Sharing Structure and Function in Biological Design with SBOL 2.0

ACS Synthetic Biology

Volumn 5, Issue 6, 2016, Pages 498-506

  Roehner, Nicholas ^a   Beal, Jacob ^b   Clancy, Kevin ^c   Bartley, Bryan ^d   Misirli, Goksel ^e   Grünberg, Raik ^f   Oberortner, Ernst ^g   Pocock, Matthew ^h   Bissell, Michael ⁱ   Madsen, Curtis ^e   Nguyen, Tramy ^j   Zhang, Michael ^j   Zhang, Zhen ^j   Zundel, Zach ^j   Densmore, Douglas ^a   Gennari, John H ^k   Wipat, Anil ^e   Sauro, Herbert M ^d   Myers, Chris J ^j  

^a Boston University   (United States)

^b BBN TECHNOLOGIES   (United States)

^c Thermo Fisher Scientific   (United States)

^d University of Washington   (United States)

^e NEWCASTLE UNIVERSITY   (United Kingdom)

^f INSTITUTE FOR RESEARCH IN IMMUNOLOGY AND CANCER   (Canada)

^g DOE JOINT GENOME INSTITUTE   (United States)

^h Turing Ate My Hamster Ltd   (United Kingdom)

ⁱ Amyris Inc   (United States)

^j Department of Electrical and Computer Engineering   (United States)

^k UNIVERSITY OF WASHINGTON   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

DNA; MICRORNA; RNA;

ARTICLE; BIOENGINEERING; BIOTECHNOLOGY; COMPUTER AIDED DESIGN; MOLECULAR INTERACTION; PRIORITY JOURNAL; SYNTHETIC BIOLOGY; WORKFLOW; COMPUTER LANGUAGE; GENE REGULATORY NETWORK; SOFTWARE; STANDARDS;

DNA; GENE REGULATORY NETWORKS; PROGRAMMING LANGUAGES; RNA; SOFTWARE; SYNTHETIC BIOLOGY; WORKFLOW;

EID: 84975297281     PISSN: None     EISSN: 21615063     Source Type: Journal    
DOI: 10.1021/acssynbio.5b00215     Document Type: Article

References (49)

