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Advances in semantic representation for multiscale biosimulation: a case study in merging models

Neal, Maxwell L and Gennari, John H and Arts, Theo and Cook, Daniel L (2009) Advances in semantic representation for multiscale biosimulation: a case study in merging models. In Proceedings, Pacific Symposium on Biocomputing, pages pp. 304-315.

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Abstract

As a case-study of biosimulation model integration, we describe our experiences applying the SemSim methodology to integrate independently-developed, multiscale models of cardiac circulation. In particular, we have integrated the CircAdapt model (written by T. Arts for MATLAB) of an adapting vascular segment with a cardiovascular system model (written by M. Neal for JSim). We report on three results from the model integration experience. First, models should be explicit about simulations that occur on different time scales. Second, data structures and naming conventions used to represent model variables may not translate across simulation languages. Finally, identifying the dependencies among model variables is a non-trivial task. We claim that these challenges will appear whenever researchers attempt to integrate models from others, especially when those models are written in a procedural style (using MATLAB, Fortran, etc.) rather than a declarative format (as supported by languages like SBML, CellML or JSim’s MML).

Item Type:Conference Paper
Projects:Ontology of Physics for Biology, Ontology Views
Subjects:SIG Publications
ID Code:241
Deposited By:Franklin, Joshua Daniel
Deposited On:26 February 2010