Tutorials / Examples
The following files may be of interest as you start using SynBioSS DS to create models of synthetic gene networks.
- SynBioSS DS Users Manual
- ICSB 2008 Tutorial
- Excel file with functions for binning the output and creating a histogram. (Word 97-2003 format) (OOXML format)
- SynBioSS Bioinformatics Article Supplementary Material
- The birth-death system of the Discrete Stochastic Model Test Suite: dsmts-001-01.xml.
- The oscillator of (Tuttle et al., Biophys J, 2005) and (Tomshine & Kaznessis, Biophys J, 2006): osc_seed.nc.
- The Heat Shock Response of (Sotiropoulos & Kaznessis, J Chem Phys, 2008): heatschock.nc.
- Several Tetracycline-inducible networks were described by Sotiropoulos & Kaznessis (Sotiropoulos & Kaznessis, BMC Syst Biol, 2007). One of the models from this paper can be found here: (Hy3S NetCDF) (SBML).
- The AND gate of Ramalingam, Tomshine, Maynard, and Kaznessis (4 different promoter configurations as NetCDF files for download) as submitted to Synthetic Biology: