Simulator

As synthetic biology operates in femtoliter volumes, even modest concentrations equate to fewer than one million molecules per cell. Importantly, genomic DNA exists with precisely one copy per cell and the number of plasmids is often countable. Such systems are far from the thermodynamic limit and consequently cannot be accurately modeled using deterministic integrators (McAdams and Arkin, 1999; McQuarrie, et al., 1964). While the exact Stochastic Simulation Algorithm (Gillespie, 1976) can be easily overwhelmed by the multiple time scales present in protein-DNA interactions, many accelerated methods exist (Kaznessis, 2007). Both the graphical desktop and command-line supercomputer simulators in SynBioSS are based on Hy3S (Salis, et al., 2006), a hybrid jump-continuous Markov process integrator. This algorithm maintains accuracy while significantly accelerating time-consuming high-concentration interactions such as protein-protein and protein-inducer interactions. Hy3S is written in FORTRAN90 utilizing NetCDF for data storage and MPI for message passing on supercomputing clusters.

Desktop Simulator (DS) [download] [download business card .iso]

SynBioSS is developed in group of Yiannis Kaznessis at the University of Minnesota. Please reference the following paper: “SynBioSS: the synthetic biology software suite”, A. Hill et al. Bioinformatics 2008 24(21):2551-2553

The desktop version of the SynBioSS simulator is implemented in Python using GTK+ and PyGTK to provide a graphical interface. These choices enable cross-platform deployment of the same code.

SynBioSS DS uses libSBML (Bornstein, et al., 2008) to read models specified in SBML and can also read models created directly for Hy3S as NetCDF files. Models can then be edited or, alternatively, created within the model interface and saved. The simulator includes default simulation parameters for stable simulation of E. coli. After setting parameters, the user then may either run the simulation locally or export a NetCDF file appropriate for the supercomputer simulator. If simulated locally, the results may be exported as either an ASCII comma-separated-value (CSV) file for import into any spreadsheet program, or as a NetCDF file appropriate for MatLab.

Supercomputer Simulator [download]

The supercomputer simulator uses MPI to coordinate parallel execution of multiple trajectories on multiple processors. Such parallel execution is an example of a trivially parallelizable problem, where perfect scaling is achieved and the number of processors utilized is limited only by the number of trajectories simulated. Parallel execution may be necessary for algorithms to determine the optimum set of biological parts for a synthetic network to match a targeted biological phenotype (Tomshine and Kaznessis, 2006). Once completed, the simulation results are stored in a NetCDF file and can be loaded into MatLab or converted to an ASCII CSV file.


SynBioSS work is supported by the U.S. National Science Foundation (CBET-0644792 ). Significant contributions made by Anthony Hill, Jonathan Tomshine, Emma Weeding, Vassilios Sotiropoulos and Howard Salis.

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