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

Pac Symp Biocomput. 2008:414-25.


Currently, biosimulation researchers use a variety of computational environments and languages to model biological processes. Ideally, researchers should be able to semiautomatically merge models to more effectively build larger, multi-scale models. However, 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 demonstrates 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 muscle. 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.

Publication types

  • Comparative Study
  • Research Support, N.I.H., Extramural

MeSH terms

  • Biophysical Phenomena
  • Biophysics
  • Calcium / metabolism
  • Cardiovascular Physiological Phenomena
  • Computational Biology
  • Computer Simulation
  • Heart Rate / physiology
  • Humans
  • Ion Transport
  • Models, Biological*
  • Models, Cardiovascular
  • Muscle, Smooth, Vascular / physiology
  • Pressoreceptors / physiology
  • Semantics
  • Software
  • Systems Biology


  • Calcium