Harvard:Synthetic Biology Nanocourse/2007

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=Synthetic Biology: Cellular and Molecular Engineering=
=Synthetic Biology: Cellular and Molecular Engineering=
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*[http://idb.med.harvard.edu/content/category/6/88/27/ link to idb website for this nanocourse]
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<br>
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==Instructors==
==Instructors==
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*Nanocourse Director: [[User:PamSilver|Pamela Silver]] ([[User_talk:PamSilver|talk]])
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*Nanocourse Lecturers: [[User:Geochurch|George Church]] ([http://arep.med.harvard.edu/gmc/email.html talk]), [[User:wmshih|William Shih]] ([[User_talk:wmshih|talk]]) (co-director), and [[User:PamSilver|Pamela Silver]] ([[User_talk:PamSilver|talk]]) (co-director)
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*Nanocourse Lecturers: [[User:Geochurch|George Church]] ([http://arep.med.harvard.edu/gmc/email.html talk]), [[User:wmshih|William Shih]] ([[User_talk:wmshih|talk]]), and [[User:PamSilver|Pamela Silver]] ([[User_talk:PamSilver|talk]])
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<br>
<br>
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*Second Meeting: Friday, 2007 October 26th, 12pm&ndash;2pm  
*Second Meeting: Friday, 2007 October 26th, 12pm&ndash;2pm  
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**Location: TBD
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**Location: Warren Alpert Building 436
<br>
<br>
==Course Project==
==Course Project==
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*For those enrolled in the nanocourse, the course project will be a short proposal (800&ndash;1000 words plus figures) describing a synthetic biology project that can be completed by a graduate student in three years or less. The proposals, in Adobe PDF form, must be posted on this wiki page by noon on Thursday, 2007 October 25.
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*The course project will be a 1-2 page proposal describing a synthetic biology project. Feel free to use figures in your proposal if it can clarify critical concepts for your readers. You should use the course lectures, course readings and your own experience to come up with a proposal. Your grade in this nanocourse will '''not''' be based on the validity of this proposal. Rather, we just ask that you make a best effort to propose a set of experiments to address an important problem. We will discuss these proposals during the discussion section of the course.
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*Registered students and instructors will read the proposals and meet on Friday, 2007 October 26 at noon to critique the proposals (see above).
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*All students should post their proposal, in Adobe PDF form, to this wiki page by noon on Thursday, 2007 October 25. (This is the day before the discussion section).
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*To see some potential project ideas, please browse through the project and brainstorming pages of former iGEM teams. If you decide to adopt one of those ideas, you need to propose a significant improvement or alteration that represents value added to the original idea. Be sure to credit the sources for your inspirations. Here are some example links (everyone, please feel free to add more or to reorganize):
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*Students and instructors should do their best to read each proposal before class on Friday. On Friday, 2007 October 26, each student will have a chance to informally present their proposed experiments to the entire class. Currently there are 8 students registered to participate on the second day, so we should be able to get through every student proposal.
 +
*To see some potential project ideas, please browse through the project and brainstorming pages of former iGEM teams. If you decide to adopt one of those ideas, you should propose a significant improvement or alteration that represents value added to the original idea. Be sure to credit the sources for your inspirations. Here are some example links (everyone, please feel free to add more or to reorganize):
**http://parts.mit.edu/wiki/index.php/Schools_Participating_in_iGEM_2006
**http://parts.mit.edu/wiki/index.php/Schools_Participating_in_iGEM_2006
**http://openwetware.org/wiki/IGEM:Harvard/2007/Brainstorming
**http://openwetware.org/wiki/IGEM:Harvard/2007/Brainstorming
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**http://openwetware.org/wiki/IGEM:MIT/2007
**http://openwetware.org/wiki/IGEM:MIT/2007
**http://openwetware.org/wiki/IGEM:MIT/2006/System_brainstorming
**http://openwetware.org/wiki/IGEM:MIT/2006/System_brainstorming
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<br>
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==Reading List==
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===Lecture 1 (Silver)===
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*Recommended review articles
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<biblio>
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# pas1 pmid=17289915
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# pas2 pmid=16978856
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# pas3 pmid=16738572
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</biblio>
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<br>
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*Additional papers of interest in the field
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<biblio>
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# pas4 pmid=17108985
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# pas5 pmid=16330045
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# pas6 pmid=17662949
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# pas7 pmid=17875664
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# pas8 pmid=15858574
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# pas9 pmid=10659856
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</biblio>
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<br>
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===Lecture 2 (Shih)===
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*Recommended review articles
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<biblio>
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# wms1 pmid=17710092
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# wms2 pmid=17269482
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# wms3 pmid=15602549
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# wms4 pmid=12540916
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</biblio>
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<br>
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*Additional papers of interest in the field
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<biblio>
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# wms5 pmid=14631033
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# wms6 pmid=15218149
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#
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#
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# wms7 pmid=16541064
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# wms8 pmid=17404217
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</biblio>
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<br>
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===Lecture 3 (Church)===
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*Recommended review articles
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<biblio>
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# gmc1 pmid=17151344
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# gmc2 pmid=17557094
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</biblio>
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<br>
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*Additional papers of interest in the field
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<biblio>
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# gmc3 pmid=17600181
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# gmc4 pmid=17086184
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</biblio>
<br>
<br>
==Uploaded Proposals==
==Uploaded Proposals==
<br>
<br>
 +
Remember to upload a PDF of your file by Thursday, October 25th by noon. Uploading your file on time means that your fellow classmates and instructors will have ample time to carefully read all of the proposals. Please name your files something meaningful. I suggest the following format... NameofStudent_syntheticbiology2007.

