SBROME: A scalable optimization and module matching framework for automated biosystems design

ACS Synthetic Biology

Volumn 2, Issue 5, 2013, Pages 263-273

  Huynh, Linh ^a   Tsoukalas, Athanasios ^a   Köppe, Matthias ^a   Tagkopoulos, Ilias ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

biodesign automation; CAD tool; computer aided design; modular design; module matching; multiplexer; part selection

Indexed keywords

LIGAND; PROTEIN; RNA;

ALGORITHM; ARTICLE; AUTOMATION; DATA BASE; GENE EXPRESSION; OSCILLATOR; PRIORITY JOURNAL;

COMPUTER SIMULATION; DATABASE MANAGEMENT SYSTEMS; DATABASES, FACTUAL; MODELS, BIOLOGICAL; PROGRAMMING LANGUAGES; SOFTWARE; SYNTHETIC BIOLOGY; SYSTEMS INTEGRATION;

EID: 84878026511     PISSN: None     EISSN: 21615063     Source Type: Journal    
DOI: 10.1021/sb300095m     Document Type: Article

References (54)

1. Purnick, P. E. M. and Weiss, R. (2009) The second wave of synthetic biology: from modules to systems Nat. Rev. Mol. Cell Biol. 10, 410-422
2. Cooling, M. T., Rouilly, V., Misirli, G., Lawson, J. R., 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
3. Landrain, T. E., Carrera, J., Kirov, B., Rodrigo, G., and Jaramillo, A. (2009) Modular model-based design for heterologous bioproduction in bacteria Curr. Opin. Biotechnol. 20, 272-279
4. Anderson, J. C., Voigt, C. A., and Arkin, A. P. (2007) Environmental signal integration by a modular AND gate Mol. Syst. Biol. 10.1038/msb4100173 (Pubitemid 47258528)
5. Wang, B., Kitney, R. I., Joly, N., and Buck, M. (2011) Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology Nat. Commun. 2, 508+
6. Tamsir, A., Tabor, J. J., and Voigt, C. A. (2011) Robust multicellular computing using genetically encoded NOR gates and chemical "wires Nature 469, 212-215
7. Lou, C. (2010) Synthesizing a novel genetic sequential logic circuit: a push-on push-off switch Mol. Syst. Biol. 10.1038/msb.2010.2
8. Miller, M., Hafner, M., Sontag, E., Davidsohn, N., Subramanian, S., Purnick, P. E. M., Lauffenburger, D., and Weiss, R. (2012) Modular design of artificial tissue homeostasis: robust control through synthetic cellular heterogeneity PLoS Comput. Biol. 8 e1002579
9. Gardner, T. S., Cantor, C. R., and Collins, J. J. (2000) Construction of a genetic toggle switch in Escherichia coli Nature 403, 339-342 (Pubitemid 30062394)
10. Litcofsky, K., Afeyan, R., R., K., Khalil, A., and Collins, J. (2012) Iterative plug-and-play methodology for constructing and modifying synthetic gene networks Nat. Methods 9, 1077-1080
11. Ginkel, M., Kremling, A., Nutsch, T., Rehner, R., and Gilles, E. D. (2003) Modular modeling of cellular systems with ProMoT/Diva Bioinformatics 19, 1169-1176 (Pubitemid 36790021)
12. Smith, L. P., Bergmann, F. T., Chandran, D., and Sauro, H. M. (2009) Antimony: a modular model definition language Bioinformatics 25, 2452-2454
13. Chandran, D. and Sauro, H. M. (2012) Hierarchical modeling for synthetic biology ACS Synth. Biol. 1, 353-364
14. Pedersen, M. and Phillips, A. (2009) Towards programming languages for genetic engineering of living cells J. R. Soc., Interface 6, S437-S450
15. 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
16. Goler, J. A. (2004) BioJADE: a design and simulation tool for synthetic biological systems, AI Technical Report 2004-003, MIT Computer Science and Artificial Intelligence Laboratory, Cambridge.
