Publications

Publications About SBOL

N. Hillson, H. Plahar, J. Beal, and R. Prithviraj, “Improving Synthetic Biology: Recommended Practices for Visual Depiction and Digital Submission of Genetic Designs”,  ACS Synthetic Biology, vol. 5, no. 6, pp. 449-451, Jun. 2016. doi: 10.1021/acssynbio.6b00146

N. Roehner, J. Beal, K. Clancy, B. Bartley, G. Misirli, R. Grunberg, E. Oberortner, M. Pocock, M. Bissell, C. Madsen, T. Nguyen, M. Zhang, Z. Zhang, Z. Zundel, D. Densmore, J. Gennari, A. Wipat, H. Sauro, and C. Myers. “Sharing structure and function in biological design with SBOL 2.0,” ACS Synthetic Biology, vol. 5, no. 6, pp. 498-506, Apr. 2016. doi: 10.1021/acssynbio.5b00215

Z. Zhang, T. Nguyen, N. Roehner, G. Misirli, M. Pocock, E. Oberortner, M. Samineni, Z. Zundel, J. Beal, K. Clancy, A. Wipat, and C. Myers. “libSBOLj 2.0: A Java Library to Support SBOL 2.0,IEEE Life Sciences Letters, vol. 1, no. 4, pp. 34-37, Mar. 2016. doi:10.1109/LLS.2016.2546546

J. Y. Quinn, R. S. Cox, A. Adler, J. Beal, S. Bhatia, Y. Cai, J. Chen, K. Clancy, M. Galdzicki, N. J. Hillson, N. L. Novère, A.J. Maheshwari, J. A. McLaughlin, C. Myers, P. Umesh, M. Pocock, C. Rodriguez, L. Soldatova, G.B. Stan, N. Swainston, A. Wipat, and H. Sauro. “SBOL Visual: A Graphical Language for Genetic Designs,” PLoS Biol, vol. 13, no. 12, Dec. 2015. doi:10.1371/journal.pbio.1002310

C. Myers, K. Clancy, G. Misirli, E. Oberortner, M. Pocock, J. Quinn, N. Roehner, H. Sauro. “The synthetic biology open language, ” Methods in Molecular Biology, vol. 1244, pp. 323-336, Sep. 2015. doi: 10.1007/978-1-4939-1878-2_16

B. Bartley, J. Beal, K. Clancy, N. Hillson, G. Misirli, N. Roehner, H. Sauro, E. Oberortner, C. Madsen, M. Pocock, A. Wipat, T. Nguyen, Z. Zhang, C. Myers, J. Gennari, and M. Bissell. “Synthetic Biology Open Language (SBOL) Version 2.0.0,” Journal of Integrative Bioinformatics, vol. 12, no. 2, pp. 272, Sep. 2015. doi: 10.2390/biecoll-jib-2015-272..

N. Roehner, E. Oberortner, M. Pocock, J. Beal, K. Clancy, C. Madsen, G. Misirli, A. Wipat, H. Sauro, and C. Myers. “Proposed data model for the next version of the Synthetic Biology Open Language,” ACS Synthetic Biology, vol. 4, no. 1, pp. 57-71, Jun. 2014. doi: 10.1021/sb500176h

M. Galdzicki, K. Clancy, E. Oberortner, M. Pocock, J. Quinn, C. Rodriguez, N. Roehner, M. L. Wilson, L. Adam, C. Anderson, B. Bartley, J. Beal, D. Chandran, J. Chen, D. Densmore, D. Endy, R. Grünberg, J. Hallinan, N.J. Hillson, J. D. Johnson, A. Kuchinsky, M. Lux, G. Misirli, J. Peccoud, H. Plahar, E. Sirin, G.B Stan, A. Villalobos, A. Wipat, J. Gennari, C. Myers, and H. Sauro. “The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology,” Nature Biotechnology, vol. 32, pp. 545-550, Jun. 2014. doi:10.1038/nbt.2891

Reviews and Other Publications Featuring SBOL

ERASynBio. “Next steps for European synthetic biology: a strategic vision from ERASynBio,” Apr. 2014. http://www.erasynbio.eu/lw_resource/datapool/_items/item_53/erasynbiostrategicvision-announcement.pdf

D. Ewen Cameron, C. Bashor, and J. Collins. “A brief history of synthetic biology,” Nature Reviews Microbiology, Apr. 2014. doi:10.1038/nrmicro3239

M. Lux, B. Bramlett, D. Ball, and J. Peccoud. “Genetic design automation: engineering fantasy or scientific renewal?” Trends in Biotechnology, vol. 30, no. 2, pp. 120-126, 2012. doi:10.1016/j.tibtech.2011.09.001

