Programming languages for synthetic biology

Systems and Synthetic Biology

Volumn 4, Issue 4, 2010, Pages 265-269

  Umesh, P ^a   Naveen, F ^b   Rao, Chanchala Uma Maheswara ^c   Nair, Achuthsankar S ^a  

^a UNIVERSITY OF KERALA   (India)

^b Travancore Analytics   (India)

^c TATA CONSULTANCY SERVICES   (India)

Author keywords

Computational biology; Design and construction of organisms; Programming language; Synthetic biology

Indexed keywords

EID: 79953182968     PISSN: 18725325     EISSN: 18725333     Source Type: Journal    
DOI: 10.1007/s11693-011-9070-y     Document Type: Article

References (16)

1. Bashor CJ, Horwitz AA, Peisajovich SG, Lim WA (2010) Rewiring cells: synthetic biology as a tool to interrogate the organizational principles of living systems. Rev Lit Arts Am. doi: 10. 1146/annurev. biophys. 050708. 133652.
2. Cai Y, Hartnett B, Gustafsson C, Peccoud J (2007) A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts. Bioinformatics 23(20): 2760.
3. Chandran D, Bergmann FT, Sauro HM (2009) TinkerCell: modular CAD tool for synthetic biology. J Biol Eng 3: 19. doi: 10. 1186/1754-1611-3-19.
4. Clancy K, Voigt CA (2010) Programming cells: towards an automated 'genetic compiler'. Curr Opin Biotechnol 572-581. doi: 10. 1016/j. copbio. 2010. 07. 005.
5. Czar MJ, Cai Y, Peccoud J (2009) Writing DNA with GenoCAD TM. Grammars 37: 40-47. doi: 10. 1093/nar/gkp361.
6. Elowitz MB, Leibler S (2000) A synthetic oscillatory network of transcriptional regulators. Nature 403(6767): 335-338.
7. Endler L, Rodriguez N, Juty N, Chelliah V, Laibe C, Li C et al. (2009) Designing and encoding models for synthetic biology rapid response designing and encoding models for synthetic biology. J R Soc. doi: 10. 1098/rsif. 2009. 0035. focus.
8. Gardner TS, Cantor CR, Collins JJ (2000) Construction of a genetic toggle switch in Escherichia coli. Nature 339-342.
9. Goler JA (2004) BioJADE: a design and simulation tool for synthetic biological systems. MIT Computer Science and Artificial Intelligence Laboratory AT Technical Report 2004-003.
10. Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A et al (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19: 524-531.
11. Khalil AS, Collins JJ (2010) Synthetic biology: applications come of age, 11. doi: 10. 1038/nrg2775.
12. Machisio MA, Stelling J (2009) Computational design tools for synthetic biology. Science Direct 20(4): 479-485.
13. Pedersen M, Phillips A, Pedersen M, Phillips A (2009) Towards programming languages for genetic engineering of living cells Towards programming languages for genetic engineering of living cells. Interface. doi: 10. 1098/rsif. 2008. 0516. focus.
14. Purnick PE, Weiss R (2009) The second wave of synthetic biology: from modules to systems. Nature Publishing Group 10(6): 410-422. doi: 10. 1038/nrm2698.
15. Smith LP, Bergmann FT, Chandran D, Sauro HM (2009) Antimony: a modular model definition language. Bioinformatics 25(18): 2452-2454. doi: 10. 1093/bioinformatics/btp401.
16. Young E, Alper H (2010) Synthetic biology: tools to design, build, and optimize cellular processes. J Biomed Biotechnol. doi: 10. 1155/2010/130781.