17. Slusarczyk, A. L., Lin, A., and Weiss, R. (2012) Foundations for the design and implementation of synthetic genetic circuits Nat. Rev. Genet. 13, 406-420
18. Beal, J., Weiss, R., Densmore, D., Adler, A., Appleton, E., Babb, J., Bhatia, S., Davidsohn, N., Haddock, T., Loyall, J., Schantz, R., Vasilev, V., and Yaman, F. (2012) An end-to-end workflow for engineering of biological networks from high-level specifications ACS Synth. Biol. 1, 317-331
19. Chandran, D., Bergmann, F., and Sauro, H. (2009) TinkerCell: modular CAD tool for synthetic biology J. Biol. Eng 3, 19
20. Marchisio, M. A. and Stelling, J. (2011) Automatic design of digital synthetic gene circuits PLoS Comput. Biol. 7, e1001083
21. Rodrigo, G., Carrera, J., and Jaramillo, A. (2007) Genetdes: automatic design of transcriptional networks Bioinformatics 23, 1857-1858 (Pubitemid 47250327)
22. Wu, C.-H., Lee, H.-C., and Chen, B.-S. (2011) Robust synthetic gene network design via library-based search method Bioinformatics 27, 2700-2706
23. Rodrigo, G. and Jaramillo, A. (2013) AutoBioCAD: full biodesign automation of genetic circuits ACS Synth. Biol. 1, 1-2
24. Yaman, F., Bhatia, S., Adler, A., Densmore, D., and Beal, J. (2012) Automated selection of synthetic biology parts for genetic regulatory networks ACS Synth. Biol. 1, 332-344
25. Miyamoto, T., Razavi, S., DeRose, R., and Inoue, T. (2012) Synthesizing biomolecule-based Boolean logic gates ACS Synth. Biol. 2, 72-82
26. Hunyh, L. and Tagkopoulos, I. (2012) A robust, library-based, optimization-driven method for automatic gene circuit design, in Computational Advances in Bio and Medical Sciences, 2012 IEEE 2nd International Conference, pp 1-6, IEEE, New York.
27. Huynh, L., Kececioglu, J., Köppe, M., and Tagkopoulos, I. (2012) Automatic design of synthetic gene circuits through mixed integer non-linear programming PLoS ONE 7 e35529
28. Ullmann, J. R. (1976) An Algorithm for Subgraph Isomorphism J. Assoc. Comput. Mach. 23, 31-42
29. Messmer, B. (1995) Efficient graph matching algorithms for preprocessed model graphs. Ph.D. thesis, University of Bern, Switzerland.
30. Hao, J. and Orlin, J. B. (1994) A faster algorithm for finding the minimum cut in a directed graph J. Algorithms 17, 424-446
31. Newman, M. E. J. (2004) Fast algorithm for detecting community structure in networks Phys. Rev. E 69, 066133+
32. Karypis, G. and Kumar, V. (1998) A fast and high quality multilevel scheme for partitioning irregular graphs SIAM J. Sci. Comput. 20, 359-392 (Pubitemid 128689516)
33. Tagkopoulos, I., Liu, Y. C., and Tavazoie, S. (2008) Predictive behavior within microbial genetic networks Science 320, 1313-1317 (Pubitemid 351929462)
34. Mozhayskiy, V., Miller, B., Ma, K.-L., and Tagkopoulos, I. (2011) A scalable multi-scale framework for parallel simulation and visualization of microbial evolution, in Proceedings of the 2011 TeraGrid Conference: Extreme Digital Discovery, 7:1-7:8, Association for Ccomputing Machinery, New York.
35. Mozhayskiy, V. and Tagkopoulos, I. (2012) Horizontal gene transfer dynamics and distribution of fitness effects during microbial in silico evolution BMC Bioinformatics 13, S13
36. Karr, J. R., Sanghvi, J. C., Macklin, D. N., Gutschow, M. V., Jacobs, J. M., Bolival, B., Assad-Garcia, N., Glass, J. I., and Covert, M. W. (2012) A whole-cell computational model predicts phenotype from genotype Cell 150, 389-401
