Improving synthetic biology communication: Recommended practices for visual depiction and digital submission of genetic designs

ACS Synthetic Biology

Volumn 5, Issue 6, 2016, Pages 449-451

  Hillson, Nathan J ^a,b,c,d   Plahar, Hector A ^a,b,d   Beal, Jacob ^e   Prithviraj, Ranjini ^f  

^a JOINT BIOENERGY INSTITUTE   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c DOE JOINT GENOME INSTITUTE   (United States)

^d Synthetic Biology Engineering Research Center   (United States)

^e BBN TECHNOLOGIES   (United States)

^f AMERICAN CHEMICAL SOCIETY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PRIORITY JOURNAL; PUBLICATION; REPRODUCIBILITY; REVIEW; SYNTHETIC BIOLOGY; WORKFLOW; GENETICS; HUMAN; PUBLISHING; RESEARCH; SEQUENCE ANALYSIS; STANDARDS;

GENETICS; HUMANS; PUBLISHING; RESEARCH; SEQUENCE ANALYSIS; SYNTHETIC BIOLOGY; WORKFLOW;

EID: 85009080868     PISSN: None     EISSN: 21615063     Source Type: Journal    
DOI: 10.1021/acssynbio.6b00146     Document Type: Review

References (19)

1. Slattery, W. J. (1971) An Index of US Voluntary Engineering Standards; Covering Those Standards, Specifications, Test Methods, and Recommended Practices Issued by National Standardization Organizations in the United States, Vol. 329, National Bureau of Standards. Office of Engineering Standards Services, United States.
2. Quinn, J. B., Bhatia, S., Cai, P., Chen, J., Hill, N., Clancy, K., Maheshwari, A., Umesh, P., Pocock, M., Rodriguez, C., Stan, G.-B., and Endy, D. (2013) Synthetic Biology Open Language Visual (SBOL Visual), version 1.0.0, BioBricks Foundation Request for Comments (BBF RFC).
3. Quinn, J. Y., Cox, R. S., 3rd, Adler, A., Beal, J., Bhatia, S., Cai, Y., Chen, J., Clancy, K., Galdzicki, M., Hillson, N. J., Le Novere, N., Maheshwari, A. J., McLaughlin, J. A., Myers, C. J., P, U., Pocock, M., Rodriguez, C., Soldatova, L., Stan, G. B., Swainston, N., Wipat, A., and Sauro, H. M. (2015) SBOL Visual: A Graphical Language for Genetic Designs. PLoS Biol. 13, e1002310.
4. Galdzicki, M., Chandran, D., Gennari, J. H., and Sauro, H. M. (2011) Data Model Standardization for Synthetic Biomolecular Circuits and Systems, In Design and Analysis of Biomolecular Circuits: Engineering Approaches to Systems and Synthetic Biology (Koeppl, H., Setti, G., di Bernardo, M., and Densmore, D., Eds.), pp 281-293, Springer: New York.
5. Peccoud, J., Anderson, J. C., Chandran, D., Densmore, D., Galdzicki, M., Lux, M. W., Rodriguez, C. A., Stan, G. B., and Sauro, H. M. (2011) Essential information for synthetic DNA sequences. Nat. Biotechnol. 29, 22.
6. Blaxter, M., Danchin, A., Savakis, B., Fukami-Kobayashi, K., Kurokawa, K., Sugano, S., Roberts, R. J., Salzberg, S. L., and Wu, C.-I. (2016) Reminder to deposit DNA sequences. Science 352, 780-780.
7. ACS Synthetic Biology Information for Authors. http://pubs. acs.org/paragonplus/submission/asbcd6/asbcd6-Authguide.pdf.
8. Bartley, B., Beal, J., Clancy, K., Misirli, G., Roehner, N., Oberortner, E., Pocock, M., Bissell, M., Madsen, C., Nguyen, T., Zhang, Z., Gennari, J. H., Myers, C., Wipat, A., and Sauro, H. (2015) Synthetic Biology Open Language (SBOL) Version 2.0.0. J. Integr Bioinform 12, 272.
9. Roehner, N., Beal, J., Clancy, K., Bartley, B., Misirli, G., Grunberg, R., Oberortner, E., Pocock, M., Bissell, M., Madsen, C., Nguyen, T., Zhang, M., Zhang, Z., Zundel, Z., Densmore, D., Gennari, J. H., Wipat, A., Sauro, H. M., and Myers, C. J. (2016) Sharing Structure and Function in Biological Design with SBOL 2.0. ACS Synth. Biol., DOI: 10.1021/acssynbio.5b00215.
10. Galdzicki, M., Clancy, K. P., Oberortner, E., Pocock, M., Quinn, J. Y., Rodriguez, C. A., Roehner, N., Wilson, M. L., Adam, L., Anderson, J. C., Bartley, B. A., Beal, J., Chandran, D., Chen, J., Densmore, D., Endy, D., Grunberg, R., Hallinan, J., Hillson, N. J., Johnson, J. D., Kuchinsky, A., Lux, M., Misirli, G., Peccoud, J., Plahar, H. A., Sirin, E., Stan, G. B., Villalobos, A., Wipat, A., Gennari, J. H., Myers, C. J., and Sauro, H. M. (2014) The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology. Nat. Biotechnol. 32, 545-550.
11. SynBioHub: A parts repository for synthetic biology. http://sbolhub.org/.
12. Registry of Standard Biological Parts. http://parts.igem.org.
13. Cooling, M. T., Rouilly, V., Misirli, G., Lawson, J., Yu, T., Hallinan, J., and Wipat, A. (2010) Standard virtual biological parts: A repository of modular modeling components for synthetic biology. Bioinformatics 26, 925-931.
14. Ham, T. S., Dmytriv, Z., Plahar, H., Chen, J., Hillson, N. J., and Keasling, J. D. (2012) Design, implementation and practice of JBEIICE: An open source biological part registry platform and tools. Nucleic Acids Res. 40, e141.
15. Kamens, J. (2015) The Addgene repository: An international nonprofit plasmid and data resource. Nucleic Acids Res. 43, D1152- 1157.
16. SBOL Software Tools. http://sbolstandard.org/software/tools/.
17. SBOL Validator/Converter tool. http://www.async.ece.utah. edu/sbol-validator/.
18. ICE Platform Tutorial Video YouTube Playlist. https://www. youtube.com/playlist-list=PLAkVdehjfmfLLYSdU2lJq6XZIWNiz-Fev.
19. Bhatia, S., and Densmore, D. (2013) Pigeon: A design visualizer for synthetic biology. ACS Synth. Biol. 2, 348-350.