Synthetic Biology:Documents: Difference between revisions
From OpenWetWare
Jump to navigationJump to search
No edit summary |
No edit summary |
||
| (15 intermediate revisions by 6 users not shown) | |||
| Line 1: | Line 1: | ||
<wikionly> | |||
Go to [http://syntheticbiology.org/ http://syntheticbiology.org/] | |||
</wikionly> | |||
<div style="padding: 10px; width: 730px; color: #ffffff; background-color: #181860"> | |||
<font face="trebuchet ms" style="color:#ffffff"> | |||
'''<big>Synthetic Biology</big> is '''<br> | |||
'''A) the design and construction of new biological parts, devices, and systems, and'''<br> | |||
'''B) the re-design of existing, natural biological systems for useful purposes.''' | |||
</font> | |||
</div> | |||
<div>[[Image:Cells-to-gears-big.png|750px|Synthetic Biology Logo]]</div> | |||
{{Synthetic biology top}} | {{Synthetic biology top}} | ||
<div style="padding: 10px; color: #000000; background-color: #ccccff; width:730px" > | <div style="padding: 10px; color: #000000; background-color: #ccccff; width:730px" > | ||
<wikionly>'''Please add other publications in the area of Synthetic Biology here.'''</wikionly> | |||
===Papers=== | ===Papers=== | ||
*[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. | |||
*Special issue on synthetic biology in [http://www.nature.com/nature/journal/v438/n7067/index.html Nature] | |||
**[[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]] | ||
* [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). | |||
* [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) | |||
*[ | |||
*[ | |||
===Theses=== | ===Theses=== | ||
| Line 15: | Line 30: | ||
*[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]] | ||
===Technical | ===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]] | ||
*[http:// | *[http://hdl.handle.net/1721.1/39832 BioBricks++: Simplifying Assembly of Standard DNA Components] by [[Austin Che]] | ||
*[http://hdl.handle.net/1721.1/32535 A New Biobrick Assembly Strategy Designed for Facile Protein Engineering] by [[Ira Phillips]] and [[Pam Silver]] | |||
===Reports=== | |||
*[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 | |||
===White papers=== | |||
*[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=== | ||
* 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]) | |||
* Laurie Zoloth's recent [http://progressive.playstream.com/nakfi/progressive/life%20engineering/zoloth/zoloth.html lecture] on ethics & Synthetic Biology. | |||
* 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. | ||
===Thesis | ===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=== | ||
*[http://hdl.handle.net/1721.1/29799 Design and Evolution of Engineered Biological Systems] by [[Jason Kelly]], [[Josh Michener]] and [[Drew Endy]] | |||
*[http://hdl.handle.net/1721.1/29804 Engineered Post-Translational Logic (PTL)] by [[Samantha Sutton]], Sara Neves, Lauren Leung and [[Drew Endy]] | |||
*[http://hdl.handle.net/1721.1/29802 Engineering the Interface Between Cellular Chassis and Integrated Biological Systems] by [[Barry Canton]] and [[Drew Endy]] | |||
*[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]] | ||
===Working | ===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)] | ||
===Comics=== | |||
*[http://www.nature.com/nature/comics/syntheticbiologycomic/index.html Adventures in Synthetic Biology] with [[Adventure Background | background]]. | |||
===Other compilations=== | |||
*Recent Synthetic Biology papers: [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&term=%22synthetic%20biology%22&DB=pubmed PubMed], [http://www.citeulike.org/tag/synthetic_biology Cite-U-Like] | |||
* [http://ec.europa.eu/research/fp6/nest/pdf/nest_pathfinder_projects_en.pdf Project fact sheets] of 4 European synthetic biology projects | |||
*MIT DSpace Synthetic Biology Archive | |||
**[https://dspace.mit.edu/handle/1721.1/18185/browse-date by date] | |||
**[https://dspace.mit.edu/handle/1721.1/18185/browse-author by author] | |||
*[http://www.princeton.edu/~rweiss/bio-programming/ Ron Weiss' work on Programming Cells] | |||
</div> | </div> | ||
{{Synthetic biology bottom}} | {{Synthetic biology bottom}} | ||
Latest revision as of 16:57, 22 December 2007
<wikionly> Go to http://syntheticbiology.org/ </wikionly>
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.
