Integration and Automation of Modeling of Biological Cell Processes

Abstract The System Biology Markup Language (SBML) has been used to build numerous models of biological processes. Here we introduce a new method to translate SBML specifications of cellular models into formal specifications for analysis and simulation. To do so we define a generic biological model architecture that can be instantiated with different parameters for different types of cells and at different levels of detail using the information available in SBML models. We discuss said architecture, a prototype implementation and different examples of use of the method with a synthetic model and model of E. coli.