Peer Reviewed

Michal Galdzicki, Kevin P. Clancy, Ernst Oberortner, Matthew Pocock, Jacqueline Quinn, Cesar A. Rodriguez, Nicholas    Roehner, Mandy L. Wilson, Laura Adam, J. Christopher Anderson, Bryan A. Bartley, Jacob Beal, Deepak Chandran, Joanna Chen, Douglas Densmore, Drew Endy, Raik Grünberg, Jennifer Hallinan, Nathan J. Hillson, Jeffrey D. Johnson, Allan Kuchinsky, Matthew Lux, Goksel Misirli, Jean Peccoud, Hector A. Plahar, Evren Sirin, Guy-Bart Stan, Alan Villalobos, Anil Wipat, John H. Gennari, Chris J. Myers, and Herbert M. Sauro. SBOL: A community standard for communicating designs in synthetic biology. Figshare, 2013; doi:10.6084/m9.figshare.762451

Michal Galdzicki, Cesar Rodriguez, Deepak Chandran, Herbert M. Sauro, and John H. Gennari (2011) Standard Biological Parts Knowledgebase. PLoS ONE. 6(2): e17005. doi:10.1371/journal.pone.0017005

Letter to the Editor

Jean Peccoud, J Christopher Anderson, Deepak Chandran, Douglas Densmore, Michal Galdzicki, Matthew W Lux, Cesar A Rodriguez, Guy-Bart Stan, and Herbert M Sauro (2011) Essential information for synthetic DNA sequences. Nature Biotechnology. 29, 22. doi:10.1038/nbt.1753

BioBrick Foundation Request for Comments Documents

Jacqueline Quinn, Jacob Beal, Swapnil Bhatia, Patrick Cai, Joanna Chen, Kevin Clancy, Nathan Hillson, Michal Galdzicki, Akshay Maheshwari, Umesh P, Matthew Pocock, Cesar Rodriguez, Guy-Bart Stan, Drew Endy, (2013) Synthetic Biology Open Language Visual (SBOL Visual), version 1.0.0 BBF RFC #93 doi: 1721.1/78249

Michal Galdzicki, Mandy Wilson, Cesar A. Rodriguez, Matthew R. Pocock, Ernst Oberortner, Laura Adam, Aaron Adler; J. Christopher Anderson, Jacob Beal, Yizhi Cai, Deepak Chandran, Douglas Densmore, Omri A. Drory, Drew Endy, John H. Gennari, Raik Grünberg, Timothy S. Ham, Nathan J. Hillson, Jeffrey D. Johnson, Allan Kuchinsky, Matthew Lux, Curtis Madsen, Goksel Misirli, Chris J. Myers, Carlos Olguin, Jean Peccoud, Hector Plahar, Darren Platt, Nicolas Roehner, Evren Sirin, Travor F. Smith, Guy-Bart Stan, Alan Villabos, Anil Wipat,Herbert M. Sauro, (2012) Synthetic Biology Open Language (SBOL) Version 1.1.0 BBF RFC #87 doi: 1721.1/73909

Michal Galdzicki, Mandy L. Wilson, Cesar A. Rodriguez, Laura Adam, Aaron Adler, J. Christopher Anderson, Jacob Beal, Deepak Chandran, Douglas Densmore, Omri A. Drory, Drew Endy, John H. Gennari, Raik Grünberg, Timothy S. Ham, Allan Kuchinsky, Matthew W. Lux, Curtis Madsen, Goksel Misirli, Chris J. Myers, Jean Peccoud, Hector Plahar, Matthew R. Pocock, Nicholas Roehner, Trevor F. Smith, Guy-Bart Stan, Alan Villalobos, Anil Wipat, and Herbert M. Sauro (2011) Synthetic Biology Open Language (SBOL) Version 1.0.0. BBF RFC #84 doi: 1721.1/66172

Jeff Johnson, Michal Galdzicki, Herbert Sauro (2010) Standard for the Electronic Distribution of SBOLv Diagrams. BBF RFC #68. doi: 1721.1/60086

