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. 2017 Apr;9(4):a023978. doi: 10.1101/cshperspect.a023978

Figure 3.

Figure 3.

Figure 3.

Modeling and simulation results of a genetic AND gate and dual-feedback oscillator. (A) SBML models are created in iBioSim for the AND gate and oscillator. The AND gate’s model is automatically generated by converting the SBOL file produced by Cello to SBML. This model is then extended to include the regulation by the proteins LacI and TetR, the complex formation of LacI and TetR with the small molecules IPTG and aTc, respectively, and the regulation of the florescent protein YFP. The oscillator model is reconstructed using information (e.g., parameter values, rate constants) from the SBML generated by GEC. (B) Simulations are performed using both COPASI and iBioSim. Deterministic simulations are performed using the LSODA ODE solver in COPASI. Stochastic simulations are performed in iBioSim using an implementation of Gillespie’s SSA.