Difference between revisions of "Summer 2012 SynBio Project (Davidson and MWSU)"

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**[http://eccc.hpi-web.de/static/books/A_Simple_Introduction_to_Computable_Analysis_Fragments_of_a_Book/] Part of a textbook on computation theory
 
**[http://eccc.hpi-web.de/static/books/A_Simple_Introduction_to_Computable_Analysis_Fragments_of_a_Book/] Part of a textbook on computation theory
 
**[http://hrl.harvard.edu/analog/] Harvard analog computing
 
**[http://hrl.harvard.edu/analog/] Harvard analog computing
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**[http://www.cs.princeton.edu/theory/index.php/Compbook/Draft] Free draft of Princeton text on computational complexity
  
  

Revision as of 18:20, 30 May 2012

Summer 2012 Synthetic Biology Project: MWSU and Davidson College


  1. Davidson Protocols
  2. MWSU_protocols
  3. GCAT-alog Freezer Stocks
  4. Laboratory_Notebooks
  5. Golden Gate


Student Proposals from Ind. Studies

-I think the use of Phytochromes might be a good way to have either a continual stimulus that would repress/express certain genes that could be turned off and on depending on what we want them to do. There are other aspects of the research in this proposal that if not used outright, could be adapted to our continuing projects as either controls or feedback mechanisms. As for the proposed Salis RBS sites, I would like to see more information in the efficacy of the predicted RBS sequence. Possibly if we could use some of the C-Dog information based on a few known sequences to determine if the computer can predict those RBS's we know to be effective then we might be able to count on the calculator as a tool for our experimental design. -Caleb Carr



PPT Presentations

  • This PPT file contains all the slides from student presentations addressing the idea proposed by MWSU.

Media:Reports_on_Circuits.pptx

  • This PPT contains slides summarizing some of the best and most complicated papers from Week 11.

Media:Week_11.pptx

Papers

Methods Papers

  • DNA assembly for synthetic biology: from parts to pathways and beyond

Tom Ellis, Tom Adieac and Geoff S. Baldwin
Integr. Biol., 2011, 3, 109–118

  • Everyone should watch this 5 minute video on optogenetics. Combine that video with the 2010 champoinship iGEM invention of E. glowi.


Older Lab Papers

  • Engineering bacteria to solve the Burnt Pancake Problem.

Haynes, Karmella, et al.
Journal of Biological Engineering. Vol. 2(8): 1 – 12.

  • Solving a Hamiltonian Path Problem with a Bacterial Computer.

Baumgardner, Jordan et al.
Journal of Biological Engineering. Vol. 3:11

  • Bacterial Hash Function Using DNA-Based XOR Logic Reveals Unexpected Behavior of the LuxR Promoter.

Brianna Pearson*, Kin H. Lau* et al.
Interdisciplinary Bio Central. Vol. 3, article no. 10.
Time Delayed Growth Movie


Network Papers

Jonathan M. Raser and Erin K. O’Shea
Science. Vol. 309, page 2010

Please post pdf.

Nagarajan Nandagopal and Michael B. Elowitz
Science. Vol. 333, page 1244.

Please post pdf.

R. Milo, S. Shen-Orr, et al
Science. Vol. 298, page 824.

Please post pdf.

Yang-Yu Liu, Jean-Jacques Slotine, & Albert-La ́szlo ́ Baraba ́si
Nature. 2011. Vol. 473, page 167.

Please post pdf.


Ethics Papers

Colin Mcilswain
Nature. Vol 465, page 867.

-This paper does a great job at highlighting the importance of socio-political legitimation in the funding of science. It seems that all new sciences must survive a period during which their only funding comes from public sources under the condition that those conducting it can make some kind of promises of future benefit to the society as a whole. After proving itself not only useful but also profitable, private money may then start flowing in, though by that point, the nature of that field may arguably have changed for better or worse. I think we would all agree that synthetic biology holds more promise than we can currently even imagine, both for advancing the public good and for providing opportunity for profit (in more than just pharmaceuticals), but it's not enough for us to believe it. Those of us who will someday pursue grants and/or private investments in synthetic biology must learn to speak not only the rational language of the science of synthetic biology but also the politically-driven language of the social benefits of synthetic biology, the socially conscious language of the ethics of synthetic biology, and the profit-driven language of the (future) business of synthetic biology (and possibly others). -Eddie Miles

Questions to Consider About Network Pathways

  • Are they naturally occurring or synthetic?
  • Do they involve screening or selection?
  • Are they anabolic or catabolic?
  • How many steps are in each pathway?
  • How can they relate to cell fitness?
  • What specific challenges would need to be addressed if we worked with the pathway?

Network Pathways Chart

Cellular Automata

  • [1] General CA introduction
  • [2], [3] Elementary Cellular Automata
  • [4] Good explanation of how elementary CAs work
  • [5] Rule 110

Peptides

Environmental factors that enhance the action of the cell penetrating peptide pep-1 - A spectroscopic study using lipidic vesicles [[7]]

Assembly and Library

[8]iGEM Introduction to Gibson Assembly

[9]Enzymatic assembly of DNA molecules up to several hundred kilobases

[10] Supplemental Methods for Enzymatic assembly of DNA molecules up to several hundred kilobases

[11] LIBRARY: Degradation Tags with Gfp protein reporters - research paper

[12]Assembly of BioBricks by the Gibson Method

Selection Modules

Light

Other Ideas



Communication

Neural Networks

General

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