Jannetta S. Steyn, Anil Wipat, Jennifer Hallinan, Matthew Pocock, Rachel May Boyd, Harsh Sheth, Alan Koh, Phil Hall, Deena Tsu, Steven Woodhouse and Younus Essa (2010) A RESTful API for Supporting Automated BioBrick Model Assembly. BBF RFC #66. doi: 1721.1/60085

Cesar Rodriguez, Suzie Bartram, Anusuya Ramasubramanian, and Drew Endy Synthetic Biology Open Language Visual (SBOLv) Specification. BBF RFC #16. doi: 1721.1/49523 2009

Michal Galdzicki, Deepak Chandran, Alec Nielsen, Jason Morrison, Mackenzie Cowell, Raik Grunberg, Sean Sleight, Herbert Sauro (2009) Provisional BioBrick Language (PoBoL). BBF RFC #31. doi: 1721.1/45537

Raik Grünberg (2009) Draft of an RDF-based framework for the exchange and integration of Synthetic Biology data. BBF RFC #30 doi: 1721.1/45143 2009

Conference Abstracts

Michal Galdzicki, Ernst Oberortner, Mathew Pocock, Jacqueline Quinn, Mandy Wilson, Evan Appleton, Bryan Bartley, Jacob Beal, Swapnil Bhatia, Robert Cox, Raik Grunberg, Goskel Misirli, Hector Plahar, Nicholas Roehner, Larisa Soldotova, Guy-Bart Stan, Doug Densmore, Chris Myers, Herbert Sauro and Anil Wipat. (2013) Recent Advances in the Synthetic Biology Open Language. The 5th International Workshop on Bio-Design Automation (IWBDA), London, UK, July 12-13, 2013.

Jacqueline Quinn, Jacob Beal, Swapnil Bhatia, Patrick Cai, Joanna Chen, Kevin Clancy, Robert Sidney Cox, Michal Galdzicki, Nathan Hillson, Akshay Maheshwari, Chris Myers, Umesh P, Matthew Pocock, Cesar Rodriguez, Herbert Sauro, Larisa Soldatova, Guy-Bart Stan, Mandy Wilson, Drew Endy. (2013) Synthetic Biology Open Language Visual: An Open-Source Graphical Notation for Synthetic Biology. The 5th International Workshop on Bio-Design Automation (IWBDA), London, UK, July 12-13, 2013.

Michal Galdzicki, Laura Adam, J. Christopher Anderson, Deepak Chandran, Douglas Densmore, Drew Endy, John H Gennari, Raik Gruenberg, Timothy Ham, Matthew Lux, Akshay Maheshwari, Barry Moore, Chris J. Myers, Jean Peccoud, Cesar A. Rodriguez, Nicholas Roehner, Guy-Bart Stan, Mandy Wilson, Herbert M. Sauro. (2011) Synthetic Biology Open Language: A standardized information exchange framework for synthetic biologists. The 5th International Meeting on Synthetic Biology, Stanford University, Stanford, CA, June 15-17, 2011.

Michal Galdzicki, Cesar Rodriguez, Herbert Sauro, Laura Adam, J. Christopher Anderson, Deepak Chandran, Douglas Densmore, Drew Endy, John H. Gennari, Raik Gruenberg, Timothy Ham, Matthew Lux, Akshay Maheshwari, Barry Moore, Chris J. Myers, Jean Peccoud, Nicholas Roehner, Guy-Bart Stan, Mandy Wilson, Herbert M. Sauro. (2011) Evolution of SBOL: design information exchange standard. The 3rd International Workshop on Bio-Design and Automation 2011, San Diego Convention Center, San Diego, CA, June 6-7, 2011.

Cesar Rodriguez, Michal Galdzicki. (2011) Design, Implementation, and Deployment of Electronic Datasheets. The 3rd International Workshop on Bio-Design and Automation 2011, San Diego Convention Center, San Diego, CA, June 6-7, 2011.

