VisBOL: Web-Based Tools for Synthetic Biology Design Visualization

ACS Synthetic Biology

Volumn 5, Issue 8, 2016, Pages 874-876

  McLaughlin, James Alastair ^a   Pocock, Matthew ^b   Mlslrll, Göksel ^a   Madsen, Curtis ^a   Wipat, Anil ^a  

^a NEWCASTLE UNIVERSITY   (United Kingdom)

^b Turing Ate My Hamster Ltd   (United Kingdom)

Author keywords

genetic circuits; SBOL Visual; synthetic biology; Synthetic Biology Open Language; visualization

Indexed keywords

ARTICLE; BIOINFORMATICS; DATA BASE; PRIORITY JOURNAL; PUBLICATION; SYNTHETIC BIOLOGY; WEB BROWSER; BIOLOGY; COMPUTER LANGUAGE; HUMAN; INTERNET; NUCLEIC ACID DATABASE; PROCEDURES; SOFTWARE;

COMPUTATIONAL BIOLOGY; DATABASES, NUCLEIC ACID; HUMANS; INTERNET; PROGRAMMING LANGUAGES; SOFTWARE; SYNTHETIC BIOLOGY;

EID: 84983273873     PISSN: None     EISSN: 21615063     Source Type: Journal    
DOI: 10.1021/acssynbio.5b00244     Document Type: Article

References (14)

1. Van Assche, E., Van Puyvelde, S., Vanderleyden, J., and Steenackers, H. P. (2015) RNA-binding proteins involved in post-transcriptional regulation in bacteria Front. Microbiol. 10.3389/fmicb.2015.00141
2. Brophy, J. A. and Voigt, C. A. (2014) Principles of genetic circuit design Nat. Methods 11, 508-520 10.1038/nmeth.2926
3. Kushwaha, M. and Salis, H. M. (2015) A portable expression resource for engineering cross-species genetic circuits and pathways Nat. Commun. 6, 7832 10.1038/ncomms8832
4. Quinn, J., Beal, J., Bhatia, S., Cai, P., Chen, J., Clancy, K., Hillson, N., Galdzicki, M., Maheshwari, A., and Umesh, P. (2013) Synthetic Biology Open Language Visual (SBOL Visual).
5. Bhatia, S. and Densmore, D. (2013) Pigeon: a design visualizer for synthetic biology ACS Synth. Biol. 2, 348-350 10.1021/sb400024s
6. Chandran, D., Bergmann, F. T., and Sauro, H. M. (2009) TinkerCell: modular CAD tool for synthetic biology J. Biol. Eng. 3, 19 10.1186/1754-1611-3-19
7. Clark & Parsia, SBOL Design Tool Powered by Semantic Technologies, http://clarkparsia.github.io/sbol/.
8. Galdzicki, M. et al. 2014, The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology Nat. Biotechnol. 32, 545-550 10.1038/nbt.2891
9. Galdzicki, M. et al., (2012) Synthetic Biology Open Language (SBOL), Version 1.1.0.
10. 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
11. 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
12. Ecma International (2013) ECMA-404: The JSON Data Interchange Format.
13. Ferraiolo, J., Jun, F., and Jackson, D. (2000) Scalable Vector Graphics (SVG) 1.0 Specification, iuniverse.
14. Hart, P. E., Nilsson, N. J., and Raphael, B. (1968) A formal basis for the heuristic determination of minimum cost paths Systems Science and Cybernetics, IEEE Transactions on 4 4, 100-107 10.1109/TSSC.1968.300136