1. Benenson, Y. (2012) Biomolecular computing systems: principles, progress and potential Nat. Rev. Genet. 13, 455-468 10.1038/nrg3197
2. Woolston, B., Edgar, S., and Stephanopoulos, G. (2013) Metabolic Engineering: past and future Annu. Rev. Chem. Biomol. Eng. 4, 259-288 10.1146/annurev-chembioeng-061312-103312
3. Markson, J. and Elowitz, M. (2014) Synthetic Biology of Multicellular Systems: New Platforms and Applications for Animal Cells and Organisms ACS Synth. Biol. 3, 875-876 10.1021/sb500358y
4. Rhodius, V., Segall-Shapiro, T., Sharon, B., Ghodasara, A., Orlova, E., Tabakh, H., Burkhardt, D. H., Clancy, K., Peterson, T., Gross, C., and Voigt, C. (2013) Design of orthogonal genetic switches based on a crosstalk map of σs, anti-σs, and promoters Mol. Syst. Biol. 9, 702 10.1038/msb.2013.58
5. Stanton, B., Nielsen, A., Tamsir, A., Clancy, K., Peterson, T., and Voigt, C. (2014) Genomic mining of prokaryotic repressors for orthogonal logic gates Nat. Chem. Biol. 10, 99-105 10.1038/nchembio.1411
6. Chen, Y.-J., Liu, P., Nielsen, A., Brophy, J., Clancy, K., Peterson, T., and Voigt, C. (2013) Characterization of 582 natural and synthetic terminators and quantification of their design constraints Nat. Methods 10, 659-664 10.1038/nmeth.2515
7. Temme, K., Zhao, D., and Voigt, C. (2012) Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca Proc. Natl. Acad. Sci. U. S. A. 109, 7085-7090 10.1073/pnas.1120788109
8. Cummings, M., Breitling, R., and Takano, E. (2014) Steps towards the synthetic biology of polyketide biosynthesis FEMS Microbiol. Lett. 351, 116-125 10.1111/1574-6968.12365
9. Kim, E., Moore, B. S., and Yoon, Y. (2015) Reinvigorating natural product combinatorial biosynthesis with synthetic biology Nat. Chem. Biol. 11, 649-659 10.1038/nchembio.1893
10. Casini, A., Storch, M., Baldwin, G. S., and Ellis, T. (2015) Bricks and blueprints: methods and standards for DNA assembly Nat. Rev. Mol. Cell Biol. 16, 568-576 10.1038/nrm4014
11. Appleton, E., Tao, J., Haddock, T., and Densmore, D. (2014) Interactive assembly algorithms for molecular cloning Nat. Methods 11, 657-662 10.1038/nmeth.2939
12. Wilson, E. H., Sagawa, S., Weis, J. W., Schubert, M. G., Bissell, M., Hawethorne, B., Reeves, C. D., Dean, J., and Platt, D. (2016) Genotype specification language ACS Synth. Biol. 10.1021/acssynbio.5b00194
13. Bartley, B., Beal, J., Kevin, C., Goksel, M., 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. Bioinf. 12, 272 10.2390/biecoll-jib-2015-272
14. Galdzicki, M. (2014) SBOL: A community standard for communicating designs in synthetic biology Nat. Biotechnol. 32, 545 10.1038/nbt.2891
15. Oberortner, E., Bhatia, S., Lindgren, E., and Densmore, D. (2014) A Rule-Based Design Specification Language for Synthetic Biology J. Emerg. Technol. Comput. Syst. 11, 1-19 10.1145/2641571
16. Bilitchenko, L., Liu, A., Cheung, S., Weeding, E., Xia, B., Leguia, M., Anderson, J. C., and Densmore, D. (2011) Eugene-a domain specific language for specifying and constraining synthetic biological parts, devices, and systems PLoS One 6, e18882 10.1371/journal.pone.0018882
17. Beal, J., Lu, T., and Weiss, R. (2011) Automatic compilation from high-level biologically-oriented programming language to genetic regulatory networks PLoS One 6, e22490 10.1371/journal.pone.0022490
18. Stattery, W. (1971) An Index of US Voluntary Engineering Standards National Standards Organizations in the US 10.6028/NBS.SP.329
19. Ham, T. S., Dmytriv, Z., Plahar, H., Chen, J., Hillson, N. J., and Keasling, J. D. (2012) Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools Nucleic Acids Res. 40, e141 10.1093/nar/gks531
20. iGEM Foundation, Registry of Standard Biological Parts. http://parts.igem.org (accessed October 1, 2015).
21. Madsen, C., Misirli, G., Pocock, M., Hallinan, J., and Wipat, A. (2015) SBOL Stack: The One-stop-shop for Storing and Publishing Synthetic Biology Designs, 5th International Workshop on Bio-Design Automation, London, UK, July 12-13, 2013.
22. Cardinale, S. and Arkin, A. P. (2012) Contextualizing context for synthetic biology-identifying causes of failure of synthetic biological systems Biotechnol. J. 7, 856-866 10.1002/biot.201200085
23. Pearson, W. R. and Lipman, D. J. (1988) Improved tools for biological sequence comparison Proc. Natl. Acad. Sci. U. S. A. 85, 2444-2448 10.1073/pnas.85.8.2444
24. Bilofsky, H. S. and Christian, B. (1988) The GenBank genetic sequence data bank Nucleic Acids Res. 16, 1861-1863 10.1093/nar/16.5.1861
