SynBioSS

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

Examples

• 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:
  • TTL
    
  • TLT
  • LTT
  • LTL