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Synthetic Biology Fall 2012 - SOSwiki

From SOSwiki

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Current revision (17:26, 6 December 2012) (view source)
(Schedule)
 
* 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
-
*** No office hours on 10/23. They have been reschedule to 8:30-10:20 on 10/24
+
*** Office hours on 11/13 are 10am - noon.
-
*** Office hours on 10/25 are as usual.
+
* 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
   <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>
<tr>
<tr>
   <td>11/1</td>
   <td>11/1</td>
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   <td>[http://depts.washington.edu/soslab/sbf12/16-biowarefare.pdf 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>
<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>[[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>
<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>
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</tr>
</tr>
<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>
<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>
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Amimeur<br>
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Vines
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</td>
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<td>
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[http://www.nature.com/msb/journal/v7/n1/full/msb201121.html Engineering microbial biofuel tolerance and export using efflux pumps]<br>
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[http://www.nature.com/nature/journal/v467/n7312/abs/nature09333.html Fundamental limits on the suppression of molecular fluctuations]<br>
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[http://www.pnas.org/content/102/10/3581.short Ultrasensitivity and noise propagation in a synthetic transcriptional cascade]<br>
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[http://www.sciencedirect.com/science/article/pii/S0022283605013380 EnvironmentallyControlled Invasion of Cancer Cells by Engineered Bacteria]
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</td>
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   <td>[[SBF12_A8|A8]], due 12/12</td>
   <td></td>
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</tr>
</tr>
   <td rowspan=3 class="big">11</td>
   <td rowspan=3 class="big">11</td>
   <td>12/3</td>
   <td>12/3</td>
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  <td>Grad Presentations</td>
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<td>
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  <td></td>
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Rose<br>
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Kooiman<br>
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Bolten<br>
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Younger
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</td>
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<td>
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[http://www.ncbi.nlm.nih.gov/pubmed/23039994 Designing synthetic regulatory networks capable of self-organizing cell polarization]<br>
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[http://stke.sciencemag.org/cgi/content/abstract/sci;319/5862/482 The Frequency Dependence of Osmo-Adaptation in Saccharomyces cerevisiae]<br>
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[http://www.nature.com/nbt/journal/v30/n11/full/nbt.2401.html Ribozyme-based insulator parts buffer synthetic circuits from genetic context]<br>
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[http://stke.sciencemag.org/cgi/content/abstract/sci;301/5630/213 A B Cell-Based Sensor for Rapid Identification of Pathogens]
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</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>
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Stevens<br>
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Pfeuffer<br>
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Parks
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</td>
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<td>
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[asd asd]<br>
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[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>
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[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>
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[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>
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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 ==
* 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.
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== 16 Ethics, Biosafety, Biowarfare ==
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* American experience material on biowarfare: http://www.pbs.org/wgbh/americanexperience/features/timeline/weapon-timeline/
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* Video on polio reconstruction: http://www.youtube.com/watch_popup?v=hfElVabRh2Y&vq=medium#t=31.
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* The CDC's biosafety guidlines: http://www.cdc.gov/biosafety/publications/bmbl5/index.htm
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* Presidential commission on synthetic biology: http://www.bioethics.gov/documents/synthetic-biology/PCSBI-Synthetic-Biology-Report-12.16.10.pdf
= Links =
= Links =

Current revision