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Integration of multi-scale biosimulation models via light-weight semantics

John H, Gennari and Maxwell L, Neal and Brian E, Carlson and Daniel L, Cook (2008) Integration of multi-scale biosimulation models via light-weight semantics. In Proceedings, Pacific Symposium on Biocomputing, Hawaii.

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Currently, biosimulation researchers use a variety of computational environments and languages to model biological processes. Ideally, researchers should be able to semi- automatically merge models to more effectively build larger, multi-scale models. How- ever, current modeling methods do not capture the underlying semantics of these models sufficiently to support this type of model construction. In this paper, we both propose a general approach to solve this problem, and we provide a specific example that demon- strates the benefits of our methodology. In particular, we describe three biosimulation models: (1) a cardio-vascular fluid dynamics model, (2) a model of heart rate regulation via baroreceptor control, and (3) a sub-cellular-level model of the arteriolar smooth mus- cle. Within a light-weight ontological framework, we leverage reference ontologies to match concepts across models. The light-weight ontology then helps us combine our three models into a merged model that can answer questions beyond the scope of any single model.

Item Type:Conference Paper
Projects:Ontology of Physics for Biology, Ontology Views
Subjects:SIG Publications
ID Code:242
Deposited By:Franklin, Joshua Daniel
Deposited On:01 April 2010