<wikionly>Please add other publications in the area of Synthetic Biology here.</wikionly>
Papers
- Synthetic Biology: Navigating the Challenges Ahead by Arjun Bhutkar in The Journal of Biolaw & Business vol.8, no.2, 2005.
- Special issue on synthetic biology in Nature
- 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
- Refactoring bacteriophage T7 by Leon Chan, Sriram Kosuri and Drew Endy
- Engineering novel life commentary by Tom Knight
- Engineering life through Synthetic Biology by Paras Chopra and Akhil Kamma. In Silico Biol. 6, 0038 (2006).
- Public will fear biological accidents, not just attacks by Markus Schmidt in Nature, 2006, vol. 441, no. 7097 (Correspondence)
Theses
- BioJADE: A Design and Simulation Tool for Synthetic Biological Systems by Jonathan Goler
- Fluorescence assay for polymerase arrival rates by Austin Che
Technical reports
- Idempotent Vector Design for Standard Assembly of BioBricks by Tom Knight
- DARPA BioComp Plasmid Distribution 1.00 of Standard Biobrick Components by Tom Knight
- BioBricks++: Simplifying Assembly of Standard DNA Components by Austin Che
- A New Biobrick Assembly Strategy Designed for Facile Protein Engineering by Ira Phillips and Pam Silver
Reports
- Synthetic Biology: Applying Engineering to Biology Report of a NEST High-Level Expert Group. Published by the European Commission 2005
White papers
- From Understanding to Action: Community-Based Options for Improving Safety and Security in Synthetic Biology by Stephen M. Maurer, Keith V. Lucas & Starr Terrell, Goldman School of Public Policy, University of California at Berkeley
Presentations
- Pamela Silver's lecture & Lisa Geller's discussion on Synthetic Biology (mp3 file)
- Laurie Zoloth's recent lecture on ethics & Synthetic Biology.
- Paul Rabinow's recent lecture on security & Synthetic Biology.
- The Next Step in Bioevolution: Engineering the Microbial World by Austin Che
- A set of presentation slides and video from various talks by Drew Endy, many of which focus on the engineering of biology.
Thesis proposals
- Engineering the Interface Between Cellular Chassis and Integrated Biological Systems by Barry Canton
- Design and Evolution of Engineered Biological Systems by Jason Kelly
Posters
- Design and Evolution of Engineered Biological Systems by Jason Kelly, Josh Michener and Drew Endy
- Engineered Post-Translational Logic (PTL) by Samantha Sutton, Sara Neves, Lauren Leung and Drew Endy
- Engineering the Interface Between Cellular Chassis and Integrated Biological Systems by Barry Canton and Drew Endy
- Engineering transcription-based digital logic devices by Reshma Shetty and Tom Knight
- BioBricks++: Mindless Module Manipulation by Monkeys by Austin Che
Working drafts
- Draft 1: Regulatory Schemes in Biological Networks to Produce Desired Response and Stability. The genetic inverter: A computational case study
- Draft 2: Recombineering: Homologous Recombination-Mediated DNA Engineering in E. coli
- Draft 3: Electrical Models for Genetic Regulatory Elements
- Draft 4: Plasmid Engineering (pdf) (doc)
Comics
Other compilations
- Recent Synthetic Biology papers: PubMed, Cite-U-Like
- Project fact sheets of 4 European synthetic biology projects
- MIT DSpace Synthetic Biology Archive
- Ron Weiss' work on Programming Cells
This site is hosted on OpenWetWare and can be edited by all members of the Synthetic Biology community.
Making life better, one part at a time.
