Genetdes

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.

Genetdes: automatic design of transcriptional networks.

The software tool 'Genetdes' is a tool designed to help with the rational design of transcriptional networks with specific targeted behavior, using a simulated annealing optimization algorithm. The software outputs a transcriptional network with corresponding kinetic parameters in SBML format and can be applied to design networks with multiple external input and output genes.

Genetdes

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