Advances in semantic representation for multiscale biosimulation: a case study in merging models.
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).
Neal
Maxwell Lewis
ML
Biomedical & Health Informatics, University of Washington, Seattle, WA 98195, USA.
Gennari
John H
JH
Arts
Theo
T
Cook
Daniel L
DL
D001699:Biometry; D002320:Cardiovascular Physiological Phenomena; D003198:Computer Simulation; D003199:Computer Systems; D006801:Humans; D008955:Models, Cardiovascular; D012660:Semantics; D012984:Software