We present walkthrough examples of using SynBioSS to design, model, and simulate synthetic gene regulatory networks. SynBioSS stands for Synthetic Biology Software Suite, a platform that is publicly available with Open Licenses at www.synbioss.org. An important aim of computational synthetic biology is the development of a mathematical modeling formalism that is applicable to a wide variety of simple synthetic biological constructs. SynBioSS-based modeling of biomolecular ensembles that interact away from the thermodynamic limit and not necessarily at steady state affords for a theoretical framework that is generally applicable to known synthetic biological systems, such as bistable switches, AND gates, and oscillators. Here, we discuss how SynBioSS creates links between DNA sequences and targeted dynamic phenotypes of these simple systems.
|Original language||English (US)|
|Title of host publication||Methods in Enzymology|
|Publisher||Academic Press Inc.|
|Number of pages||16|
|State||Published - 2011|
|Name||Methods in Enzymology|
Bibliographical noteFunding Information:
This work was supported by a grant from the National Science Foundation (CBET-0425882 and CBET-0644792), the National Institutes of Health (American Recovery and Reinvestment Act grant R01GM086865), and the University of Minnesota Biotechnology Institute. Computational support from the Minnesota Supercomputing Institute (MSI) is gratefully acknowledged. This work was also supported by the National Computational Science Alliance under TG-MCA04N033. In addition, the author thanks Jon Tomshine, Ben Swiniarski, and Kostas Biliouris for help with the illustrations.
- Biochemical networks
- Hybrid stochastic simulation
- Markov processes
- Stochastic chemical kinetics