Abstract
SYNBADm is a Matlab toolbox for the automated design of biocircuits using a model-based optimization approach. It enables the design of biocircuits with pre-defined functions starting from libraries of biological parts. SYNBADm makes use of mixed integer global optimization and allows both single and multi-objective design problems. Here we describe a basic protocol for the design of synthetic gene regulatory circuits. We illustrate step-by-step how to solve two different problems: (1) the (single objective) design of a synthetic oscillator and (2) the (multi-objective) design of a circuit with switch-like behavior upon induction, with a good compromise between performance and protein production cost.
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References
Marchisio MA, Stelling J (2009) Computational design tools for synthetic biology. Curr Opin Biotechnol 20(4):479–485
Rodrigo G, Landrain TE, Shen S, Jaramillo A (2013) A new frontier in synthetic biology: automated design of small RNA devices in bacteria. Trends Genet 29(9):529–536
Nielsen AAK, Der BS, Shin J, Vaidyanathan P, Paralanov V, Strychalski EA, Ross D, Densmore D, Voigt CA (2016) Genetic circuit design automation. Science 352(6281):aac7341
Otero-Muras I, Henriques D, Banga JR (2016) Synbadm: a tool for optimization-based automated design of synthetic gene circuits. Bioinformatics 32(21):3360–3362
Xiang Y, Dalchau N, Wang B (2018) Scaling up genetic circuit design for cellular computing: advances and prospects. Nat Comput 17(4):833–853
Otero-Muras I, Banga JR (2017) Automated design framework for synthetic biology exploiting Pareto optimality. ACS Synth Biol 6(7):1180–1193
Egea JA, Marti R, Banga JR (2010) An evolutionary method for complex-process optimization. Comput Oper Res 37:315–324
Exler O, Schittkowski K (2007) A trust region SQP algorithm for mixed-integer nonlinear programming. Optim Lett 1(3):269–280
Exler O, Antelo LT, Egea JA, Alonso AA, Banga JR (2008) A Tabu search-based algorithm for mixed-integer nonlinear problems and its application to integrated process and control system design. Comput Chem Eng 32(8):1877–1891
Schlueter M, Egea JA, Banga JR (2009) Extended ant colony optimization for non-convex mixed integer nonlinear programming. Comput Oper Res 36(7):2217–2229
Hansen P, Mladenovic N, Moreno-Perez JA (2010) Variable neighbourhood search: methods and applications. Ann Oper Res 175(1):367–407
Pedersen M, Phillips A (2009) Towards programming languages for genetic engineering of living cells. J R Soc Interface 6:S437–S450
Otero-Muras I, Banga JR (2016) Design principles of biological oscillators through optimization: Forward and reverse analysis. PLoS ONE 11(12):e0166867
Dasika MS, Maranas CD (2008) Optcircuit: an optimization based method for computational design of genetic circuits. BMC Syst Biol 2:24
Szekely P, Sheftel H, Mayo A, Alon U (2013) Evolutionary tradeoffs between economy and effectiveness in biological homeostasis systems. PLoS Comput Biol 9(8):e1003163
Otero-Muras I, Banga JR (2014) Multicriteria global optimization for biocircuit design. BMC Syst Biol 8:113
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Otero-Muras, I., Banga, J.R. (2021). Automated Biocircuit Design with SYNBADm. In: Menolascina, F. (eds) Synthetic Gene Circuits . Methods in Molecular Biology, vol 2229. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1032-9_4
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DOI: https://doi.org/10.1007/978-1-0716-1032-9_4
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