The Role of Composition and Aggregation in Modeling Macromolecular Regulatory Networks

Today´s macromolecular regulatory network models are small compared to the amount of information known about a particular cellular pathway, in part because current modeling languages and tools are unable to handle significantly larger models. Thus, most pathway modeling work today focuses on building small models of individual pathways since they are easy to construct and manage. The hope is someday to put these pieces together to create a more complete picture of the underlying molecular machinery. While efforts to make large models benefit from reusing existing components, unfortunately, there currently exists little tool or representational support for combining or composing models. We have identified four distinct modeling processes related to model composition: fusion, composition, aggregation, and flattening. We present concrete proposals for implementing all four processes in the context of the Systems Biology Markup Language (SBML)