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Bioinformatics Advance Access published online on May 7, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm237
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Genetdes: automatic design of transcriptional networks

Guillermo Rodrigo a, Javier Carrera a and Alfonso Jaramillo b,*

aDep. de Matematica Aplicada, Universidad Politecnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain, bLab. de Biochimie, CNRS - UMR 7654, Ecole Polytechnique, Route de Saclay, 91128 Palaiseau, France

*To whom correspondence should be addressed. Prof. Alfonso Jaramillo, E-mail: Alfonso.Jaramillo{at}polytechnique.edu


  Abstract

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

Associate Editor: Prof. Alfonso Valencia

Received on February 28, 2007; revised on April 22, 2007; accepted on April 26, 2007

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