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Sebastian Nähring, Carsten Maus, Roland Ewald, and Adelinde M Uhrmacher (2013)

From Standardized Modeling Formats to Modeling Languages and back --- an Exploration based on SBML and ML-Rules

In: Proceedings of the 2013 Winter Simulation Conference, ed. by R. Pasupathy, S.-H. Kim, A. Tolk, R. Hill, and M. E. Kuhl, Institute of Electrical and Electronics Engineers, Inc.

 

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.
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