Computational Systems Biology
Sauro Lab
University of Washington
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maintained by Frank Bergmann

Synthetic Biology

Synthetic biology has been described as the design and construction of new biological entities such as enzymes, genetic circuits, and cells, or the redesign of existing biological systems. It is a useful tool to investigate the dynamics of small biological networks and to assess our capacity to predict their behavior from computational models. We are currently engaged in several synthetic biology efforts.

The first is development of a software application to optimize design of new biological networks. Our software system will allow synthetic biologists to:

  • Construct genetic networks and metabolic/signaling networks that can be exported into standard formats (e.g. SBML)
  • Obtain simulated behavior of the network
  • Search a database for genetic “parts” to fit the network
  • Save a genetic network or sub-network in a standard format for later use
  • Obtain a plasmid sequence for individual genetic parts or the entire genetic network

The second effort is the organization of an international workshop to bring together leaders in the synthetic biology field in order to discuss issues pertaining to how parts might be specified, organized, and constructed.

We have also recently built small genetic circuits in E. coli to test our ability to go from in silico design to implementation (Entus et al. 2007, in press). This work involved the construction of three different genetic circuits that act as concentration band detectors (i.e. circuits that switch on when the concentration of an input signal is in a specific range). We built three circuits to test different methods of construction, one based on utilizing components from the methionine regulatory system, another based on anti-RNA binding, and another on lysozyme inhibition. All circuits were based on a feed-forward regulatory loop. Also, a synthetic feedback amplifier and other designs are in the works.

sysbio/synthetic_biology.txt · Last modified: 2008/01/12 17:38 (external edit)

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