K. Temme, D. Zhaob, and C. Voigt. “Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca, ” Proceedings of the National Academy of Science, Apr. 2012. doi:10.1073/pnas.1120788109

J. Peccoud, J. Anderson, D. Chandran, D. Densmore, M. Galdzicki, M. Lux, C. Rodriguez, G.B. Stan, and H. Sauro. “Essential information for synthetic DNA sequences,” Nature Biotechnology, vol. 29, no. 22, 2011. doi:10.1038/nbt.1753

Y. Zheng and G. Sriram. “Mathematical Modeling: Bridging the Gap between Concept and Realization in Synthetic Biology,” Journal of Biomedicine and Biotechnology, vol. 2010, 2010. doi:10.1155/2010/541609

Publications About Software Support for SBOL

C. Madsen, J.A. McLaughlin, G. Mısırlı, M. Pocock, K. Flanagan, J. Hallinan, and A. Wipat. “The SBOL Stack: A Platform for Storing, Publishing, and Sharing Synthetic Biology Designs,” ACS Synthetic Biology, vol. 5, no. 6, pp. 487-497, Jun. 2016. doi: 10.1021/acssynbio.5b00210 

J.A. McLaughlin, M. Pocock, G. Mısırlı, C. Madsen, and A. Wipat. “VisBOL: Web-Based Tools for Synthetic Biology Design Visualization,” ACS Synthetic Biology, Jan. 2016. doi: 10.1021/acssynbio.5b00244

T. Nguyen, N. Roehner, Z. Zundel, and C. Myers. “A Converter from the Systems Biology Markup Language to the Synthetic Biology Open Language,” ACS Synthetic Biology, vol. 5, no. 6, pp. 479-486, Dec. 2015. doi: 10.1021/acssynbio.5b00212

N. Roehner, Z. Zhang, T. Nguyen, C. Myers. “Generating Systems Biology Markup Language Models from the Synthetic Biology Open Language, ” ACS Synthetic Biology, vol. 4, no. 8, pp. 873-879, Apr. 2015. doi: 10.1021/sb5003289 

E. Appleton, J, Tao, T. Haddock, and D. Densmore. “Interactive assembly algorithms for molecular cloning, ” Nature Methods, Apr. 2014. doi:10.1038/nmeth.2939

N. Roehner and C. Myers. “Directed acyclic graph-based technology mapping of genetic circuit models, ” ACS Synthethic Biology, Mar. 2014. doi: 10.1021/sb400135t

N. Roehner and C. Myers. “A methodology to annotate Systems Biology Markup Language Models with the Synthetic Biology Open Language,” ACS Synthetic Biology, vol. 3, no. 2, pp. 57-66, 2013. doi: 10.1021/sb400066m

J. Stevens and C. Myers. “Dynamic Modeling of Cellular Populations with iBioSim,” ACS Synthetic Biology, vol. 2, no. 5, pp. 223-229, 2013. doi:10.1021/sb300082b

S. Bhatia and D. Densmore. “Pigeon: A Design Visualizer for Synthetic Biology,” ACS Synthetic Biology, vol. 2, no. 6, pp. 348–350, 2013. doi:10.1021/sb400024s

J. Beal, R.Weiss, D. Densmore, A. Adler, E. Appleton, J. Babb, S. Bhatia, N. Davidsohn, T. Haddock, J. Loyall, R. Schantz, V. Vasilev, and F. Yaman. “An End-to-End Workflow for Engineering of Biological Networks from High-Level Specifications, “ ACS Synthetic Biology, vol. 1, no. 8, pp. 317-331, 2012. doi:10.1021/sb300030d

F. Yaman, S. Bhatia, A. Adler, D. Densmore, and J. Beal. “Automated Selection of Synthetic Biology Parts for Genetic Regulatory Networks,” ACS Synthetic Biology, vol. 1, no. 8, pp. 332-334, 2012. doi:10.1021/sb300032y

T. Ham, Z. Dmytriv, H. Plahar, J. Chen, N. Hillson, and J. Keasling. “Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools, ” Nucleic Acid Res, vol. 40, no. 18: e141. doi:10.1093/nar/gks531

J. Chen, D. Densmore, T. Ham, J. Keasling, and N. Hillson. “DeviceEditor visual biological CAD canvas,” Journal of Biological Engineering, vol. 6, no. 1. doi:10.1186/1754-1611-6-1