37. Moon, T. S., Clarke, E. J., Groban, E. S., Tamsir, A., Clark, R. M., Eames, M., Kortemme, T., and Voigt, C. A. (2011) Construction of a genetic multiplexer to toggle between chemosensory pathways in Escherichia coli J. Mol. Biol. 406, 215-227
38. Pasotti, L., Quattrocelli, M., Galli, D., De Angelis, M. G. C., and Magni, P. (2011) Multiplexing and demultiplexing logic functions for computing signal processing tasks in synthetic biology Biotechnol. J. 6, 784-795
39. Berkeley 2006 iGEM Team. Constitutive promoter family(retrieved August, (2012). http://partsregistry.org/Promoters/Catalog/Anderson.
40. Ellis, T., Wang, X., and Collins, J. (2009) Diversity-based, model-guided construction of synthetic gene networks with predicted functions Nat. Biotechnol. 27, 465-471
41. Cordella, L. P., Foggia, P., Sansone, C., and Vento, M. (2004) A (sub)graph isomorphism algorithm for matching large graphs IEEE Trans. Pattern Anal. Mach. Intell. 26, 1367-1372
42. Messmer, B. T. and Bunke, H. (2000) Efficient subgraph isomorphism detection: a decomposition approach IEEE Trans. Knowl. Data Eng. 12, 307-323
43. Ohlrich, M., Ebeling, C., Ginting, E., and Sather, L. (1993) SubGemini: identifying subcircuits using a fast subgraph isomorphism algorithm, in Proceedings of the 30th international Conference on Design Automation, pp 31-37, IEEE, New York (Pubitemid 23673292)
44. Del Vecchio, D., Ninfa, A. J., and Sontag, E. D. (2008) Modular cell biology: retroactivity and insulation Mol. Syst. Biol. 4, 161
45. Saez-Rodriguez, J., Gayer, S., Ginkel, M., and Gilles, E. D. (2008) Automatic decomposition of kinetic models of signaling networks minimizing the retroactivity among modules Bioinformatics 24, i213-i219
46. Voigt, C., Ed. (2011) Synthetic Biology: Methods for Building and Programming Life, Methods in Enzymology Vol. 497, Academic Press, New York.
47. Hooshangi, S., Thiberge, S., and Weiss, R. (2005) Ultrasensitivity and noise propagation in a synthetic transcriptional cascade Proc. Natl. Acad. Sci. U.S.A. 102, 3581-3586 (Pubitemid 40354655)
48. Guido, N. J., Wang, X., Adalsteinsson, D., Mcmillen, D., Hasty, J., Cantor, C. R., Elston, T. C., and Collins, J. J. (2006) A bottom-up approach to gene regulation Nature 439, 856-60 (Pubitemid 43255704)
49. Tabor, J. J., Salis, H. M., Simpson, Z. B., Chevalier, A. A., Levskaya, A., Marcotte, E. M., Voigt, C. A., and Ellington, A. D. (2009) A synthetic genetic edge detection program Cell 137, 1272-1281
50. Canton, B., Labno, A., and Endy, D. (2008) Refinement and standardization of synthetic biological parts and devices Nat. Biotechnol. 26, 787-793 (Pubitemid 351961452)
51. Sayut, D. J., Niu, Y., and Sun, L. (2009) Construction and enhancement of a minimal genetic AND logic gate Appl. Environ. Microbiol. 75, 637-642
52. Elowitz, M. B. and Leibler, S. (2000) A synthetic oscillatory network of transcriptional regulators Nature 403, 335-338 (Pubitemid 30062393)
53. Stricker, J., Cookson, S., Bennett, M. R., Mather, W. H., Tsimring, L. S., and Hasty, J. (2008) A fast, robust and tunable synthetic gene oscillator Nature 456, 516-519 (Pubitemid 352759003)
54. Atkinson, M. R., Savageau, M. A., Myers, J. T., and Ninfa, A. J. (2003) Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli Cell 113, 597-607 (Pubitemid 36694185)