Current revision

Intellectual Unit: Experimental Tools for Biological Discovery

Contents

Synthetic Biology: Cellular and Molecular Engineering


Instructors


Course Description

Synthetic biology explores the design rules for building artificial behavior of biomolecular systems through cycles of construction and comparison of intended versus observed behaviors. The ability to synthesize biomimetic behavior is an important benchmark for biological understanding. This course will introduce strategies for engineering cellular and molecular systems and will explore current and future applications for synthetic biology approaches.

Meeting Times

  • First Meeting: Monday, 2007 October 22nd, 1:30pm–4:30pm
    • Location: Goldenson 122 (on the HMS quad)
  • Second Meeting: Friday, 2007 October 26th, 12pm–2pm
    • Location: Warren Alpert Building 436


Course Project

  • The course project will be a 1-2 page proposal describing a synthetic biology project. Feel free to use figures in your proposal if it can clarify critical concepts for your readers. You should use the course lectures, course readings and your own experience to come up with a proposal. Your grade in this nanocourse will not be based on the validity of this proposal. Rather, we just ask that you make a best effort to propose a set of experiments to address an important problem. We will discuss these proposals during the discussion section of the course.
  • All students should post their proposal, in Adobe PDF form, to this wiki page by noon on Thursday, 2007 October 25. (This is the day before the discussion section).
  • Students and instructors should do their best to read each proposal before class on Friday. On Friday, 2007 October 26, each student will have a chance to informally present their proposed experiments to the entire class. Currently there are 8 students registered to participate on the second day, so we should be able to get through every student proposal.
  • To see some potential project ideas, please browse through the project and brainstorming pages of former iGEM teams. If you decide to adopt one of those ideas, you should propose a significant improvement or alteration that represents value added to the original idea. Be sure to credit the sources for your inspirations. Here are some example links (everyone, please feel free to add more or to reorganize):


Reading List

Lecture 1 (Silver)

  • Recommended review articles
  1. Drubin DA, Way JC, and Silver PA. . pmid:17289915. PubMed HubMed [pas1]
  2. Voigt CA. . pmid:16978856. PubMed HubMed [pas2]
  3. Andrianantoandro E, Basu S, Karig DK, and Weiss R. . pmid:16738572. PubMed HubMed [pas3]
All Medline abstracts: PubMed HubMed


  • Additional papers of interest in the field
  1. Chang MC and Keasling JD. . pmid:17108985. PubMed HubMed [pas4]
  2. Anderson JC, Clarke EJ, Arkin AP, and Voigt CA. . pmid:16330045. PubMed HubMed [pas5]
  3. Deans TL, Cantor CR, and Collins JJ. . pmid:17662949. PubMed HubMed [pas6]
  4. Ajo-Franklin CM, Drubin DA, Eskin JA, Gee EP, Landgraf D, Phillips I, and Silver PA. . pmid:17875664. PubMed HubMed [pas7]
  5. Basu S, Gerchman Y, Collins CH, Arnold FH, and Weiss R. . pmid:15858574. PubMed HubMed [pas8]
  6. Elowitz MB and Leibler S. . pmid:10659856. PubMed HubMed [pas9]
All Medline abstracts: PubMed HubMed


Lecture 2 (Shih)

  • Recommended review articles
  1. Yeh BJ and Lim WA. . pmid:17710092. PubMed HubMed [wms1]
  2. Alvizo O, Allen BD, and Mayo SL. . pmid:17269482. PubMed HubMed [wms2]
  3. Breaker RR. . pmid:15602549. PubMed HubMed [wms3]
  4. Seeman NC. . pmid:12540916. PubMed HubMed [wms4]
All Medline abstracts: PubMed HubMed


  • Additional papers of interest in the field
  1. Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, and Baker D. . pmid:14631033. PubMed HubMed [wms5]
  2. Dwyer MA, Looger LL, and Hellinga HW. . pmid:15218149. PubMed HubMed [wms6]
  3. Rothemund PW. . pmid:16541064. PubMed HubMed [wms7]
  4. Douglas SM, Chou JJ, and Shih WM. . pmid:17404217. PubMed HubMed [wms8]
All Medline abstracts: PubMed HubMed


Lecture 3 (Church)

  • Recommended review articles
  1. Forster AC and Church GM. . pmid:17151344. PubMed HubMed [gmc1]
  2. Bügl H, Danner JP, Molinari RJ, Mulligan JT, Park HO, Reichert B, Roth DA, Wagner R, Budowle B, Scripp RM, Smith JA, Steele SJ, Church G, and Endy D. . pmid:17557094. PubMed HubMed [gmc2]
All Medline abstracts: PubMed HubMed


  • Additional papers of interest in the field
  1. Lartigue C, Glass JI, Alperovich N, Pieper R, Parmar PP, Hutchison CA 3rd, Smith HO, and Venter JC. . pmid:17600181. PubMed HubMed [gmc3]
  2. Herring CD, Raghunathan A, Honisch C, Patel T, Applebee MK, Joyce AR, Albert TJ, Blattner FR, van den Boom D, Cantor CR, and Palsson BØ. . pmid:17086184. PubMed HubMed [gmc4]
All Medline abstracts: PubMed HubMed


Uploaded Proposals


Remember to upload a PDF of your file by Thursday, October 25th by noon. Uploading your file on time means that your fellow classmates and instructors will have ample time to carefully read all of the proposals. Please name your files something meaningful. I suggest the following format... NameofStudent_syntheticbiology2007.

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