Synthetic Biology:Documents

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<wikionly>
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Go to [http://syntheticbiology.org/ http://syntheticbiology.org/]
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'''<big>Synthetic Biology</big> is '''<br>
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'''A) the design and construction of new biological parts, devices, and systems, and'''<br>
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'''B) the re-design of existing, natural biological systems for useful purposes.'''
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<div>[[Image:Cells-to-gears-big.png|750px|Synthetic Biology Logo]]</div>
{{Synthetic biology top}}
{{Synthetic biology top}}
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<wikionly>'''Please add other publications in the area of Synthetic Biology here.'''</wikionly>
===Papers===
===Papers===
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*[http://openwetware.org/images/0/02/Aj_bhutkar_synth_bio_jbb_2005.pdf Synthetic Biology: Navigating the Challenges Ahead] by Arjun Bhutkar in ''The Journal of Biolaw & Business'' vol.8, no.2, 2005.
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*Special issue on synthetic biology in [http://www.nature.com/nature/journal/v438/n7067/index.html Nature]
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**[[Media:Levskaya_2005.pdf|Engineering ''Escherichia coli'' to see light]] by A. Levskaya, A.A. Chevalier, J.J. Tabor, Z.B. Simpson, L.A. Lavery, M.Levy, E.A. Davidson, A.Scouras, A.D. Ellington, E.M. Marcotte, and C.A. Voigt
*[http://www.nature.com/msb/journal/v1/n1/full/msb4100025.html Refactoring bacteriophage T7] by [[Leon Chan]], [[Sriram Kosuri]] and [[Drew Endy]]  
*[http://www.nature.com/msb/journal/v1/n1/full/msb4100025.html Refactoring bacteriophage T7] by [[Leon Chan]], [[Sriram Kosuri]] and [[Drew Endy]]  
**[http://www.nature.com/msb/journal/v1/n1/full/msb4100028.html Engineering novel life] commentary by [[Tom Knight]]
**[http://www.nature.com/msb/journal/v1/n1/full/msb4100028.html Engineering novel life] commentary by [[Tom Knight]]
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* [http://www.bioinfo.de/isb/2006/06/0038/ Engineering life through Synthetic Biology] by [[Paras Chopra]] and Akhil Kamma. In Silico Biol. 6, 0038 (2006).
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===DSpace Synthetic Biology Archive===
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* [http://www.nature.com/nature/journal/v441/n7097/full/4411048d.html Public will fear biological accidents, not just attacks] by [http://openwetware.org/wiki/User:Mschmidt Markus Schmidt] in Nature, 2006, vol. 441, no. 7097 (Correspondence)
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*[https://dspace.mit.edu/handle/1721.1/18185/browse-date by date]
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*[https://dspace.mit.edu/handle/1721.1/18185/browse-author by author]
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===Theses===
===Theses===
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*[http://hdl.handle.net/1721.1/16618 Fluorescence assay for polymerase arrival rates] by [[Austin Che]]
*[http://hdl.handle.net/1721.1/16618 Fluorescence assay for polymerase arrival rates] by [[Austin Che]]
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===Technical Reports===
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===Technical reports===
*[http://hdl.handle.net/1721.1/21168 Idempotent Vector Design for Standard Assembly of BioBricks] by [[Tom Knight]]
*[http://hdl.handle.net/1721.1/21168 Idempotent Vector Design for Standard Assembly of BioBricks] by [[Tom Knight]]
*[http://hdl.handle.net/1721.1/21167 DARPA BioComp Plasmid Distribution 1.00 of Standard Biobrick Components] by [[Tom Knight]]
*[http://hdl.handle.net/1721.1/21167 DARPA BioComp Plasmid Distribution 1.00 of Standard Biobrick Components] by [[Tom Knight]]
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*[http://austin.che.name/docs/bbpp.pdf BioBricks++: Simplifying Assembly of Standard DNA Components] by [[Austin Che]]
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*[http://hdl.handle.net/1721.1/39832 BioBricks++: Simplifying Assembly of Standard DNA Components] by [[Austin Che]]
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*[http://hdl.handle.net/1721.1/32535 A New Biobrick Assembly Strategy Designed for Facile Protein Engineering] by [[Ira Phillips]] and [[Pam Silver]]
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===Reports===
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*[ftp://ftp.cordis.lu/pub/nest/docs/syntheticbiology_b5_eur21796_en.pdf Synthetic Biology: Applying Engineering to Biology] Report of a NEST High-Level Expert Group. Published by the European Commission 2005
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===White papers===
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*[http://gspp.berkeley.edu/iths/UC%20White%20Paper.pdf From Understanding to Action: Community-Based Options for Improving Safety and Security in Synthetic Biology] by [[User:Smaurer | Stephen M. Maurer]], Keith V. Lucas & Starr Terrell, Goldman School of Public Policy, University of California at Berkeley
===Presentations===
===Presentations===
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* Pamela Silver's lecture & Lisa Geller's discussion [http://www.aaas.org/spp/dser/seminar/2005/111005syntheticbio.shtml/ on Synthetic Biology] ([http://www.aaas.org/spp/dser/seminar/2005/synbiology11102005.mp3 mp3 file])
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* Laurie Zoloth's recent [http://progressive.playstream.com/nakfi/progressive/life%20engineering/zoloth/zoloth.html lecture] on ethics & Synthetic Biology.
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* Paul Rabinow's recent [http://63.251.167.36/nakfi/progressive/Life%20Engineering/rabinow/rabinow.html lecture] on security & Synthetic Biology.
*[http://austin.che.name/docs/dangerous_ideas.pdf The Next Step in Bioevolution: Engineering the Microbial World] by [[Austin Che]]
*[http://austin.che.name/docs/dangerous_ideas.pdf The Next Step in Bioevolution: Engineering the Microbial World] by [[Austin Che]]
*A set of [http://openwetware.mit.edu/index.php?title=Endy:Talks presentation slides and video] from various talks by [[Drew Endy]], many of which focus on the engineering of biology.
*A set of [http://openwetware.mit.edu/index.php?title=Endy:Talks presentation slides and video] from various talks by [[Drew Endy]], many of which focus on the engineering of biology.
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===Thesis Proposals===
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===Thesis proposals===
*[http://hdl.handle.net/1721.1/19813 Engineering the Interface Between Cellular Chassis and Integrated Biological Systems] by [[Barry Canton]]
*[http://hdl.handle.net/1721.1/19813 Engineering the Interface Between Cellular Chassis and Integrated Biological Systems] by [[Barry Canton]]
*[http://hdl.handle.net/1721.1/21169 Design and Evolution of Engineered Biological Systems] by [[Jason Kelly]]
*[http://hdl.handle.net/1721.1/21169 Design and Evolution of Engineered Biological Systems] by [[Jason Kelly]]
===Posters===
===Posters===
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*[http://hdl.handle.net/1721.1/29799 Design and Evolution of Engineered Biological Systems] by [[Jason Kelly]], [[Josh Michener]] and [[Drew Endy]]
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*[http://hdl.handle.net/1721.1/29804 Engineered Post-Translational Logic (PTL)] by [[Samantha Sutton]], Sara Neves, Lauren Leung and [[Drew Endy]]
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*[http://hdl.handle.net/1721.1/29802 Engineering the Interface Between Cellular Chassis and Integrated Biological Systems] by [[Barry Canton]] and [[Drew Endy]]
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*[http://hdl.handle.net/1721.1/29800 Engineering transcription-based digital logic devices] by [[Reshma Shetty]] and [[Tom Knight]]
*[http://austin.che.name/docs/bbpp_poster.pdf BioBricks++: Mindless Module Manipulation by Monkeys] by [[Austin Che]]
*[http://austin.che.name/docs/bbpp_poster.pdf BioBricks++: Mindless Module Manipulation by Monkeys] by [[Austin Che]]
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*[http://openwetware.mit.edu/images/2/22/BCwisconsin05.pdf Engineering the Interface Between Cellular Chassis and Integrated Biological Systems] by [[Barry Canton]]
 
