Genetic design automation

Electronic design automation (EDA) tools have facilitated the design of ever more complex integrated circuits each year. Synthetic biology would also benefit from the development of genetic design automation (GDA) tools. Existing GDA tools require biologists to design genetic circuits at the molecular level, roughly equivalent to designing electronic circuits at the layout level. Analysis of these circuits is also performed at this very low level. This paper presents the background and issues involved in the development of such a GDA tool for modeling, analysis, and design.

[1]  M. Elowitz,et al.  A synthetic oscillatory network of transcriptional regulators , 2000, Nature.

[2]  Michael A. Gibson,et al.  Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels , 2000 .

[3]  Timothy S. Ham,et al.  Production of the antimalarial drug precursor artemisinic acid in engineered yeast , 2006, Nature.

[4]  Chris J. Myers,et al.  Learning Genetic Regulatory Network Connectivity from Time Series Data , 2011, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[5]  Chris J. Myers,et al.  Engineering Genetic Circuits , 2009 .

[6]  Victor de Lorenzo,et al.  Genetically modified organisms for the environment: stories of success and failure and what we have learned from them. , 2005, International microbiology : the official journal of the Spanish Society for Microbiology.

[7]  Gregory D. Peterson,et al.  Engineering in the biological substrate: information processing in genetic circuits , 2004, Proceedings of the IEEE.

[8]  Michael S. Samoilov,et al.  Automated Abstraction Methodology for Genetic Regulatory Networks , 2006, Trans. Comp. Sys. Biology.

[9]  R. Sarpeshkar,et al.  Brain power - borrowing from biology makes for low power computing [bionic ear] , 2006, IEEE Spectrum.

[10]  J. Collins,et al.  Construction of a genetic toggle switch in Escherichia coli , 2000, Nature.

[11]  Leonore Fleischer,et al.  Brain power , 2016, Nature.

[12]  D. Gillespie Exact Stochastic Simulation of Coupled Chemical Reactions , 1977 .

[13]  Chris J. Myers,et al.  Tablet—next generation sequence assembly visualization , 2009, Bioinform..

[14]  A. Arkin,et al.  Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells. , 1998, Genetics.

[15]  Christopher A. Voigt,et al.  Environmentally controlled invasion of cancer cells by engineered bacteria. , 2006, Journal of molecular biology.

[16]  Linda R. Petzold,et al.  Improved leap-size selection for accelerated stochastic simulation , 2003 .

[17]  Chris J. Myers,et al.  The Design of a Genetic Muller C-Element , 2007, 13th IEEE International Symposium on Asynchronous Circuits and Systems (ASYNC'07).

[18]  M. Ptashne A Genetic Switch , 1986 .

[19]  Nigel Shadbolt,et al.  Brain power , 2003, IEEE Intelligent Systems.

[20]  Kiyoshi Oguri,et al.  Asynchronous Circuit Design , 2001 .