From standardized modeling formats to modeling languages and back — An exploration based on SBML and ML-Rules

Standardized model exchange formats give practitioners the freedom to choose the most suitable tool and facilitate both cross-validation and reproduction of simulation results. On the other hand, standardization necessarily implies a compromise between the capabilities of individual modeling languages and a common ground of concepts and underlying assumptions of the given application domain. This compromise often leads to a mismatch of expressiveness between modeling language and exchange format, which should be resolved automatically, e.g., by offering a transformation. We explore the challenges of such an approach for the Systems Biology Markup Language (SBML), a well-established model format in systems biology, and ML-Rules, a rule-based modeling language for describing cell biological systems at multiple interrelated levels. Our transformation approach can be extended both in terms of the heuristics it employs and in terms of the modeling formalisms it supports.