Dynamic modeling of cellular populations within iBioSim

ACS Synthetic Biology

Volumn 2, Issue 5, 2013, Pages 223-229

  Stevens, Jason T ^a,b   Myers, Chris J ^a  

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

^b University of Washington   (United States)

Author keywords

dynamic modeling; genetic circuits; multicellular modeling; SBML; spatial modeling; stochastic simulation

Indexed keywords

DNA;

ALGORITHM; ARTICLE; AUTOMATION; BIOLOGICAL MODEL; CELL POPULATION; COMPUTER INTERFACE; COMPUTER PROGRAM; POPULATION DYNAMICS; PRIORITY JOURNAL; SIMULATION;

ANIMALS; CELL PHYSIOLOGICAL PHENOMENA; COMPUTER SIMULATION; HUMANS; MODELS, BIOLOGICAL; PROGRAMMING LANGUAGES; SOFTWARE; SYNTHETIC BIOLOGY; USER-COMPUTER INTERFACE;

EID: 84878047546     PISSN: None     EISSN: 21615063     Source Type: Journal    
DOI: 10.1021/sb300082b     Document Type: Article

References (29)

1. Ruder, W. C., Lu, T., and Collins, J. J. (2011) Synthetic biology moving into the clinic Science 333, 1248-1252
2. Basu, S., Gerchman, Y., Collins, C. H., Arnold, F. H., and Weiss, R. (2005) A synthetic multicellular system for programmed pattern formation Nature 434, 1130-1134 (Pubitemid 40663491)
3. Liu, C., Fu, X., Liu, L., Ren, X., Chau, C. K., Li, S., Xiang, L., Zeng, H., Chen, G., Tang, L. H., Lenz, P., Cui, X., Huang, W., Hwa, T., and Huang, J. D. (2011) Sequential establishment of stripe patterns in an expanding cell population Science 334, 238-241
4. Tamsir, A., Tabor, J., and Voigt, C. (2011) Robust multicellular computing using genetically encoded NOR gates and chemical wires Nature 469, 212-215
5. Cai, Y., Hartnett, B., Gustafsson, C., and Peccoud, J. (2007) A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts Bioinformatics 23, 2760-2767 (Pubitemid 350048342)
6. Weeding, E., Houle, J., and Kaznessis, Y. N. (2010) SynBioSS designer: a web-based tool for the automated generation of kinetic models for synthetic biological constructs Briefings Bioinf. 11, 394-402
7. Chandran, D., Bergmann, F. T., and Sauro, H. M. (2009) TinkerCell: modular CAD tool for synthetic biology J. Biol. Eng. 3, 19
8. Hillson, N. J., Rosengarten, R. D., and Keasling, J. D. (2012) j5 DNA Assembly Design Automation Software ACS Synth. Biol. 1, 14-21
9. Xia, B., Bhatia, S., Bubenheim, B., Dadgar, M., Densmore, D., and Anderson, J. C. (2011) in Synthetic Biology, Part B Computer Aided Design and DNA Assembly (Voigt, C., Ed.) Methods in Enzymology, Vol. 498; pp 97-135, Academic Press, New York.
10. Cickovski, T. M., Huang, C., Chaturvedi, R., Glimm, T., Hentschel, H. G., Alber, M. S., Glazier, J. A., Newman, S. A., and Izaguirre, J. A. (2005) A framework for three-dimensional simulation of morphogenesis IEEE/ACM Trans. Comput. Biol. Bioinf. 2, 273-288
11. Meir, E., Munro, E. M., Odell, G. M., and Von Dassow, G. (2002) Ingeneue: a versatile tool for reconstituting genetic networks, with examples from the segment polarity network J. Exp. Zool. 294, 216-251 (Pubitemid 35181256)
12. Le Novere, N. and Shimizu, T. S. (2001) STOCHSIM: modelling of stochastic biomolecular processes Bioinformatics 17, 575-576 (Pubitemid 32600510)
13. Jang, S. S., Oishi, K. T., Egbert, R. G., and Klavins, E. (2012) Specification and simulation of synthetic multicelled behaviors ACS Synth. Biol. 1, 365-374
14. Rudge, T. J., Steiner, P. J., Phillips, A., and Haseloff, J. (2012) Computational modeling of synthetic microbial biofilms ACS Synth. Biol. 1, 345-352
15. 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
16. Madsen, C., Myers, C., Patterson, T., Roehner, N., Stevens, J., and Winstead, C. (2012) Design and test of genetic circuits using iBioSim IEEE Design Test Comput. 29 (3) 32-39
17. Hucka, M. 2003, The Systems Biology Markup Language (SBML): A medium for representation and exchange of biochemical network models Bioinformatics 19, 524-531 (Pubitemid 36336519)
18. Galdzicki, M. (2011) Synthetic Biology Open Language (SBOL) Version 1.0.0., DOI: 1721.1/66172.
19. Kuwahara, H., Myers, C., Barker, N., Samoilov, M., and Arkin, A. (2006) Automated abstraction methodology for genetic regulatory networks Trans. Comp. Syst. Biol. VI, 150-175 (Pubitemid 351150658)
20. Kuwahara, H. (2007) Model abstraction and temporal behavior analysis of genetic regulatory networks. Ph.D. thesis, University of Utah.
21. Kuwahara, H., Myers, C., and Samoilov, M. (2010) Temperature control of fimbriation circuit switch in uropathogenic Escherichia coli: quantitative analysis via automated model abstraction PLoS Comput. Biol. 6, e1000723
22. Kuwahara, H., Madsen, C., Mura, I., Myers, C., Tejeda, A., and Winstead, C. (2010) in Stochastic Control (Myers, C., Ed.) Sciyo, http://sciyo.com/.
23. Madsen, C., Myers, C., Roehner, N., Winstead, C., and Zhang, Z. (2012) Utilizing stochastic model checking to analyze genetic circuits, in 2012 Computational Intelligence in Bioinformatics and Computational Biology; IEEE, New York.
24. Nguyen, N., Myers, C., Kuwahara, H., Winstead, C., and Keener, J. (2010) Design and analysis of a robust genetic Muller C-element J. Theor. Biol. 264, 174-187
25. Slepoy, A., Thompson, A. P., and Plimpton, S. J. (2008) A constant-time kinetic Monte Carlo algorithm for simulation of large biochemical reaction networks J. Chem. Phys. 128, 205101
26. JGraphX. http://www.jgraph.com/jgraphdownload.html.
27. GNU Trove. http://sourceforge.net/projects/trove4j/.
28. Jafama. http://sourceforge.net/projects/jafama/.
29. Flanagan, M. T. Michael Thomas Flanagan's Java Scientific Library. http://www.ee.ucl.ac.uk/mflanaga/java/.