title: Genetdes: automatic design of transcriptional networks.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  The software, a tutorial manual, parameter sets and examples are freely available at http://synth-bio.yi.org/genetdes.html.
authors.affiliation: Dep. de Matematica Aplicada, Universidad Politecnica de Valencia, Camino de Vera s/n, 46022 Valencia, Spain.
authors.forename: Guillermo
authors.initials: G
authors.lastname: Rodrigo
authors.forename: Javier
authors.initials: J
authors.lastname: Carrera
authors.forename: Alfonso
authors.initials: A
authors.lastname: Jaramillo
mesh_terms: D000465:Algorithms; D001331:Automation; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D007700:Kinetics; D008954:Models, Biological; D015233:Models, Statistical; D009991:Oscillometry; D011401:Promoter Regions, Genetic; D012984:Software; D049490:Systems Biology / Q000295:instrumentation*; D014158:Transcription, Genetic