Synthetic Biology:Documents

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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.

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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

• Adventures in Synthetic Biology with background.

Other compilations

• Recent Synthetic Biology papers: PubMed, Cite-U-Like
• Project fact sheets of 4 European synthetic biology projects
• MIT DSpace Synthetic Biology Archive
  • by date
  • by author
• Ron Weiss' work on Programming Cells

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