Model transformation of metabolic networks using a Petri net based framework

Abstract

The different modeling approaches in Systems Biology create models with different levels of detail. The transformation techniques in Petri net theory can provide a solid framework for zooming between these different levels of abstraction and refinement. This work presents a Petri net based approach to Metabolic Engineering that implements model reduction methods to reduce the complexity of large-scale metabolic networks. These methods can be complemented with kinetics inference to build dynamic models with a smaller number of parameters. The central carbon metabolism model of E. coli is used as a test-case to illustrate the application of these concepts. Model transformation is a promising mechanism to facilitate pathway analysis and dynamic modeling at the genome-scale level.