A module-based approach to biomodel engineering with Petri Nets

Based on Petri nets as formal language for biomodel engineering, we describe the general concept of a modular modelling approach that considers the functional coupling of modules representing components of the genome, the transcriptome, and the proteome in the form of an executable model. The composable, metadata-containing Petri net modules are organized in a database with version control and accessible through a web interface. The effects of genes and their mutated alleles on downstream components are modelled by gene modules coupled to protein modules through RNA modules by specific interfaces designed for the automatic, database-assisted composition. Automatically assembled models may integrate forward and reverse engineered modules and consider cell type-specific gene expression patterns. Prospects for automatic model generation including its application to systems biology, synthetic biology, and to functional genomics are discussed.