25. Hucka, M. et al. 2003, The Systems Biology Markup Language (SBML): a medium for representation and exchange of biochemical network models Bioinformatics 19, 524-531 10.1093/bioinformatics/btg015
26. Demir, E. et al. 2010, The BioPAX community standard for pathway data sharing Nat. Biotechnol. 28, 935-942 10.1038/nbt.1666
27. Endy, D. (2005) Foundations for engineering biology Nature 438, 449-453 10.1038/nature04342
28. Roehner, N., Oberortner, E., Pocock, M., Beal, J., Clancy, K., Madsen, C., Misirli, G., Wipat, A., Sauro, H., and Myers, C. J. (2014) Proposed data model for the next version of the Synthetic Biology Open Language ACS Synth. Biol. 4, 57-71 10.1021/sb500176h
29. Galdzicki, M., et al., (2013) Recent Advances in the Synthetic Biology Open Language, 7th International Workshop on Bio-Design Automation, Seattle, WA, August 19-21, 2015.
30. Xie, Z., Wroblewska, L., Prochazka, L., Weiss, R., and Benenson, Y. (2011) Multi-input RNAi-based logic circuit for identification of specific cancer cells Science 333, 1307-1311 10.1126/science.1205527
31. Moon, T. S., Lou, C., Tamsir, A., Stanton, B. C., and Voigt, C. A. (2012) Genetic programs constructed from layered logic gates in single cells Nature 491, 249-253 10.1038/nature11516
32. Garny, A., Nickerson, D., Cooper, J., dos Santos, R. W., Miller, A., McKeever, S., Nielsen, P., and Hunter, P. (2008) CellML and associated tools and techniques Philos. Trans. R. Soc., A 366, 3017-43 10.1098/rsta.2008.0094
33. Quinn, J. Y. et al. 2015, SBOL Visual: A Graphical Language for Genetic Designs PLoS Biol. 13, e1002310 10.1371/journal.pbio.1002310
34. Quinn, J., Beal, J., Bhatia, S., Cai, P., Chen, J., Clancy, K., Hillson, N. J., Galdzicki, M., 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. BBF RFC 93, http://hdl.handle.net/1721.1/78249.
35. Eilbeck, K., Lewis, S. E., Mungall, C. J., Yandell, M., Stein, L., Durbin, R., and Ashburner, M. (2005) The Sequence Ontology: a tool for the unification of genome annotations Genome Biology 6, R44 10.1186/gb-2005-6-5-r44
36. Juty, N. and Novere, N. (2013) Encyclopedia of Systems Biology, pp 2063-2063, Springer, New York.
37. Myers, C. J., Barker, N., Jones, K., Kuwahara, H., Madsen, C., and Nguyen, N.-P. D. (2009) iBioSim: a tool for the analysis and design of genetic circuits Bioinformatics 25, 2848-2849 10.1093/bioinformatics/btp457
38. Zhang, Z., Nguyen, T., Roehner, N., Misirli, G., Pocock, M., Oberortner, E., Samineni, M., Zundel, Z., Beal, J., Clancy, K., Wipat, A., and Myers, C. (2015) IEEE Life Science Letters 1, 34 10.1109/LLS.2016.2546546
39. Nielsen, A. A. K., Der, B. S., Shin, J., Vaidyanathan, P., Paralanov, V., Strychalski, E. A., Ross, D., Densmore, D., and Voigt, C. A. (2016) Genetic circuit design automation Science 352, aac7341 10.1126/science.aac7341
40. Vaidyanathan, P., Der, B., Bhatia, S., Roehner, N., Silva, R., Voigt, C., and Densmore, D. (2015) A Framework for Genetic Logic Synthesis Proc. IEEE 103, 1-12 10.1109/JPROC.2015.2443832
41. Roehner, N. and Myers, C. J. (2014) A methodology to annotate Systems Biology Markup Language Models with the Synthetic Biology Open Language ACS Synth. Biol. 3, 57-66 10.1021/sb400066m
42. Hedley, W. J., Nelson, M. R., Bellivant, D. P., and Nielsen, P. F. (2001) A short introduction to CellML Philos. Trans. R. Soc., A 359, 1073-1089 10.1098/rsta.2001.0817
43. Hucka, M., Bergmann, F. T., Hoops, S., Keating, S. M., Sahle, S., Schaff, J. C., Smith, L. P., and Wilkinson, D. J. (2010) The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core. SBML Specification, http://sbml.org/Documents/Specifications#SBML-Level-3-Version-1-Core.
44. Faeder, J. R., Blinov, M. L., and Hlavacek, W. S. (2009) Systems Biology, pp 113-167, Springer.
45. IEEE Standard for Verilog Hardware Description Language, IEEE Std 1364-2005 (Revision of IEEE Std 1364-2001), 2006, pp 1-560.
46. Nguyen, T., Roehner, N., Zundel, Z., and Myers, C. J. (2016) A Converter from the Systems Biology Markup Language to the Synthetic Biology Open Language ACS Synth. Biol. 10.1021/acssynbio.5b00212
47. Roehner, N., Zhang, Z., Nguyen, T., and Myers, C. J. (2015) Generating Systems Biology Markup Language Models from the Synthetic Biology Open Language ACS Synth. Biol. 4, 873-879 10.1021/sb5003289
48. Manola, F. and Miller, E., Eds. (2004) RDF Primer, W3C Recommendation, World Wide Web Consortium.
49. Prud'hommeaux, E. and Seaborne, A. (2008) SPARQL Query Language for RDF. W3C Recommendation; http://www.w3.org/TR/rdf-sparql-query/.