C. Madsen, C. Myers, T. Patterson, N. Roehner, J. Stevens, and C. Winstead. “Design and Test of Genetic Circuits using iBioSim. Design & Test of Computers,” vol. 29, no. 3, pp. 32-39, Feb. 2012. doi:10.1109/MDT.2012.2187875

M. Galdzicki, C. Rodriguez, D. Chandran, H. Sauro, and J. Gennari. “Standard Biological Parts Knowledgebase,” PLoS ONE, vol. 6, no. 2, 2011. doi:10.1371/journal.pone.0017005

L. Bilitchenko, A. Liu, S. Cheung, E. Weeding, B. Xia, M. Leguia, C. Anderson, and D. Densmore. “Eugene – A Domain Specific Language for Specifying and Constraining Synthetic Biological Parts, Devices, and Systems,” PLoS ONE, vol. 6, no. 4, 2011. doi:10.1371/journal.pone.0018882

D. Chandran, F. Bergmann, and H. Sauro. “TinkerCell: modular CAD tool for synthetic biology, ” Journal of Biological Engineering, vol. 3, no. 19, 2009. doi:10.1186/1754-1611-3-19

BioBrick Foundation Request for Comments Documents

B. Bartley, J. Beal, K. Clancy, N. Hillson, G. Misirli, N. Roehner, H. Sauro, E. Oberortner, C. Madsen, M. Pocock, A. Wipat, T. Nguyen, Z. Zhang, C. Myers, J. Gennari, and M. Bissell. “Synthetic Biology Open Language (SBOL) Version 2.0.0,” BBF RFC #108, 2015. doi: (pending)

J. Quinn, J. Beal, S. Bhatia, P. Cai, J. Chen, K. Clancy, N. Hillson, M. Galdzicki, A. Maheshwari, P. Umesh, M. Pocock, C. Rodriguez, G.B. Stan, and D. Endy. “Synthetic Biology Open Language Visual (SBOL Visual), version 1.0.0,” BBF RFC #93, 2013. doi: 1721.1/78249

M. Galdzicki, M. Wilson, C. Rodriguez, M. Pocock, E. Oberortner, L. Adam, A. Adler, C. Anderson, J. Beal, Y. Cai, D. Chandran, D. Densmore, O. Drory, D. Endy, J. Gennari, R. Grünberg, T. Ham, N. Hillson, J. Johnson, A. Kuchinsky, M. Lux, C. Madsen, G. Misirli, C. Myers, C. Olguin, J. Peccoud, H. Plahar, D. Platt, N. Roehner, E. Sirin, T. Smith, G.B. Stan, A. Villabos, A.Wipat, and H. Sauro. “Synthetic Biology Open Language (SBOL) Version 1.1.0,” BBF RFC #87, 2012. doi: 1721.1/73909

M. Galdzicki, M. Wilson, C. Rodriguez, L. Adam, A. Adler, C. Anderson, J. Beal, D. Chandran, D. Densmore, O.Drory, D. Endy, J. Gennari, R. Grünberg, T. Ham, A. Kuchinsky, M. Lux, C. Madsen, G. Misirli, C. Myers, J. Peccoud, H. Plahar, M. Pocock, N. Roehner, T. Smith, G.B. Stan, A. Villalobos, A. Wipat, and H. Sauro. “Synthetic Biology Open Language (SBOL) Version 1.0.0,” BBF RFC #84, 2011. doi: 1721.1/66172

J. Johnson, M. Galdzicki, and H. Sauro. “Standard for the Electronic Distribution of SBOLv Diagrams,” BBF RFC #68, 2010. doi: 1721.1/60086

J. Steyn, A. Wipat, J. Hallinan, M. Pocock, R. Boyd, H. Sheth, A. Koh, P. Hall, D. Tsu, S. Woodhouse and Y. Essa. “A RESTful API for Supporting Automated BioBrick Model Assembly,” BBF RFC #66, 2010. doi: 1721.1/60085

M. Galdzicki, D. Chandran, A. Nielsen, J. Morrison, M. Cowell, R. Grunberg, S. Sleight, and H. Sauro. “Provisional BioBrick Language (PoBoL),” BBF RFC #31, 2009. doi: 1721.1/45537

R. Grünberg. “Draft of an RDF-based framework for the exchange and integration of Synthetic Biology data,” BBF RFC #30, 2009. doi: 1721.1/45143 2009

C. Rodriguez, S. Bartram, A. Ramasubramanian, and D. Endy. “Synthetic Biology Open Language Visual (SBOLv) Specification,” BBF RFC #16, 2009. doi: 1721.1/49523

Documents