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===Working Drafts===
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===Working drafts===
*Draft 1: [http://docs.syntheticbiology.org/LacOperator.doc Regulatory Schemes in Biological Networks to Produce Desired Response and Stability.  The genetic inverter: A computational case study]
*Draft 1: [http://docs.syntheticbiology.org/LacOperator.doc Regulatory Schemes in Biological Networks to Produce Desired Response and Stability.  The genetic inverter: A computational case study]
*Draft 2: [http://docs.syntheticbiology.org/HomologRecomb.pdf Recombineering: Homologous Recombination-Mediated DNA Engineering in E. coli]
*Draft 2: [http://docs.syntheticbiology.org/HomologRecomb.pdf Recombineering: Homologous Recombination-Mediated DNA Engineering in E. coli]
*Draft 3: [http://www.swiss.ai.mit.edu/~gjs/syntheticbiology/models.pdf Electrical Models for Genetic Regulatory Elements]
*Draft 3: [http://www.swiss.ai.mit.edu/~gjs/syntheticbiology/models.pdf Electrical Models for Genetic Regulatory Elements]
*Draft 4: Plasmid Engineering [http://docs.syntheticbiology.org/PlasmidEngineering.pdf (pdf)] [http://docs.syntheticbiology.org/PlasmidEngineering.doc (doc)]
*Draft 4: Plasmid Engineering [http://docs.syntheticbiology.org/PlasmidEngineering.pdf (pdf)] [http://docs.syntheticbiology.org/PlasmidEngineering.doc (doc)]
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===Comics===
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*[http://www.nature.com/nature/comics/syntheticbiologycomic/index.html Adventures in Synthetic Biology] with [[Adventure Background | background]].
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===Other compilations===
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*Recent Synthetic Biology papers: [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&amp;term=%22synthetic%20biology%22&amp;DB=pubmed PubMed], [http://www.citeulike.org/tag/synthetic_biology Cite-U-Like]
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* [http://ec.europa.eu/research/fp6/nest/pdf/nest_pathfinder_projects_en.pdf Project fact sheets] of 4 European synthetic biology projects 
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*MIT DSpace Synthetic Biology Archive
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**[https://dspace.mit.edu/handle/1721.1/18185/browse-date by date]
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**[https://dspace.mit.edu/handle/1721.1/18185/browse-author by author]
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*[http://www.princeton.edu/~rweiss/bio-programming/ Ron Weiss' work on Programming Cells]
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{{Synthetic biology bottom}}
{{Synthetic biology bottom}}

Current revision

Go to http://syntheticbiology.org/

Synthetic Biology is
A) the design and construction of new biological parts, devices, and systems, and
B) the re-design of existing, natural biological systems for useful purposes.

Synthetic Biology Logo

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Please add other publications in the area of Synthetic Biology here.

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Theses

Technical reports

Reports

White papers

Presentations

Thesis proposals

Posters

Working drafts

Comics

Other compilations

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