A hybrid approach to piecewise modelling of biochemical systems
PPSN'12 Proceedings of the 12th international conference on Parallel Problem Solving from Nature - Volume Part I
Bacterially inspired evolving system with an application to time series prediction
Applied Soft Computing
Synthetic Biology and Microdevices: A Powerful Combination
ACM Journal on Emerging Technologies in Computing Systems (JETC) - Special Issue on Bioinformatics
Natural Computing: an international journal
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Motivation: The rational design of biological networks with prescribed functions is limited to gene circuits of a few genes. Larger networks involve complex interactions with many parameters and the use of automated computational tools can be very valuable. We propose a new tool to design transcriptional networks with targeted behavior that could be used to better understand the design principles of genetic circuits. Results: We have implemented a Simulated Annealing optimization algorithm that explores throughout the space of transcription networks to obtain a specific behavior. The software outputs a transcriptional network with all the corresponding kinetic parameters in SBML format. We provide examples of transcriptional circuits with logical and oscillatory behaviors. Our tool can also be applied to design networks with multiple external input and output genes. Availability: The software, a tutorial manual, parameter sets and examples are freely available at http://synth-bio.yi.org/genetdes.html Contact: Alfonso.Jaramillo@polytechnique.edu