbl5/index.htm
 +
* Presidential commission on synthetic biology: http://www.bioethics.gov/documents/synthetic-biology/PCSBI-Synthetic-Biology-Report-12.16.10.pdf
= Links =
= Links =

Current revision


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.


Schedule

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 Robust 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
10/31 MIDTERM
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 A6 Solution
11/9 Computation See my notes and also the paper by Soloveichik et al.
8 11/12 Vetrans Day
11/14 Molecular Programming Adleman's Paper. Qian and Winfree's Paper A7, due 11/21
11/16 Chemotaxis and Reaction/Diffusion
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

Olson
Rao
Amimeur
Vines

Engineering microbial biofuel tolerance and export using efflux pumps
Fundamental limits on the suppression of molecular fluctuations
Ultrasensitivity and noise propagation in a synthetic transcriptional cascade
EnvironmentallyControlled Invasion of Cancer Cells by Engineered Bacteria

A8, due 12/12
11 12/3

Rose
Kooiman
Bolten
Younger

Designing synthetic regulatory networks capable of self-organizing cell polarization
The Frequency Dependence of Osmo-Adaptation in Saccharomyces cerevisiae
Ribozyme-based insulator parts buffer synthetic circuits from genetic context
A B Cell-Based Sensor for Rapid Identification of Pathogens

12/5

Brettner
Stevens
Pfeuffer
Parks

[asd asd]
Modular Design of Artificial Tissue Homeostasis: Robust Control through Synthetic Cellular Heterogeneity
Sequestration-based bistability enables tuning of the switching boundaries and design of a latch
A design principle underlying the synchronization of oscillations in cellular systems

12/7 FINAL
12/12 FINAL MEETING : Simulation presentations!

Reading

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

Links