ADVANCES IN SEMANTIC REPRESENTATION FORMULTISCALE BIOSIMULATION: A CASE STUDY IN MERGING MODELS

Pacific Symposium on Biocomputing 2009

MAXWELL LEWIS NEAL ; JOHN H. GENNARI ; THEO ARTS ; DANIEL L. COOK

Others  :  http://psb.stanford.edu/psb-online/proceedings/psb09/neal.pdf
PID  :  19855

来源: CEUR

【 摘 要 】

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 timescales. 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).