The Synthetic Biology Software Suite (SynBioSS) is a software suite for the generation, storing, retrieval and quantitative simulation of synthetic biological networks. SynBioSS facilitates computational synthetic biology and consists of three independent components: the Desktop Simulator (DS), the Wiki, and the Designer.
SynBioSS is detailed in “Hill et al. Bioinformatics 24 (21): 2551. (2008).”
In a recent published work “Ramalingam et al. Biochemical Engineering Journal 47 (2009) 38-47“, synthetic biological AND gates are simulated with SynBioSS and constructed and tested in E. coli. The results provide a good proof of concept. A pdf of this manuscript is here.
Downloadable Desktop Simulator
The SynBioSS DS is a set of multiscale algorithms for modeling and simulating reaction networks, such as gene regulatory networks. It combines routines for modeling systems stochastically and discretely (kinetic Monte Carlo) and/or stochastically and continuously (stochastic differential equations). SynBioSS has a user friendly graphical user interface, and it reads and writes SBML and .nc models. SynBioSS DS can run on Windows, Mac OS, and Linux/UNIX. It is an Open Source software and can be downloaded at SourceForge. Click here to download SynBioSS DS.
Please remember to cite the following “Hill et al. Bioinformatics 24 (21): 2551. (2008).”
SynBioSS Designer is a web service to transform a sequence of BioBricks, or any other set of biomolecular components, to a set of reactions that can be simulated dynamically in SynBioSS DS. The user simply inputs the Biobricks and their relationships and Designer builds a reaction network using biological interactions rules. Click here to go to the Designer.
SynBioSS Wiki is a web service to collect the kinetic parameters necessary to create a model that can be simulated by SynBioSS DS. If you want to create a model in from the SynBioSS Wiki reaction by reaction, click here to go to the SynBioSS Wiki. Also, if you want to add or edit any information on biochemical species and / or the reactions in which they participate, go to the Wiki.
SynBioSS Desktop Simulator Examples(DS)
If you are not quite sure how to get started making a model, or just want to see what SynBioSS DS can do, here are some example models that can be loaded into SynBioSS DS.
- An oscillator has been previously described in the literature. Here are two references: (Tuttle et al., Biophys J, 2005) and (Tomshine & Kaznessis, Biophys J, 2006). Here is the model: osc_seed.nc.
- The Heat Shock Response was modeled as a part of a paper by Sotiropoolos & Kaznessis (Sotiropoulos & Kaznessis, J Chem Phys, 2008). The model is here: 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: Net1Add2000Tc10510100split.nc.zip.
SynBioSS DS uses Hy3S. The Hy3S project can be found here. http://hysss.sourceforge.net.
SynBioSS work is supported by the National Science Foundation (CAREER award to Yiannis Kaznessis). Our work and this website are also supported by the University of Minnesota Supercomputing Institute.