Genetdes: automatic design of transcriptional networks.

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.
Document type :
Journal articles
Complete list of metadatas

https://hal-polytechnique.archives-ouvertes.fr/hal-00767379
Contributor : Denis Roura <>
Submitted on : Friday, January 4, 2013 - 1:00:12 PM
Last modification on : Wednesday, July 10, 2019 - 7:14:02 PM

Links full text

Identifiers

Collections

Citation

G. Rodrigo, J. Carrera, A. Jaramillo. Genetdes: automatic design of transcriptional networks.. Bioinformatics, Oxford University Press (OUP), 2007, 23 (14), pp.1857-8. ⟨10.1093/bioinformatics/btm237⟩. ⟨hal-00767379⟩

Share

Metrics

Record views

122