Modular Modeling of Genetic Circuits in SBML Level 3.

The System Biology Markup Language (SBML) Level 2 has been used extensively to make models for biological systems of different complexity. However, the lack of modularity was a serious hurdle for its application to Synthetic Biology where genetic circuits are preferably modeled by putting together the models of their components. SBML Level 3 with the Hierarchical Composition Package overcame this limit. Here, we describe how to realize a modular model for a eukaryotic AND gate in SBML Level 3. Circuit modules, such as transcription units and pools of molecules, are modeled separately and connected, to close the circuit, via Python scripts that utilize the libSBML API. Circuit simulations with COPASI confirm the validity of this modeling approach.