In order to design the synthetic gene regulatory circuits that implement new functions, we first model and simulate them. The simulations give us useful insight that assist in engineering the bacteria without resorting to traditional trial and error molecular biology techniques.
Visit our publications webpage and consult the following manuscript for more details on one example of bacterial AND gates:
Ramalingam, KI, Tomshine, JR, Maynard, JA, Kaznessis YN. " Forward engineering of synthetic bio-logical AND gates" Biochemical Engineering Journal, 2009, 47(1-3):38-47
Synthetic Biology Software Suite
In order to assist synthetic biologists, we developed the Synthetic Biology Software Suite, a suite of modeling tools that connect DNA sequences to dynamic behaviors. We have launched the Synthetic Biology Software Suite on www.synbioss.org.
SynBioSS users can now quickly design, construct and simulate synthetic gene networks. SynBioSS can also use BioBricks as input and automatically generate a reaction network that can model the dynamic behavior of the BioBrick.
SynBioSS is explained in detail in the following publications:
Weeding E, Houle J, Kaznessis YN SynBioSS Designer: A Web-Based Tool for the Automated Generation of Kinetic Models for Synthetic Biological Constructs Briefings in Bioinformatics, 2010.
Kaznessis YN. "Computational Methods in Synthetic Biology", Biotechnology Journal, 2009, Volume 4(10):1392-1405.
A. Hill, J. Tomshine, E. Wedding, V. Sotiropoulos, Y. Kaznessis, "SynBioSS: the Synthetic Biology Modeling Suite", Bioinformatics 2008, 24(21):2551-3.
Kaznessis YN. "Models for synthetic biology." BMC Syst Biol. 2007 Nov 6;1(1):47