Michal Galdzicki, Cesar Rodriguez, Deepak Chandran, John Gennari and Herbert Sauro. (2010) A Semantic Knowledge Base of Standard Biological Parts. The 2nd International Workshop on Bio-Design and Automation (IWBDA) 2010, Anaheim, CA

Michal Galdzicki, Deepak Chandran, Herbert Sauro, Daniel Cook, and John Gennari. (2009) Bridging Synthetic Biology Models and Experiments using PoBoL. The 1st International Workshop on Bio-Design and Automation (IWBDA) 2009, San Francisco, CA

Deepak Chandran, Michal Galdzicki, and Alec Nielsen. (2009) Bridging Synthetic Biology Design and Experiments using PoBoL. The 1st International Workshop on Bio-Design and Automation 2009, San Francisco, CA

Publications Citing SBOL

D. Ewen Cameron, Caleb J. Bashor, and James J. Collins. (2014) A brief history of synthetic biology. Nature Reviews Microbiology, 01 April 2014 online. doi:10.1038/nrmicro3239

Swapnil Bhatia and Douglas Densmore. (2013) Pigeon: A Design Visualizer for Synthetic Biology,  (Technical Note) ACS Synthetic Biology, 2013, 2 (6), pp 348–350, doi:10.1021/sb400024s

Jason T. Stevens, Chris J. Myers. (2013) Dynamic Modeling of Cellular Populations with iBioSim. ACS Synthetic Biology, 2013, 2 (5), pp 223-229. doi:10.1021/sb300082b

Jacob Beal, Ron Weiss, Douglas Densmore, Aaron Adler, Evan Appleton, Jonathan Babb, Swapnil Bhatia, Noah Davidsohn, Traci Haddock, Joseph Loyall, Richard Schantz, Viktor Vasilev, and Fusun Yaman. (2012) An End-to-End Workflow for Engineering of Biological Networks from High-Level Specifications. ACS Synthetic Biology, 2012, 1 (8), pp 317-331. doi:10.1021/sb300030d

Funsun Yaman, Swapnil Bhatia, Aaron Adler, Douglas Densmore, and Jacob Beal. (2012) Automated Selection of Synthetic Biology Parts for Genetic Regulatory Networks. ACS Synthetic Biology, 2012, 1(8), pp 332-334. doi:10.1021/sb300032y

TS Ham, Z Dmytriv, H Plahar, J Chen, NJ Hillson, JD and Keasling. (2012) Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools. Nucleic Acid Res, 40(18): e141. doi:10.1093/nar/gks531

Karsten Temme, Dehua Zhaob, Christopher A. Voigt. (2012) Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca. Proceedings of the National Academy of Science, Online Publication April 16, 2012. doi:10.1073/pnas.1120788109 

Joanna Chen, Douglas Densmore, Timothy S Ham, Jay D Keasling, and Nathan J Hillson. (2012) DeviceEditor visual biological CAD canvas. Journal of Biological Engineering, 6:1.  doi:10.1186/1754-1611-6-1

Matthew W Lux, Brian W Bramlett, David A Ball, Jean Peccoud. (2012) Genetic design automation: engineering fantasy or scientific renewal? Trends in Biotechnology, 30(2), 120-126. doi:10.1016/j.tibtech.2011.09.001

Madsen C, Myers C J, Patterson T, Roehner N, Stevens J T, Winstead C. (2012) Design and Test of Genetic Circuits using iBioSim. Design & Test of Computers, PP(99), 1 - 1. doi:10.1109/MDT.2012.2187875 

Lesia Bilitchenko, Adam Liu, Sherine Cheung, Emma Weeding, Bing Xia, Mariana Leguia, J. Christopher Anderson, Douglas Densmore. (2011) Eugene – A Domain Specific Language for Specifying and Constraining Synthetic Biological Parts, Devices, and Systems. PLoS ONE 6(4): e18882. doi:10.1371/journal.pone.0018882

Yuting Zheng and Ganesh Sriram, “Mathematical Modeling: Bridging the Gap between Concept and Realization in Synthetic Biology,” Journal of Biomedicine and Biotechnology, vol. 2010, Article ID 541609, 16 pages, 2010. doi:10.1155/2010/541609

Deepak Chandran, Frank T Bergmann, Herbert M Sauro. TinkerCell: modular CAD tool for synthetic biology. Journal of Biological Engineering 2009, 3:19 doi:10.1186/1754-1611-3-19